2024 |
Iliopoulou, Elisavet; Papadogiannis, Vasileios; Tsigenopoulos, Costas S; Manousaki, Tereza Extensive Loss and Gain of Conserved Noncoding Elements During Early Teleost Evolution Journal Article Genome Biology and Evolution, 16 (4), pp. evae061, 2024, ISSN: 1759-6653. @article{iliopoulou_extensive_2024, title = {Extensive Loss and Gain of Conserved Noncoding Elements During Early Teleost Evolution}, author = {Elisavet Iliopoulou and Vasileios Papadogiannis and Costas S Tsigenopoulos and Tereza Manousaki}, editor = {Bonnie Fraser}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/04/2024-Iliopoulou-GBE-23.pdf https://academic.oup.com/gbe/article/doi/10.1093/gbe/evae061/7655401}, doi = {10.1093/gbe/evae061}, issn = {1759-6653}, year = {2024}, date = {2024-04-24}, urldate = {2024-04-24}, journal = {Genome Biology and Evolution}, volume = {16}, number = {4}, pages = {evae061}, abstract = {Abstract Conserved noncoding elements in vertebrates are enriched around transcription factor loci associated with development. However, loss and rapid divergence of conserved noncoding elements has been reported in teleost fish, albeit taking only few genomes into consideration. Taking advantage of the recent increase in high-quality teleost genomes, we focus on studying the evolution of teleost conserved noncoding elements, carrying out targeted genomic alignments and comparisons within the teleost phylogeny to detect conserved noncoding elements and reconstruct the ancestral teleost conserved noncoding elements repertoire. This teleost-centric approach confirms previous observations of extensive vertebrate conserved noncoding elements loss early in teleost evolution, but also reveals massive conserved noncoding elements gain in the teleost stem-group over 300 million years ago. Using synteny-based association to link conserved noncoding elements to their putatively regulated target genes, we show the most teleost gained conserved noncoding elements are found in the vicinity of orthologous loci involved in transcriptional regulation and embryonic development that are also associated with conserved noncoding elements in other vertebrates. Moreover, teleost and vertebrate conserved noncoding elements share a highly similar motif and transcription factor binding site vocabulary. We suggest that early teleost conserved noncoding element gains reflect a restructuring of the ancestral conserved noncoding element repertoire through both extreme divergence and de novo emergence. Finally, we support newly identified pan-teleost conserved noncoding elements have potential for accurate resolution of teleost phylogenetic placements in par with coding sequences, unlike ancestral only elements shared with spotted gar. This work provides new insight into conserved noncoding element evolution with great value for follow-up work on phylogenomics, comparative genomics, and the study of gene regulation evolution in teleosts.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Conserved noncoding elements in vertebrates are enriched around transcription factor loci associated with development. However, loss and rapid divergence of conserved noncoding elements has been reported in teleost fish, albeit taking only few genomes into consideration. Taking advantage of the recent increase in high-quality teleost genomes, we focus on studying the evolution of teleost conserved noncoding elements, carrying out targeted genomic alignments and comparisons within the teleost phylogeny to detect conserved noncoding elements and reconstruct the ancestral teleost conserved noncoding elements repertoire. This teleost-centric approach confirms previous observations of extensive vertebrate conserved noncoding elements loss early in teleost evolution, but also reveals massive conserved noncoding elements gain in the teleost stem-group over 300 million years ago. Using synteny-based association to link conserved noncoding elements to their putatively regulated target genes, we show the most teleost gained conserved noncoding elements are found in the vicinity of orthologous loci involved in transcriptional regulation and embryonic development that are also associated with conserved noncoding elements in other vertebrates. Moreover, teleost and vertebrate conserved noncoding elements share a highly similar motif and transcription factor binding site vocabulary. We suggest that early teleost conserved noncoding element gains reflect a restructuring of the ancestral conserved noncoding element repertoire through both extreme divergence and de novo emergence. Finally, we support newly identified pan-teleost conserved noncoding elements have potential for accurate resolution of teleost phylogenetic placements in par with coding sequences, unlike ancestral only elements shared with spotted gar. This work provides new insight into conserved noncoding element evolution with great value for follow-up work on phylogenomics, comparative genomics, and the study of gene regulation evolution in teleosts. |
Katirtzoglou, Aikaterini; Tsaparis, Dimitris; Kolios, Evangelos; Magoulas, Antonios; Mylonas, Constantinos C; Fakriadis, Ioannis; Manousaki, Tereza; Tsigenopoulos, Costas S Frontiers in Fish Science, 2 , pp. 1356313, 2024, ISSN: 2813-9097. @article{katirtzoglou_population_2024, title = {Population genomic analysis of the greater amberjack (\textit{Seriola dumerili}) in the Mediterranean and the Northeast Atlantic, based on SNPs, microsatellites, and mitochondrial DNA sequences}, author = {Aikaterini Katirtzoglou and Dimitris Tsaparis and Evangelos Kolios and Antonios Magoulas and Constantinos C Mylonas and Ioannis Fakriadis and Tereza Manousaki and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/03/2024-Kaitirtzoglou-frish-14.pdf https://www.frontiersin.org/articles/10.3389/frish.2024.1356313/full}, doi = {10.3389/frish.2024.1356313}, issn = {2813-9097}, year = {2024}, date = {2024-03-14}, urldate = {2024-03-14}, journal = {Frontiers in Fish Science}, volume = {2}, pages = {1356313}, abstract = {The greater amberjack ( Seriola dumerili ) has attracted considerable economic interest since the 1990s because it possesses traits that distinguish it as a promising candidate in aquaculture. However, the challenges of its successful rearing, combined with the need to develop proper management practices, underline the importance of research into the genetic diversity of both wild and farmed stocks. We aimed to decipher the genetic structure of S. dumerili in the Eastern Mediterranean and the Northeast Atlantic using three types of genetic markers (mitochondrial control region sequences, microsatellites, and single nucleotide polymorphisms, or SNPs) to evaluate the population genetic structure of the species. The results were compared to those of previous studies of the species focusing on the Central Mediterranean and confirmed the presence of two divergent mtDNA haplogroups distributed without any detectable geographical structuring within the Mediterranean and the Atlantic. However, population analyses of the genetic structure of the species using either 10 microsatellites or a set of 1,051 SNP markers suggest that the species forms three genetically distinct groups, one in the Mediterranean and two in the Atlantic. The latter has so far not been reported in the Northeast Atlantic, and that this differentiation refers to samples from the Canary Islands is surprising. Fifteen candidate outlier SNP loci were identified in the data set, one located within the tead1a /TEF-1A gene, which has been associated with temperature acclimation of the medaka. This work enriches our knowledge of the genetic diversity of wild populations of the greater amberjack in the Mediterranean and the Northeast Atlantic and attempts to investigate signs of local adaptation toward a better understanding of the species distribution patterns. Future studies should be conducted to investigate the genomic regions associated with temperature acclimation in marine organisms that have to adapt to the ongoing climate change pressures, such as sea temperature rise, in order to survive.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The greater amberjack ( Seriola dumerili ) has attracted considerable economic interest since the 1990s because it possesses traits that distinguish it as a promising candidate in aquaculture. However, the challenges of its successful rearing, combined with the need to develop proper management practices, underline the importance of research into the genetic diversity of both wild and farmed stocks. We aimed to decipher the genetic structure of S. dumerili in the Eastern Mediterranean and the Northeast Atlantic using three types of genetic markers (mitochondrial control region sequences, microsatellites, and single nucleotide polymorphisms, or SNPs) to evaluate the population genetic structure of the species. The results were compared to those of previous studies of the species focusing on the Central Mediterranean and confirmed the presence of two divergent mtDNA haplogroups distributed without any detectable geographical structuring within the Mediterranean and the Atlantic. However, population analyses of the genetic structure of the species using either 10 microsatellites or a set of 1,051 SNP markers suggest that the species forms three genetically distinct groups, one in the Mediterranean and two in the Atlantic. The latter has so far not been reported in the Northeast Atlantic, and that this differentiation refers to samples from the Canary Islands is surprising. Fifteen candidate outlier SNP loci were identified in the data set, one located within the tead1a /TEF-1A gene, which has been associated with temperature acclimation of the medaka. This work enriches our knowledge of the genetic diversity of wild populations of the greater amberjack in the Mediterranean and the Northeast Atlantic and attempts to investigate signs of local adaptation toward a better understanding of the species distribution patterns. Future studies should be conducted to investigate the genomic regions associated with temperature acclimation in marine organisms that have to adapt to the ongoing climate change pressures, such as sea temperature rise, in order to survive. |
Johnston, Ian A; Kent, Matthew P; Boudinot, Pierre; Looseley, Mark; Bargelloni, Luca; Faggion, Sara; Merino, Gabriela A; Ilsley, Garth R; Bobe, Julien; Tsigenopoulos, Costas S; Robertson, Joseph; Harrison, Peter W; Martinez, Paulino; Robledo, Diego; Macqueen, Daniel J; Lien, Sigbjørn Advancing fish breeding in aquaculture through genome functional annotation Journal Article Aquaculture, 583 , pp. 740589, 2024, ISSN: 00448486. @article{johnston_advancing_2024, title = {Advancing fish breeding in aquaculture through genome functional annotation}, author = {Ian A Johnston and Matthew P Kent and Pierre Boudinot and Mark Looseley and Luca Bargelloni and Sara Faggion and Gabriela A Merino and Garth R Ilsley and Julien Bobe and Costas S Tsigenopoulos and Joseph Robertson and Peter W Harrison and Paulino Martinez and Diego Robledo and Daniel J Macqueen and Sigbjørn Lien}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/02/2024-Johnston-AQUA-8.pdf https://linkinghub.elsevier.com/retrieve/pii/S0044848624000504}, doi = {10.1016/j.aquaculture.2024.740589}, issn = {00448486}, year = {2024}, date = {2024-02-12}, urldate = {2024-02-13}, journal = {Aquaculture}, volume = {583}, pages = {740589}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
García-Escudero, Catalina A; Tsigenopoulos, Costas S; Manousaki, Tereza; Tsakogiannis, Alexandros; Marbà, Núria; Vizzini, Salvatrice; Duarte, Carlos M; Apostolaki, Eugenia T Population genomics unveils the century-old invasion of the Seagrass Halophila stipulacea in the Mediterranean Sea Journal Article Marine Biology, 171 (2), pp. 40, 2024, ISSN: 0025-3162, 1432-1793. @article{garcia-escudero_population_2024, title = {Population genomics unveils the century-old invasion of the Seagrass Halophila stipulacea in the Mediterranean Sea}, author = {Catalina A García-Escudero and Costas S Tsigenopoulos and Tereza Manousaki and Alexandros Tsakogiannis and Núria Marbà and Salvatrice Vizzini and Carlos M Duarte and Eugenia T Apostolaki}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/01/2024-Garcia-Escudero-2.pdf https://link.springer.com/10.1007/s00227-023-04361-7}, doi = {10.1007/s00227-023-04361-7}, issn = {0025-3162, 1432-1793}, year = {2024}, date = {2024-01-11}, urldate = {2024-01-19}, journal = {Marine Biology}, volume = {171}, number = {2}, pages = {40}, abstract = {Abstract The tropical seagrass Halophila stipulacea invaded the Eastern Mediterranean Sea in the late nineteenth century and progressively spread throughout the basin ever since. Its spread is expected to continue north-westward as the Mediterranean Sea becomes warmer, potentially changing the seagrass biogeography of the basin. Given the power of genomics to assess invasion dynamics in non-model species, we report the first ddRAD-seq study of H. stipulacea and small-scale population genomic analysis addressing its century-old Mediterranean invasion. Based on 868 SNPs and 35 genotyped native (Red Sea) and exotic (from Cyprus, Greece, and Italy) samples, results suggest that genetic structure was high, especially between major geographic discontinuities, and that exotic populations maintain comparably lower genetic diversity than native populations, despite 130 years of invasion. The evidence of high heterozygosity excess, coupled with previously reported male-dominated and rare flowering records in the exotic range, suggests that clonal propagation likely played a pivotal role in the successful colonization and spread of H. stipulacea in the Mediterranean. This shift in reproductive strategy, particularly evident in the Italian populations located closest to the western boundary and representing more recent establishments, underscores the importance of this cost-effective mode of reproduction, especially during the initial stages of invasion, raising questions about the species future expansion trajectory. Our findings serve as a catalyst for future research into the species’ invasion dynamics, including deciphering the intricate roles of acclimatization and rapid adaptation, important for a comprehensive assessment of invasion risks and improving management strategies aimed at conserving seagrass ecosystems.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract The tropical seagrass Halophila stipulacea invaded the Eastern Mediterranean Sea in the late nineteenth century and progressively spread throughout the basin ever since. Its spread is expected to continue north-westward as the Mediterranean Sea becomes warmer, potentially changing the seagrass biogeography of the basin. Given the power of genomics to assess invasion dynamics in non-model species, we report the first ddRAD-seq study of H. stipulacea and small-scale population genomic analysis addressing its century-old Mediterranean invasion. Based on 868 SNPs and 35 genotyped native (Red Sea) and exotic (from Cyprus, Greece, and Italy) samples, results suggest that genetic structure was high, especially between major geographic discontinuities, and that exotic populations maintain comparably lower genetic diversity than native populations, despite 130 years of invasion. The evidence of high heterozygosity excess, coupled with previously reported male-dominated and rare flowering records in the exotic range, suggests that clonal propagation likely played a pivotal role in the successful colonization and spread of H. stipulacea in the Mediterranean. This shift in reproductive strategy, particularly evident in the Italian populations located closest to the western boundary and representing more recent establishments, underscores the importance of this cost-effective mode of reproduction, especially during the initial stages of invasion, raising questions about the species future expansion trajectory. Our findings serve as a catalyst for future research into the species’ invasion dynamics, including deciphering the intricate roles of acclimatization and rapid adaptation, important for a comprehensive assessment of invasion risks and improving management strategies aimed at conserving seagrass ecosystems. |
2023 |
Litsi-Mizan, Victoria; García-Escudero, Catalina A; Tsigenopoulos, Costas S; Tsiaras, Kostas; Gerakaris, Vasilis; Apostolaki, Eugenia T Unravelling the genetic pattern of seagrass (Posidonia oceanica) meadows in the Eastern Mediterranean Sea Journal Article Biodiversity and Conservation, 2023, ISSN: 0960-3115, 1572-9710. @article{litsi-mizan_unravelling_2023, title = {Unravelling the genetic pattern of seagrass (Posidonia oceanica) meadows in the Eastern Mediterranean Sea}, author = {Victoria Litsi-Mizan and Catalina A García-Escudero and Costas S Tsigenopoulos and Kostas Tsiaras and Vasilis Gerakaris and Eugenia T Apostolaki}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/01/2023-Litsi-Mizan-BioDivConser-66.pdf https://link.springer.com/10.1007/s10531-023-02746-0}, doi = {10.1007/s10531-023-02746-0}, issn = {0960-3115, 1572-9710}, year = {2023}, date = {2023-12-27}, urldate = {2024-01-12}, journal = {Biodiversity and Conservation}, abstract = {Abstract The genetic traits of seagrass populations are a crucial aspect of their ecology and evolution, influencing their adaptability and resilience. Here, we studied the genetic diversity, population structure, and connectivity of eighteen Posidonia oceanica meadows extending in the Eastern Mediterranean Sea (Aegean, Ionian and Cretan Seas, Greece), combining twelve microsatellite markers and Lagrangian particle drift modelling. Our findings revealed a strong genetic differentiation between the Ionian Sea and the Aegean and Cretan Seas, suggesting limited genetic exchange between these two groups. High gene flow was observed within the meadows of the Aegean and Cretan Seas, indicating a well-connected group of populations. Notably, populations of the North Aegean Sea displayed the lowest genetic diversity and the highest clonality compared to the rest of the populations. The lack of substantial oceanographic connectivity between Ionian and Aegean/Cretan Sea populations supported their genetic differentiation. However, the Lagrangian simulations did not fully support gene flow patterns in the Aegean Sea, suggesting that in addition to contemporary processes, historical events may have contributed to the formation of the observed genetic pattern. The genetic information provided here can be incorporated into management strategies aimed at identifying suitable areas as management units in conservation efforts and determining meadows that may serve as donor sites in transplantation initiatives.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract The genetic traits of seagrass populations are a crucial aspect of their ecology and evolution, influencing their adaptability and resilience. Here, we studied the genetic diversity, population structure, and connectivity of eighteen Posidonia oceanica meadows extending in the Eastern Mediterranean Sea (Aegean, Ionian and Cretan Seas, Greece), combining twelve microsatellite markers and Lagrangian particle drift modelling. Our findings revealed a strong genetic differentiation between the Ionian Sea and the Aegean and Cretan Seas, suggesting limited genetic exchange between these two groups. High gene flow was observed within the meadows of the Aegean and Cretan Seas, indicating a well-connected group of populations. Notably, populations of the North Aegean Sea displayed the lowest genetic diversity and the highest clonality compared to the rest of the populations. The lack of substantial oceanographic connectivity between Ionian and Aegean/Cretan Sea populations supported their genetic differentiation. However, the Lagrangian simulations did not fully support gene flow patterns in the Aegean Sea, suggesting that in addition to contemporary processes, historical events may have contributed to the formation of the observed genetic pattern. The genetic information provided here can be incorporated into management strategies aimed at identifying suitable areas as management units in conservation efforts and determining meadows that may serve as donor sites in transplantation initiatives. |
Kitsoulis, Christos V; Papadogiannis, Vasileios; Kristoffersen, Jon B; Kaitetzidou, Elisavet; Sterioti, Aspasia; Tsigenopoulos, Costas S; Manousaki, Tereza Near-chromosome level genome assembly of devil firefish, Pterois miles Journal Article Peer Community Journal, 3 , pp. e64, 2023, ISSN: 2804-3871. @article{kitsoulis_near-chromosome_2023, title = {Near-chromosome level genome assembly of devil firefish, Pterois miles}, author = {Christos V Kitsoulis and Vasileios Papadogiannis and Jon B Kristoffersen and Elisavet Kaitetzidou and Aspasia Sterioti and Costas S Tsigenopoulos and Tereza Manousaki}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/08/2023-Kitsoulis-PeerCJ-43.pdf https://peercommunityjournal.org/articles/10.24072/pcjournal.295/}, doi = {10.24072/pcjournal.295}, issn = {2804-3871}, year = {2023}, date = {2023-08-29}, urldate = {2023-08-31}, journal = {Peer Community Journal}, volume = {3}, pages = {e64}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Papadogiannis, Vasileios; Manousaki, Tereza; Nousias, Orestis; Tsakogiannis, Alexandros; Kristoffersen, Jon B; Mylonas, Constantinos C; Batargias, Costas; Chatziplis, Dimitrios; Tsigenopoulos, Costas S Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution Journal Article Frontiers in Genetics, 13 , pp. 1081760, 2023, ISSN: 1664-8021. @article{papadogiannis_chromosome_2023b, title = {Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution}, author = {Vasileios Papadogiannis and Tereza Manousaki and Orestis Nousias and Alexandros Tsakogiannis and Jon B Kristoffersen and Constantinos C Mylonas and Costas Batargias and Dimitrios Chatziplis and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/07/2023-Papadogiannis-FrontGen-34.pdf https://www.frontiersin.org/articles/10.3389/fgene.2022.1081760/full}, doi = {10.3389/fgene.2022.1081760}, issn = {1664-8021}, year = {2023}, date = {2023-07-03}, urldate = {2023-07-03}, journal = {Frontiers in Genetics}, volume = {13}, pages = {1081760}, abstract = {The meagre, Argyrosomus regius , has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius , produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. We use this new resource to study the evolution of the meagre genome and other Sciaenids, via a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related dmrt1 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The meagre, Argyrosomus regius , has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius , produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. We use this new resource to study the evolution of the meagre genome and other Sciaenids, via a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related dmrt1 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species. |
Antoniou, Aglaia; Manousaki, Tereza; Ramírez, Francisco; Cariani, Alessia; Cannas, Rita; Kasapidis, Panagiotis; Magoulas, Antonios; Albo‐Puigserver, Marta; Lloret‐Lloret, Elena; Bellido, Jose Maria; Pennino, Maria Grazia; Follesa, Maria Cristina; Esteban, Antonio; Saraux, Claire; Sbrana, Mario; Spedicato, Maria Teresa; Coll, Marta; Tsigenopoulos, Costas S Sardines at a junction: Seascape genomics reveals ecological and oceanographic drivers of variation in the textlessspan style= Journal Article Molecular Ecology, pp. mec.16840, 2023, ISSN: 0962-1083, 1365-294X. @article{antoniou_sardines_2023, title = {Sardines at a junction: Seascape genomics reveals ecological and oceanographic drivers of variation in the textlessspan style=}, author = {Aglaia Antoniou and Tereza Manousaki and Francisco Ramírez and Alessia Cariani and Rita Cannas and Panagiotis Kasapidis and Antonios Magoulas and Marta Albo‐Puigserver and Elena Lloret‐Lloret and Jose Maria Bellido and Maria Grazia Pennino and Maria Cristina Follesa and Antonio Esteban and Claire Saraux and Mario Sbrana and Maria Teresa Spedicato and Marta Coll and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/02/2023-Antoniou-Mol-Eco-9-1.pdf https://onlinelibrary.wiley.com/doi/10.1111/mec.16840}, doi = {10.1111/mec.16840}, issn = {0962-1083, 1365-294X}, year = {2023}, date = {2023-02-06}, urldate = {2023-02-06}, journal = {Molecular Ecology}, pages = {mec.16840}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Papadogiannis, Vasileios; Manousaki, Tereza; Nousias, Orestis; Tsakogiannis, Alexandros; Kristoffersen, Jon B; Mylonas, Constantinos C; Batargias, Costas; Chatziplis, Dimitrios; Tsigenopoulos, Costas S Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution Journal Article Frontiers in Genetics, 13 , pp. 1081760, 2023, ISSN: 1664-8021. @article{papadogiannis_chromosome_2023, title = {Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution}, author = {Vasileios Papadogiannis and Tereza Manousaki and Orestis Nousias and Alexandros Tsakogiannis and Jon B Kristoffersen and Constantinos C Mylonas and Costas Batargias and Dimitrios Chatziplis and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/01/2023-Papadogiannis-FinGenetics-4.pdf https://www.frontiersin.org/articles/10.3389/fgene.2022.1081760/full}, doi = {10.3389/fgene.2022.1081760}, issn = {1664-8021}, year = {2023}, date = {2023-01-10}, urldate = {2023-01-11}, journal = {Frontiers in Genetics}, volume = {13}, pages = {1081760}, abstract = {The meagre, Argyrosomus regius , has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius , produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. We use this new resource to study the evolution of the meagre genome and other Sciaenids, via a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related dmrt1 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The meagre, Argyrosomus regius , has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius , produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. We use this new resource to study the evolution of the meagre genome and other Sciaenids, via a comparative analysis of 25 high-quality teleost genomes. Combining a rigorous investigation of gene duplications with base-wise conservation analysis, we identify candidate loci related to immune, fat metabolism and growth adaptations in the meagre. Following phylogenomic reconstruction, we show highly conserved synteny within Sciaenidae. In contrast, we report rapidly evolving syntenic rearrangements and gene copy changes in the sex-related dmrt1 neighbourhood in meagre and other members of the family. These novel genomic datasets and findings will add important new tools for aquaculture studies and greatly facilitate husbandry and breeding work in the species. |
2022 |
Ramos-Júdez, Sandra; Danis, Theodoros; Angelova, Nelina; Tsakogiannis, Alexandros; Giménez, Ignacio; Tsigenopoulos, Costas S; Duncan, Neil; Manousaki, Tereza Transcriptome analysis of flathead grey mullet (Mugil cephalus) ovarian development induced by recombinant gonadotropin hormones Journal Article Frontiers in Physiology, 13 , pp. 1033445, 2022, ISSN: 1664-042X. @article{ramos-judez_transcriptome_2022, title = {Transcriptome analysis of flathead grey mullet (Mugil cephalus) ovarian development induced by recombinant gonadotropin hormones}, author = {Sandra Ramos-Júdez and Theodoros Danis and Nelina Angelova and Alexandros Tsakogiannis and Ignacio Giménez and Costas S Tsigenopoulos and Neil Duncan and Tereza Manousaki}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/11/2022-Ramos-Judez-fphys-75-1.pdf https://www.frontiersin.org/articles/10.3389/fphys.2022.1033445/full}, doi = {10.3389/fphys.2022.1033445}, issn = {1664-042X}, year = {2022}, date = {2022-11-14}, urldate = {2022-11-14}, journal = {Frontiers in Physiology}, volume = {13}, pages = {1033445}, abstract = {Background: Treatment with recombinant gonadotropin hormones (rGths), follicle-stimulating hormone (rFsh) and luteinizing hormone (rLh), was shown to induce and complete vitellogenesis to finally obtain viable eggs and larvae in the flathead grey mullet ( Mugil cephalus ), a teleost arrested at early stages of gametogenesis in intensive captivity conditions. This study aimed to investigate the transcriptomic changes that occur in the ovary of females during the rGths-induced vitellogenesis. Methods: Ovarian samples were collected through biopsies from the same five females at four stages of ovarian development. RNASeq libraries were constructed for all stages studied, sequenced on an Illumina HiSeq4000, and a de novo transcriptome was constructed. Differentially expressed genes (DEGs) were identified between stages and the functional properties of DEGs were characterized by comparison with the gene ontology and Kyoto Encyclopedia. An enrichment analysis of molecular pathways was performed. Results: The de novo transcriptome comprised 287,089 transcripts after filtering. As vitellogenesis progressed, more genes were significantly upregulated than downregulated. The rFsh application induced ovarian development from previtellogenesis to early-to-mid-vitellogenesis with associated pathways enriched from upregulated DEGs related to ovarian steroidogenesis and reproductive development , cholesterol metabolism, ovarian growth and differentiation, lipid accumulation, and cell-to-cell adhesion pathways. The application of rFsh and rLh at early-to-mid-vitellogenesis induced the growth of oocytes to late-vitellogenesis and, with it, the enrichment of pathways from upregulated DEGs related to the production of energy, such as the lysosomes activity . The application of rLh at late-vitellogenesis induced the completion of vitellogenesis with the enrichment of pathways linked with the switch from vitellogenesis to oocyte maturation. Conclusion: The DEGs and enriched molecular pathways described during the induced vitellogenesis of flathead grey mullet with rGths were typical of natural oogenesis reported for other fish species. Present results add new knowledge to the rGths action to further raise the possibility of using rGths in species that present similar reproductive disorders in aquaculture, the aquarium industry as well as the conservation of endangered species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background: Treatment with recombinant gonadotropin hormones (rGths), follicle-stimulating hormone (rFsh) and luteinizing hormone (rLh), was shown to induce and complete vitellogenesis to finally obtain viable eggs and larvae in the flathead grey mullet ( Mugil cephalus ), a teleost arrested at early stages of gametogenesis in intensive captivity conditions. This study aimed to investigate the transcriptomic changes that occur in the ovary of females during the rGths-induced vitellogenesis. Methods: Ovarian samples were collected through biopsies from the same five females at four stages of ovarian development. RNASeq libraries were constructed for all stages studied, sequenced on an Illumina HiSeq4000, and a de novo transcriptome was constructed. Differentially expressed genes (DEGs) were identified between stages and the functional properties of DEGs were characterized by comparison with the gene ontology and Kyoto Encyclopedia. An enrichment analysis of molecular pathways was performed. Results: The de novo transcriptome comprised 287,089 transcripts after filtering. As vitellogenesis progressed, more genes were significantly upregulated than downregulated. The rFsh application induced ovarian development from previtellogenesis to early-to-mid-vitellogenesis with associated pathways enriched from upregulated DEGs related to ovarian steroidogenesis and reproductive development , cholesterol metabolism, ovarian growth and differentiation, lipid accumulation, and cell-to-cell adhesion pathways. The application of rFsh and rLh at early-to-mid-vitellogenesis induced the growth of oocytes to late-vitellogenesis and, with it, the enrichment of pathways from upregulated DEGs related to the production of energy, such as the lysosomes activity . The application of rLh at late-vitellogenesis induced the completion of vitellogenesis with the enrichment of pathways linked with the switch from vitellogenesis to oocyte maturation. Conclusion: The DEGs and enriched molecular pathways described during the induced vitellogenesis of flathead grey mullet with rGths were typical of natural oogenesis reported for other fish species. Present results add new knowledge to the rGths action to further raise the possibility of using rGths in species that present similar reproductive disorders in aquaculture, the aquarium industry as well as the conservation of endangered species. |
Villanueva, Beatriz; Fernández, Almudena; Peiró-Pastor, Ramón; Peñaloza, Carolina; Houston, Ross D; Sonesson, Anna K; Tsigenopoulos, Costas S; Bargelloni, Luca; Gamsız, Kutsal; Karahan, Bilge; Gökçek, Emel Ö; Fernández, Jesús; Saura, María Aquaculture Reports, 24 , pp. 101145, 2022, ISSN: 23525134. @article{villanueva_population_2022, title = {Population structure and genetic variability in wild and farmed Mediterranean populations of gilthead seabream and European seabass inferred from a 60K combined species SNP array}, author = {Beatriz Villanueva and Almudena Fernández and Ramón Peiró-Pastor and Carolina Peñaloza and Ross D Houston and Anna K Sonesson and Costas S Tsigenopoulos and Luca Bargelloni and Kutsal Gamsız and Bilge Karahan and Emel Ö Gökçek and Jesús Fernández and María Saura}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Villanueva-37.pdf https://linkinghub.elsevier.com/retrieve/pii/S2352513422001417}, doi = {10.1016/j.aqrep.2022.101145}, issn = {23525134}, year = {2022}, date = {2022-06-01}, urldate = {2022-07-29}, journal = {Aquaculture Reports}, volume = {24}, pages = {101145}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sarropoulou, Xenia; Tsaparis, Dimitris; Tsagarakis, Konstantinos; Badouvas, Nicholas; Tsigenopoulos, Costas S Different patterns of population structure and genetic diversity of three mesopelagic fishes in the Greek Seas Journal Article Mediterranean Marine Science, 23 (3), pp. 536–545, 2022, ISSN: 1791-6763. @article{sarropoulou_different_2022, title = {Different patterns of population structure and genetic diversity of three mesopelagic fishes in the Greek Seas}, author = {Xenia Sarropoulou and Dimitris Tsaparis and Konstantinos Tsagarakis and Nicholas Badouvas and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Sarropoulou-MMS-49.pdf https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/28567}, doi = {10.12681/mms.28567}, issn = {1791-6763}, year = {2022}, date = {2022-06-01}, urldate = {2022-07-29}, journal = {Mediterranean Marine Science}, volume = {23}, number = {3}, pages = {536--545}, abstract = {Mesopelagic fishes are among the most abundant groups of vertebrates on Earth. Despite their unique biological and ecological traits, research in this group has been particularly scarce. The present study investigates the intraspecific genetic diversity of three mesopelagic fishes (Hygophum benoiti, Maurolicus muelleri, and Benthosema glaciale) in the Greek Seas. Analyses of three mitochondrial DNA genes (COI, 12S, and 16S) from a total of 168 samples revealed a lack of genetic structure for M. muelleri and B. glaciale across the studied area. However, H. benoiti specimens from the Corinthian Gulf were differentiated from the rest of the populations, suggesting that the limited connection between the Corinthian and neighboring seas may act as a barrier to gene flow. Furthermore, the COI data of this study were co-analyzed with publicly available sequences, demonstrating lack of phylogeographic structure for all three species through their distribution range. Therefore, even though indications of genetic differentiation were observed, the three mesopelagic fishes are generally characterized by genetic homogeneity, which may be the result of their recent evolutionary history.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Mesopelagic fishes are among the most abundant groups of vertebrates on Earth. Despite their unique biological and ecological traits, research in this group has been particularly scarce. The present study investigates the intraspecific genetic diversity of three mesopelagic fishes (Hygophum benoiti, Maurolicus muelleri, and Benthosema glaciale) in the Greek Seas. Analyses of three mitochondrial DNA genes (COI, 12S, and 16S) from a total of 168 samples revealed a lack of genetic structure for M. muelleri and B. glaciale across the studied area. However, H. benoiti specimens from the Corinthian Gulf were differentiated from the rest of the populations, suggesting that the limited connection between the Corinthian and neighboring seas may act as a barrier to gene flow. Furthermore, the COI data of this study were co-analyzed with publicly available sequences, demonstrating lack of phylogeographic structure for all three species through their distribution range. Therefore, even though indications of genetic differentiation were observed, the three mesopelagic fishes are generally characterized by genetic homogeneity, which may be the result of their recent evolutionary history. |
Vela-Avitúa, Sergio; Thorland, Ingunn; Bakopoulos, Vasileios; Papanna, Kantham; Dimitroglou, Arkadios; Kottaras, Eleftherios; Leonidas, Papaharisis; Guinand, Bruno; Tsigenopoulos, Costas S; Aslam, Muhammad L Frontiers in Genetics, 13 , pp. 804584, 2022, ISSN: 1664-8021. @article{vela-avitua_genetic_2022, title = {Genetic Basis for Resistance Against Viral Nervous Necrosis: GWAS and Potential of Genomic Prediction Explored in Farmed European Sea Bass (Dicentrarchus labrax)}, author = {Sergio Vela-Avitúa and Ingunn Thorland and Vasileios Bakopoulos and Kantham Papanna and Arkadios Dimitroglou and Eleftherios Kottaras and Papaharisis Leonidas and Bruno Guinand and Costas S Tsigenopoulos and Muhammad L Aslam}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Vela-Avitua-Frontiers-in-Gen-26.pdf}, doi = {10.3389/fgene.2022.804584}, issn = {1664-8021}, year = {2022}, date = {2022-03-01}, urldate = {2022-05-09}, journal = {Frontiers in Genetics}, volume = {13}, pages = {804584}, abstract = {Viral nervous necrosis (VNN) is an infectious disease caused by the red-spotted grouper nervous necrosis virus (RGNNV) in European sea bass and is considered a serious concern for the aquaculture industry with fry and juveniles being highly susceptible. To understand the genetic basis for resistance against VNN, a survival phenotype through the challenge test against the RGNNV was recorded in populations from multiple year classes (YC2016 and YC2017). A total of 4,851 individuals from 181 families were tested, and a subset (n∼1,535) belonging to 122 families was genotyped using a ∼57K Affymetrix Axiom array. The survival against the RGNNV showed low to moderate heritability with observed scale estimates of 0.18 and 0.25 obtained using pedigree vs. genomic information, respectively. The genome-wide association analysis showed a strong signal of quantitative trait loci (QTL) at LG12 which explained ∼33% of the genetic variance. The QTL region contained multiple genes ( ITPK1 , PLK4 , HSPA4L , REEP1 , CHMP2 , MRPL35 , and SCUBE ) with HSPA4L and/or REEP1 genes being highly relevant with a likely effect on host response in managing disease-associated symptoms. The results on the accuracy of predicting breeding values presented 20–43% advantage in accuracy using genomic over pedigree-based information which varied across model types and applied validation schemes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Viral nervous necrosis (VNN) is an infectious disease caused by the red-spotted grouper nervous necrosis virus (RGNNV) in European sea bass and is considered a serious concern for the aquaculture industry with fry and juveniles being highly susceptible. To understand the genetic basis for resistance against VNN, a survival phenotype through the challenge test against the RGNNV was recorded in populations from multiple year classes (YC2016 and YC2017). A total of 4,851 individuals from 181 families were tested, and a subset (n∼1,535) belonging to 122 families was genotyped using a ∼57K Affymetrix Axiom array. The survival against the RGNNV showed low to moderate heritability with observed scale estimates of 0.18 and 0.25 obtained using pedigree vs. genomic information, respectively. The genome-wide association analysis showed a strong signal of quantitative trait loci (QTL) at LG12 which explained ∼33% of the genetic variance. The QTL region contained multiple genes ( ITPK1 , PLK4 , HSPA4L , REEP1 , CHMP2 , MRPL35 , and SCUBE ) with HSPA4L and/or REEP1 genes being highly relevant with a likely effect on host response in managing disease-associated symptoms. The results on the accuracy of predicting breeding values presented 20–43% advantage in accuracy using genomic over pedigree-based information which varied across model types and applied validation schemes. |
García-Escudero, Catalina A; Tsigenopoulos, Costas S; Gerakaris, Vasilis; Tsakogiannis, Alexandros; Apostolaki, Eugenia T ITS DNA Barcoding Reveals That Halophila stipulacea Still Remains the Only Non-Indigenous Seagrass of the Mediterranean Sea Journal Article Diversity, 14 (2), pp. 76, 2022, ISSN: 1424-2818. @article{garcia-escudero_its_2022, title = {ITS DNA Barcoding Reveals That Halophila stipulacea Still Remains the Only Non-Indigenous Seagrass of the Mediterranean Sea}, author = {Catalina A García-Escudero and Costas S Tsigenopoulos and Vasilis Gerakaris and Alexandros Tsakogiannis and Eugenia T Apostolaki}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Garcia-Escudero-DIVERSITY-8.pdf https://www.mdpi.com/1424-2818/14/2/76}, doi = {10.3390/d14020076}, issn = {1424-2818}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {Diversity}, volume = {14}, number = {2}, pages = {76}, abstract = {Non-indigenous species (NIS) are one of the major threats to the native marine ecosystems of the Mediterranean Sea. Halophila stipulacea was the only exotic seagrass of the Mediterranean until 2018, when small patches of a species morphologically identified as Halophila decipiens were reported in Salamina Island, Greece. Given the absence of reproductive structures during the identification and the taxonomic ambiguities known to lead to misidentifications on this genus, we reassessed the identity of this new exotic record using DNA barcoding (rbcL, matK and ITS) and the recently published taxonomic key. Despite their morphologic similarity to H. decipiens based on the new taxonomic key, the specimens showed no nucleotide differences with H. stipulacea specimens (Crete) for the three barcodes and clustered together on the ITS phylogenetic tree. Considering the high species resolution of the ITS region and the common morphological variability within the genus, the unequivocal genetic result suggests that the Halophila population found in Salamina Island most likely corresponds to a morphologically variant H. stipulacea. Our results highlight the importance of applying an integrated taxonomic approach (morphological and molecular) to taxonomically complex genera such as Halophila, in order to avoid overlooking or misreporting species range shifts, which is essential for monitoring NIS introductions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Non-indigenous species (NIS) are one of the major threats to the native marine ecosystems of the Mediterranean Sea. Halophila stipulacea was the only exotic seagrass of the Mediterranean until 2018, when small patches of a species morphologically identified as Halophila decipiens were reported in Salamina Island, Greece. Given the absence of reproductive structures during the identification and the taxonomic ambiguities known to lead to misidentifications on this genus, we reassessed the identity of this new exotic record using DNA barcoding (rbcL, matK and ITS) and the recently published taxonomic key. Despite their morphologic similarity to H. decipiens based on the new taxonomic key, the specimens showed no nucleotide differences with H. stipulacea specimens (Crete) for the three barcodes and clustered together on the ITS phylogenetic tree. Considering the high species resolution of the ITS region and the common morphological variability within the genus, the unequivocal genetic result suggests that the Halophila population found in Salamina Island most likely corresponds to a morphologically variant H. stipulacea. Our results highlight the importance of applying an integrated taxonomic approach (morphological and molecular) to taxonomically complex genera such as Halophila, in order to avoid overlooking or misreporting species range shifts, which is essential for monitoring NIS introductions. |
Oikonomou, Stavroula; Samaras, Athanasios; Tekeoglou, Maria; Loukovitis, Dimitrios; Dimitroglou, Arkadios; Kottaras, Lefteris; Papanna, Kantham; Papaharisis, Leonidas; Tsigenopoulos, Costas S; Pavlidis, Michail; Chatziplis, Dimitrios Genomic Selection and Genome-Wide Association Analysis for Stress Response, Disease Resistance and Body Weight in European Seabass Journal Article Animals, 12 (3), pp. 277, 2022, ISSN: 2076-2615. @article{oikonomou_genomic_2022, title = {Genomic Selection and Genome-Wide Association Analysis for Stress Response, Disease Resistance and Body Weight in European Seabass}, author = {Stavroula Oikonomou and Athanasios Samaras and Maria Tekeoglou and Dimitrios Loukovitis and Arkadios Dimitroglou and Lefteris Kottaras and Kantham Papanna and Leonidas Papaharisis and Costas S Tsigenopoulos and Michail Pavlidis and Dimitrios Chatziplis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Oikonomou-ANIMALS-9.pdf https://www.mdpi.com/2076-2615/12/3/277}, doi = {10.3390/ani12030277}, issn = {2076-2615}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {Animals}, volume = {12}, number = {3}, pages = {277}, abstract = {The majority of the genetic studies in aquaculture breeding programs focus on commercial traits such as body weight, morphology, and resistance against diseases. However, studying stress response in European seabass may contribute to the understanding of the genetic component of stress and its future use to select broodstock whose offspring may potentially be less affected by handling. A total of 865 European seabass offspring were used to measure body weight and stress response. Moreover, a disease challenge experiment with Vibrio anguillarum was conducted in a subset (332) of the above fish to study disease resistance. Fish were genotyped with a 57k SNP array, and a Genome-Wide Association study (GWAS) was performed. Five SNPs were found to be statistically significant, three of which affect stress indicators and body weight (in a subgroup of the population), and a putative SNP affects growth performance, while no SNP associated with resistance to Vibrio was found. A moderate to high genomic heritability regarding stress indicators and body weight was estimated using the Restricted Maximum Likelihood (REML) process. Finally, the accuracy, along with the correlation between Estimated Breeding Values (EBVs) and Genomic Estimated Breeding Values (GEBVs), were calculated for all the traits.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The majority of the genetic studies in aquaculture breeding programs focus on commercial traits such as body weight, morphology, and resistance against diseases. However, studying stress response in European seabass may contribute to the understanding of the genetic component of stress and its future use to select broodstock whose offspring may potentially be less affected by handling. A total of 865 European seabass offspring were used to measure body weight and stress response. Moreover, a disease challenge experiment with Vibrio anguillarum was conducted in a subset (332) of the above fish to study disease resistance. Fish were genotyped with a 57k SNP array, and a Genome-Wide Association study (GWAS) was performed. Five SNPs were found to be statistically significant, three of which affect stress indicators and body weight (in a subgroup of the population), and a putative SNP affects growth performance, while no SNP associated with resistance to Vibrio was found. A moderate to high genomic heritability regarding stress indicators and body weight was estimated using the Restricted Maximum Likelihood (REML) process. Finally, the accuracy, along with the correlation between Estimated Breeding Values (EBVs) and Genomic Estimated Breeding Values (GEBVs), were calculated for all the traits. |
Angelova, Nelina; Danis, Theodoros; Lagnel, Jacques; Tsigenopoulos, Costas S; Manousaki, Tereza SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments Journal Article BMC Research Notes, 15 (1), pp. 98, 2022, ISSN: 1756-0500. @article{angelova_snakecube_2022, title = {SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments}, author = {Nelina Angelova and Theodoros Danis and Jacques Lagnel and Costas S Tsigenopoulos and Tereza Manousaki}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Angelova-BMC-18.pdf https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-022-05978-5}, doi = {10.1186/s13104-022-05978-5}, issn = {1756-0500}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {BMC Research Notes}, volume = {15}, number = {1}, pages = {98}, abstract = {Abstract Objective The rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift development and application of new algorithms, as well as the establishment of standardized analysis approaches that promote transparency and transferability in research. Results Here, we present SnakeCube, an automated and containerized whole de novo genome assembly pipeline that runs within isolated, secured environments and scales for use in High Performance Computing (HPC) domains. SnakeCube was optimized for its performance and tested for its effectiveness with various inputs, highlighting its safe and robust universal use in the field.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Objective The rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift development and application of new algorithms, as well as the establishment of standardized analysis approaches that promote transparency and transferability in research. Results Here, we present SnakeCube, an automated and containerized whole de novo genome assembly pipeline that runs within isolated, secured environments and scales for use in High Performance Computing (HPC) domains. SnakeCube was optimized for its performance and tested for its effectiveness with various inputs, highlighting its safe and robust universal use in the field. |
Nousias, O; Oikonomou, S; Manousaki, T; Papadogiannis, V; Angelova, N; Tsaparis, D; Tsakogiannis, A; Duncan, N; Estevez, A; Tzokas, K; Pavlidis, M; Chatziplis, D; Tsigenopoulos, C S Scientific Reports, 12 (1), pp. 5301, 2022, ISSN: 2045-2322. @article{nousias_linkage_2022, title = {Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing}, author = {O Nousias and S Oikonomou and T Manousaki and V Papadogiannis and N Angelova and D Tsaparis and A Tsakogiannis and N Duncan and A Estevez and K Tzokas and M Pavlidis and D Chatziplis and C S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Nousias-Sci-Report-27.pdf https://www.nature.com/articles/s41598-022-09289-4}, doi = {10.1038/s41598-022-09289-4}, issn = {2045-2322}, year = {2022}, date = {2022-01-01}, urldate = {2022-05-09}, journal = {Scientific Reports}, volume = {12}, number = {1}, pages = {5301}, abstract = {Abstract Meagre ( Argyrosomus regius ), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax , traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Meagre ( Argyrosomus regius ), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax , traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production. |
Oikonomou, Stavroula; Kazlari, Zoi; Papapetrou, Maria; Papanna, Kantham; Papaharisis, Leonidas; Manousaki, Tereza; Loukovitis, Dimitrios; Dimitroglou, Arkadios; Kottaras, Lefteris; Gourzioti, Evgenia; Pagonis, Charalampos; Kostandis, Andreas; Tsigenopoulos, Costas S; Chatziplis, Dimitiros Genome Wide Association (GWAS) Analysis and genomic heritability for parasite resistance and growth in European seabass Journal Article Aquaculture Reports, 24 , pp. 101178, 2022, ISSN: 23525134. @article{oikonomou_genome_2022, title = {Genome Wide Association (GWAS) Analysis and genomic heritability for parasite resistance and growth in European seabass}, author = {Stavroula Oikonomou and Zoi Kazlari and Maria Papapetrou and Kantham Papanna and Leonidas Papaharisis and Tereza Manousaki and Dimitrios Loukovitis and Arkadios Dimitroglou and Lefteris Kottaras and Evgenia Gourzioti and Charalampos Pagonis and Andreas Kostandis and Costas S Tsigenopoulos and Dimitiros Chatziplis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Oikonomou-AqRep-45.pdf https://linkinghub.elsevier.com/retrieve/pii/S2352513422001740}, doi = {10.1016/j.aqrep.2022.101178}, issn = {23525134}, year = {2022}, date = {2022-01-01}, urldate = {2022-07-29}, journal = {Aquaculture Reports}, volume = {24}, pages = {101178}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Tsaparis, Dimitrios; Lecocq, Thomas; Kyriakis, Dimitrios; Oikonomaki, Katerina; Fontaine, Pascal; Tsigenopoulos, Costas S Assessing Genetic Variation in Wild and Domesticated Pikeperch Populations: Implications for Conservation and Fish Farming Journal Article Animals, 12 (9), pp. 1178, 2022, ISSN: 2076-2615. @article{tsaparis_assessing_2022, title = {Assessing Genetic Variation in Wild and Domesticated Pikeperch Populations: Implications for Conservation and Fish Farming}, author = {Dimitrios Tsaparis and Thomas Lecocq and Dimitrios Kyriakis and Katerina Oikonomaki and Pascal Fontaine and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Tsaparis-Animals-36.pdf https://www.mdpi.com/2076-2615/12/9/1178}, doi = {10.3390/ani12091178}, issn = {2076-2615}, year = {2022}, date = {2022-01-01}, urldate = {2022-05-09}, journal = {Animals}, volume = {12}, number = {9}, pages = {1178}, abstract = {The pikeperch is a freshwater/brackish water fish species with growing interest for European aquaculture. Wild populations show signs of decline in many areas of the species natural range due to human activities. The comparative evaluation of genetic status in wild and domesticated populations is extremely useful for the future establishment of genetic breeding programs. The main objective of the present study was to assess and compare the genetic variability of 13 domesticated populations from commercial farms and 8 wild populations, developing an efficient microsatellite multiplex tool for genotyping. Partial cytochrome b gene sequences were also used to infer phylogeographic relationships. Results show that on average, the domesticated populations do not exhibit significantly lower levels of genetic diversity compared to the wild ones and do not suffer from inbreeding. Nuclear data provide evidence that pikeperch populations in Europe belong to at least two genetically differentiated groups: the first one is predominantly present in Northern Europe and around the Baltic Sea, while the second one comprises populations from Central Europe. In this second group, Hungarian origin populations constitute a differentiated stock that needs special consideration. Aquaculture broodstocks analyzed appear to contain fish of a single origin with only a few exceptions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The pikeperch is a freshwater/brackish water fish species with growing interest for European aquaculture. Wild populations show signs of decline in many areas of the species natural range due to human activities. The comparative evaluation of genetic status in wild and domesticated populations is extremely useful for the future establishment of genetic breeding programs. The main objective of the present study was to assess and compare the genetic variability of 13 domesticated populations from commercial farms and 8 wild populations, developing an efficient microsatellite multiplex tool for genotyping. Partial cytochrome b gene sequences were also used to infer phylogeographic relationships. Results show that on average, the domesticated populations do not exhibit significantly lower levels of genetic diversity compared to the wild ones and do not suffer from inbreeding. Nuclear data provide evidence that pikeperch populations in Europe belong to at least two genetically differentiated groups: the first one is predominantly present in Northern Europe and around the Baltic Sea, while the second one comprises populations from Central Europe. In this second group, Hungarian origin populations constitute a differentiated stock that needs special consideration. Aquaculture broodstocks analyzed appear to contain fish of a single origin with only a few exceptions. |
2021 |
Nousias, Orestis; Tzokas, Konstantinos; Papaharisis, Leonidas; Ekonomaki, Katerina; Chatziplis, Dimitrios; Batargias, Costas; Tsigenopoulos, Costas S Genetic Variability, Population Structure, and Relatedness Analysis of Meagre Stocks as an Informative Basis for New Breeding Schemes Journal Article Fishes, 6 (4), pp. 78, 2021, ISSN: 2410-3888. @article{nousias_genetic_2021, title = {Genetic Variability, Population Structure, and Relatedness Analysis of Meagre Stocks as an Informative Basis for New Breeding Schemes}, author = {Orestis Nousias and Konstantinos Tzokas and Leonidas Papaharisis and Katerina Ekonomaki and Dimitrios Chatziplis and Costas Batargias and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/01/2021-Nousias-Fishes-85.pdf}, doi = {10.3390/fishes6040078}, issn = {2410-3888}, year = {2021}, date = {2021-12-01}, urldate = {2022-01-12}, journal = {Fishes}, volume = {6}, number = {4}, pages = {78}, abstract = {This study evaluates the genetic diversity of different meagre broodstocks sampled in Greece. A multiplex of twelve microsatellite markers was used to genotype 946 fish from eleven stocks and batches used for broodstock selection, and the genetic data was used to calculate genetic population parameters as well as to investigate the genetic differentiation between stocks. The results from a relatedness analysis were used as the guiding lines for a fine-tuned and overall evaluation of the genetic distance between stocks, and the choice of candidate breeders from some of them. The approach implemented in this study uses well-established population genetics methods to evaluate the selection of breeder candidates in aquaculture commercial conditions utilizing a descriptive genetic data set based on microsatellite analyses, and to outline an efficient methodology for establishing the basis of new breeding schemes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study evaluates the genetic diversity of different meagre broodstocks sampled in Greece. A multiplex of twelve microsatellite markers was used to genotype 946 fish from eleven stocks and batches used for broodstock selection, and the genetic data was used to calculate genetic population parameters as well as to investigate the genetic differentiation between stocks. The results from a relatedness analysis were used as the guiding lines for a fine-tuned and overall evaluation of the genetic distance between stocks, and the choice of candidate breeders from some of them. The approach implemented in this study uses well-established population genetics methods to evaluate the selection of breeder candidates in aquaculture commercial conditions utilizing a descriptive genetic data set based on microsatellite analyses, and to outline an efficient methodology for establishing the basis of new breeding schemes. |
Oikonomou, Stavroula; Tsakogiannis, Alexandros; Kriaridou, Christina; Danis, Theodoros; Manousaki, Tereza; Chatziplis, Dimitris; Papandroulakis, Nikos; Mylonas, Constantinos C; Triantafyllidis, Alexandros; Tsigenopoulos, Costas S 21 , pp. 100855, 2021, ISSN: 23525134. @article{oikonomou_first_2021, title = {First linkage maps and a pilot QTL analysis for early growth performance in common dentex (Dentex dentex) and sharpsnout seabream (Diplodus puntazzo)}, author = {Stavroula Oikonomou and Alexandros Tsakogiannis and Christina Kriaridou and Theodoros Danis and Tereza Manousaki and Dimitris Chatziplis and Nikos Papandroulakis and Constantinos C Mylonas and Alexandros Triantafyllidis and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Oikonomou-AquaReports-68.pdf https://linkinghub.elsevier.com/retrieve/pii/S2352513421002714}, doi = {10.1016/j.aqrep.2021.100855}, issn = {23525134}, year = {2021}, date = {2021-09-01}, urldate = {2021-09-22}, volume = {21}, pages = {100855}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Peñaloza, C; Manousaki, T; Franch, R; Tsakogiannis, A; Sonesson, A K; Aslam, M L; Allal, F; Bargelloni, L; Houston, R D; Tsigenopoulos, C S Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata) Journal Article Genomics, 113 (4), pp. 2096–2107, 2021, ISSN: 08887543. @article{penaloza_development_2021, title = {Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata)}, author = {C Peñaloza and T Manousaki and R Franch and A Tsakogiannis and A K Sonesson and M L Aslam and F Allal and L Bargelloni and R D Houston and C S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/06/2021-Penaloza-Genomics-39.pdf https://linkinghub.elsevier.com/retrieve/pii/S0888754321001713}, doi = {10.1016/j.ygeno.2021.04.038}, issn = {08887543}, year = {2021}, date = {2021-07-01}, urldate = {2021-06-24}, journal = {Genomics}, volume = {113}, number = {4}, pages = {2096--2107}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Tsaparis, Dimitris; Konstantinidis, Ioannis; Palandacic, Anja; Kalogianni, Eleni; Stoumboudi, Maria Th.; Barbieri, Roberta; Vardakas, Leonidas; Koutsikos, Nicholas; Tsigenopoulos, Costas S Hydrobiologia, 848 (5), pp. 1163–1176, 2021, ISSN: 0018-8158, 1573-5117. @article{tsaparis_dna_2021, title = {DNA barcoding provides new insights on the distribution, systematics and conservation of the freshwater genus Pelasgus (Cypriniformes: Cyprinidae) in Greece}, author = {Dimitris Tsaparis and Ioannis Konstantinidis and Anja Palandacic and Eleni Kalogianni and Maria Th. Stoumboudi and Roberta Barbieri and Leonidas Vardakas and Nicholas Koutsikos and Costas S Tsigenopoulos}, url = {http://link.springer.com/10.1007/s10750-021-04526-9}, doi = {10.1007/s10750-021-04526-9}, issn = {0018-8158, 1573-5117}, year = {2021}, date = {2021-03-01}, urldate = {2021-02-24}, journal = {Hydrobiologia}, volume = {848}, number = {5}, pages = {1163--1176}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Krick, Madoka Vera; Desmarais, Erick; Samaras, Athanasios; Guéret, Elise; Dimitroglou, Arkadios; Pavlidis, Michalis; Tsigenopoulos, Costas; Guinand, Bruno Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.) Journal Article BMC Genomics, 22 (1), pp. 111, 2021, ISSN: 1471-2164. @article{krick_family-effects_2021, title = {Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.)}, author = {Madoka Vera Krick and Erick Desmarais and Athanasios Samaras and Elise Guéret and Arkadios Dimitroglou and Michalis Pavlidis and Costas Tsigenopoulos and Bruno Guinand}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021-Krick-2021_Family-effects-in-sb-BMG-Genomics-14.pdf https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07420-9}, doi = {10.1186/s12864-021-07420-9}, issn = {1471-2164}, year = {2021}, date = {2021-01-01}, urldate = {2021-02-24}, journal = {BMC Genomics}, volume = {22}, number = {1}, pages = {111}, abstract = {Abstract Background In fish, minimally invasive blood sampling is widely used to monitor physiological stress with blood plasma biomarkers. As fish blood cells are nucleated, they might be a source a potential new markers derived from ‘omics technologies. We modified the epiGBS (epiGenotyping By Sequencing) technique to explore changes in genome-wide cytosine methylation in the red blood cells (RBCs) of challenged European sea bass ( Dicentrarchus labrax ), a species widely studied in both natural and farmed environments. Results We retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% (unique best hits). Minor changes in RBC methylome appeared to manifest after the challenge test and a family-effect was detected. Only fifty-seven differentially methylated cytosines (DMCs) close to 51 distinct genes distributed on 17 of 24 linkage groups (LGs) were detected between RBCs of pre- and post-challenge individuals. Thirty-seven of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences. While further investigation remains necessary, few DMC-related genes associated to the Brain Derived Neurotrophic Factor, a protein that favors stress adaptation and fear memory, appear relevant to integrate a centrally produced stress response in RBCs. Conclusion Our modified epiGBS protocol was powerful to analyze patterns of cytosine methylation in RBCs of D. labrax and to evaluate the impact of a challenge using minimally invasive blood samples . This study is the first approximation to identify epigenetic biomarkers of exposure to stress in fish.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Background In fish, minimally invasive blood sampling is widely used to monitor physiological stress with blood plasma biomarkers. As fish blood cells are nucleated, they might be a source a potential new markers derived from ‘omics technologies. We modified the epiGBS (epiGenotyping By Sequencing) technique to explore changes in genome-wide cytosine methylation in the red blood cells (RBCs) of challenged European sea bass ( Dicentrarchus labrax ), a species widely studied in both natural and farmed environments. Results We retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% (unique best hits). Minor changes in RBC methylome appeared to manifest after the challenge test and a family-effect was detected. Only fifty-seven differentially methylated cytosines (DMCs) close to 51 distinct genes distributed on 17 of 24 linkage groups (LGs) were detected between RBCs of pre- and post-challenge individuals. Thirty-seven of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences. While further investigation remains necessary, few DMC-related genes associated to the Brain Derived Neurotrophic Factor, a protein that favors stress adaptation and fear memory, appear relevant to integrate a centrally produced stress response in RBCs. Conclusion Our modified epiGBS protocol was powerful to analyze patterns of cytosine methylation in RBCs of D. labrax and to evaluate the impact of a challenge using minimally invasive blood samples . This study is the first approximation to identify epigenetic biomarkers of exposure to stress in fish. |
Mladineo, Ivona; Hrabar, Jerko; Trumbić, Željka; Manousaki, Tereza; Tsakogiannis, Alexandros; Taggart, John B; Tsigenopoulos, Costas S Pathogens, 10 (2), pp. 100, 2021, ISSN: 2076-0817. @article{mladineo_community_2021, title = {Community Parameters and Genome-Wide RAD-Seq Loci of Ceratothoa oestroides Imply Its Transfer between Farmed European Sea Bass and Wild Farm-Aggregating Fish}, author = {Ivona Mladineo and Jerko Hrabar and Željka Trumbić and Tereza Manousaki and Alexandros Tsakogiannis and John B Taggart and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2020-Mladineo-Pathogens-7.pdf https://www.mdpi.com/2076-0817/10/2/100}, doi = {10.3390/pathogens10020100}, issn = {2076-0817}, year = {2021}, date = {2021-01-01}, urldate = {2021-02-02}, journal = {Pathogens}, volume = {10}, number = {2}, pages = {100}, abstract = {Wild fish assemblages that aggregate within commercial marine aquaculture sites for feeding and shelter have been considered as a primary source of pathogenic parasites vectored to farmed fish maintained in net pens at an elevated density. In order to evaluate whether Ceratothoa oestroides (Isopoda, Cymothoidae), a generalist and pestilent isopod that is frequently found in Adriatic and Greek stocks of farmed European sea bass (Dicentrarchus labrax), transfers between wild and farmed fish, a RAD-Seq (restriction-site-associated DNA sequencing)-mediated genetic screening approach was employed. The double-digest RAD-Seq of 310 C. oestroides specimens collected from farmed European sea bass (138) and different wild farm-aggregating fish (172) identified 313 robust SNPs that evidenced a close genetic relatedness between the “wild” and “farmed” genotypes. ddRAD-Seq proved to be an effective method for detecting the discrete genetic structuring of C. oestroides and genotype intermixing between two populations. The parasite prevalence in the farmed sea bass was 1.02%, with a mean intensity of 2.0 and mean abundance of 0.02, while in the wild fish, the prevalence was 8.1%; the mean intensity, 1.81; and the mean abundance, 0.15. Such differences are likely a consequence of human interventions during the farmed fish’s rearing cycle that, nevertheless, did not affect the transfer of C. oestroides.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Wild fish assemblages that aggregate within commercial marine aquaculture sites for feeding and shelter have been considered as a primary source of pathogenic parasites vectored to farmed fish maintained in net pens at an elevated density. In order to evaluate whether Ceratothoa oestroides (Isopoda, Cymothoidae), a generalist and pestilent isopod that is frequently found in Adriatic and Greek stocks of farmed European sea bass (Dicentrarchus labrax), transfers between wild and farmed fish, a RAD-Seq (restriction-site-associated DNA sequencing)-mediated genetic screening approach was employed. The double-digest RAD-Seq of 310 C. oestroides specimens collected from farmed European sea bass (138) and different wild farm-aggregating fish (172) identified 313 robust SNPs that evidenced a close genetic relatedness between the “wild” and “farmed” genotypes. ddRAD-Seq proved to be an effective method for detecting the discrete genetic structuring of C. oestroides and genotype intermixing between two populations. The parasite prevalence in the farmed sea bass was 1.02%, with a mean intensity of 2.0 and mean abundance of 0.02, while in the wild fish, the prevalence was 8.1%; the mean intensity, 1.81; and the mean abundance, 0.15. Such differences are likely a consequence of human interventions during the farmed fish’s rearing cycle that, nevertheless, did not affect the transfer of C. oestroides. |
Papapetrou, Maria; Kazlari, Zoi; Papanna, Kantham; Papaharisis, Leonidas; Oikonomou, Stavroula; Manousaki, Tereza; Loukovitis, Dimitrios; Kottaras, Lefteris; Dimitroglou, Arkadios; Gourzioti, Evgenia; Pagonis, Charalampos; Kostandis, Andreas; Tsigenopoulos, Costas S; Chatziplis, Dimitrios Aquaculture Reports, 20 , pp. 100767, 2021, ISSN: 23525134. @article{papapetrou_trail_2021, title = {On the trail of detecting genetic (co)variation between resistance to parasite infections (Diplectanum aequans and Lernanthropus kroyeri) and growth in European seabass (Dicentrarchus labrax)}, author = {Maria Papapetrou and Zoi Kazlari and Kantham Papanna and Leonidas Papaharisis and Stavroula Oikonomou and Tereza Manousaki and Dimitrios Loukovitis and Lefteris Kottaras and Arkadios Dimitroglou and Evgenia Gourzioti and Charalampos Pagonis and Andreas Kostandis and Costas S Tsigenopoulos and Dimitrios Chatziplis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/06/2021-Papapetrou-AquaRep-46.pdf https://linkinghub.elsevier.com/retrieve/pii/S2352513421001836}, doi = {10.1016/j.aqrep.2021.100767}, issn = {23525134}, year = {2021}, date = {2021-01-01}, urldate = {2021-06-24}, journal = {Aquaculture Reports}, volume = {20}, pages = {100767}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Superio, Joshua; Fakriadis, Ioannis; Tsigenopoulos, Costas S; Lancerotto, Stefano Adam; Rodriguez, Andrea Villena; Vervelakis, Emanuele; Mylonas, Constantinos C Spawning kinetics and parentage contribution of European sea bass (Dicentrarchus labrax) broodstocks, and influence of GnRHa-induced spawning Journal Article Aquaculture Reports, 21 , pp. 100766, 2021, ISSN: 23525134. @article{superio_spawning_2021, title = {Spawning kinetics and parentage contribution of European sea bass (Dicentrarchus labrax) broodstocks, and influence of GnRHa-induced spawning}, author = {Joshua Superio and Ioannis Fakriadis and Costas S Tsigenopoulos and Stefano Adam Lancerotto and Andrea Villena Rodriguez and Emanuele Vervelakis and Constantinos C Mylonas}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/07/2021-Superio-AquaRep-47.pdf https://linkinghub.elsevier.com/retrieve/pii/S2352513421001824}, doi = {10.1016/j.aqrep.2021.100766}, issn = {23525134}, year = {2021}, date = {2021-01-01}, urldate = {2021-07-26}, journal = {Aquaculture Reports}, volume = {21}, pages = {100766}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Zafeiropoulos, Haris; Gioti, Anastasia; Ninidakis, Stelios; Potirakis, Antonis; Paragkamian, Savvas; Angelova, Nelina; Antoniou, Aglaia; Danis, Theodoros; Kaitetzidou, Eliza; Kasapidis, Panagiotis; Kristoffersen, Jon Bent; Papadogiannis, Vasileios; Pavloudi, Christina; Ha, Quoc Viet; Lagnel, Jacques; Pattakos, Nikos; Perantinos, Giorgos; Sidirokastritis, Dimitris; Vavilis, Panagiotis; Kotoulas, Georgios; Manousaki, Tereza; Sarropoulou, Elena; Tsigenopoulos, Costas S; Arvanitidis, Christos; Magoulas, Antonios; Pafilis, Evangelos 0s and 1s in marine molecular research: a regional HPC perspective Journal Article GigaScience, 10 (8), pp. giab053, 2021, ISSN: 2047-217X. @article{zafeiropoulos_0s_2021, title = {0s and 1s in marine molecular research: a regional HPC perspective}, author = {Haris Zafeiropoulos and Anastasia Gioti and Stelios Ninidakis and Antonis Potirakis and Savvas Paragkamian and Nelina Angelova and Aglaia Antoniou and Theodoros Danis and Eliza Kaitetzidou and Panagiotis Kasapidis and Jon Bent Kristoffersen and Vasileios Papadogiannis and Christina Pavloudi and Quoc Viet Ha and Jacques Lagnel and Nikos Pattakos and Giorgos Perantinos and Dimitris Sidirokastritis and Panagiotis Vavilis and Georgios Kotoulas and Tereza Manousaki and Elena Sarropoulou and Costas S Tsigenopoulos and Christos Arvanitidis and Antonios Magoulas and Evangelos Pafilis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/08/2021-Zafeiropoulos-GiGa-63.pdf https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giab053/6353916}, doi = {10.1093/gigascience/giab053}, issn = {2047-217X}, year = {2021}, date = {2021-01-01}, urldate = {2021-08-23}, journal = {GigaScience}, volume = {10}, number = {8}, pages = {giab053}, abstract = {Abstract High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned. |
Danis, Theodoros; Papadogiannis, Vasileios; Tsakogiannis, Alexandros; Kristoffersen, Jon B; Golani, Daniel; Tsaparis, Dimitris; Sterioti, Aspasia; Kasapidis, Panagiotis; Kotoulas, Georgios; Magoulas, Antonios; Tsigenopoulos, Costas S; Manousaki, Tereza Genome Analysis of Lagocephalus sceleratus: Unraveling the Genomic Landscape of a Successful Invader Journal Article Frontiers in Genetics, 12 , pp. 2481, 2021, ISSN: 1664-8021. @article{danis_genome_2021, title = {Genome Analysis of Lagocephalus sceleratus: Unraveling the Genomic Landscape of a Successful Invader}, author = {Theodoros Danis and Vasileios Papadogiannis and Alexandros Tsakogiannis and Jon B Kristoffersen and Daniel Golani and Dimitris Tsaparis and Aspasia Sterioti and Panagiotis Kasapidis and Georgios Kotoulas and Antonios Magoulas and Costas S Tsigenopoulos and Tereza Manousaki}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/01/2021-Danis-FrontGen-84.pdf https://www.frontiersin.org/article/10.3389/fgene.2021.790850}, doi = {10.3389/fgene.2021.790850}, issn = {1664-8021}, year = {2021}, date = {2021-01-01}, urldate = {2022-01-12}, journal = {Frontiers in Genetics}, volume = {12}, pages = {2481}, abstract = {The Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. The silver-cheeked toadfish (Lagocephalus sceleratus) is a well-known “invasive sprinter” that has invaded and spread, in less than a decade, throughout the Eastern and part of the Western Mediterranean Sea from the Red Sea through the Suez Canal. In this study, we built and analysed the first near-chromosome level genome assembly of L. sceleratus and explored its evolutionary landscape. Through a phylogenomic analysis, we positioned L. sceleratus closer to T. nigroviridis, compared to other members of the family, while gene family evolution analysis revealed that genes associated with the immune response have experienced rapid expansion, providing a genetic basis for studying how L. sceleratus is able to achieve highly successful colonisation. Moreover, we found that voltage-gated sodium channel (NaV 1.4) mutations previously connected to tetrodotoxin resistance in other pufferfishes are not found in L. sceleratus, highlighting the complex evolution of this trait. The high-quality genome assembly built here is expected to set the ground for future studies on the species biology.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. The silver-cheeked toadfish (Lagocephalus sceleratus) is a well-known “invasive sprinter” that has invaded and spread, in less than a decade, throughout the Eastern and part of the Western Mediterranean Sea from the Red Sea through the Suez Canal. In this study, we built and analysed the first near-chromosome level genome assembly of L. sceleratus and explored its evolutionary landscape. Through a phylogenomic analysis, we positioned L. sceleratus closer to T. nigroviridis, compared to other members of the family, while gene family evolution analysis revealed that genes associated with the immune response have experienced rapid expansion, providing a genetic basis for studying how L. sceleratus is able to achieve highly successful colonisation. Moreover, we found that voltage-gated sodium channel (NaV 1.4) mutations previously connected to tetrodotoxin resistance in other pufferfishes are not found in L. sceleratus, highlighting the complex evolution of this trait. The high-quality genome assembly built here is expected to set the ground for future studies on the species biology. |
2020 |
Chatziplis, Dimitrios; Oikonomou, Stavroula; Loukovitis, Dimitrios; Tsiokos, Dimitrios; Samaras, Athanasios; Dimitroglou, Arkadios; Kottaras, Lefteris; Papanna, Kantham; Papaharisis, Leonidas; Tsigenopoulos, Costas; Pavlidis, Michail QTL for Stress and Disease Resistance in European Sea Bass, Dicentrarhus labrax L. Journal Article Animals, 10 (9), pp. 1668, 2020, ISSN: 2076-2615. @article{chatziplis_qtl_2020, title = {QTL for Stress and Disease Resistance in European Sea Bass, Dicentrarhus labrax L.}, author = {Dimitrios Chatziplis and Stavroula Oikonomou and Dimitrios Loukovitis and Dimitrios Tsiokos and Athanasios Samaras and Arkadios Dimitroglou and Lefteris Kottaras and Kantham Papanna and Leonidas Papaharisis and Costas Tsigenopoulos and Michail Pavlidis}, url = {https://www.mdpi.com/2076-2615/10/9/1668}, doi = {10.3390/ani10091668}, issn = {2076-2615}, year = {2020}, date = {2020-09-01}, urldate = {2020-10-05}, journal = {Animals}, volume = {10}, number = {9}, pages = {1668}, abstract = {There is a growing interest in selective breeding in European sea bass (Dicentrarchus labrax), especially regarding family selection based on growth performance. In particular, quantitative trait loci (QTL) identification in sea bass enhances the application of marker-assisted breeding for the genetic improvement of the production traits. The aims of the study were to identify potential QTL affecting stress and immunological indicators, body weight, and mortality after vibriosis injection in sea bass as well as to estimate heritability and genetic/phenotypic correlations for the aforementioned traits. To this end, stress test was performed on 960 offspring and a sub-group of them (420) was selected to explore the mortality after vibrio injection. Selective genotyping was performed in 620 offspring for 35 microsatellite markers and distributed into 6 linkage groups. The length of the genetic linkage map was 283.6 cM and the mean distance between the markers was 8.1 cM. QTL affecting body weight in three different growth periods detected on linkage groups LG1, LG4, LG6, and LG14. A QTL associated with weight in early growth stages (290–306 days post-hatching) was also identified on LG3. QTL analysis confirmed the existence of QTL affecting cortisol levels, on LG3 and LG14. Moreover, new QTL affecting only cortisol and glucose levels were detected on LG1 and LG23. No QTL affecting hormonal or biochemical marks was found on LG4 and LG6. Heritability of cortisol, lysozyme levels, and mortality were high (0.36, 0.55, and 0.38, respectively).}, keywords = {}, pubstate = {published}, tppubtype = {article} } There is a growing interest in selective breeding in European sea bass (Dicentrarchus labrax), especially regarding family selection based on growth performance. In particular, quantitative trait loci (QTL) identification in sea bass enhances the application of marker-assisted breeding for the genetic improvement of the production traits. The aims of the study were to identify potential QTL affecting stress and immunological indicators, body weight, and mortality after vibriosis injection in sea bass as well as to estimate heritability and genetic/phenotypic correlations for the aforementioned traits. To this end, stress test was performed on 960 offspring and a sub-group of them (420) was selected to explore the mortality after vibrio injection. Selective genotyping was performed in 620 offspring for 35 microsatellite markers and distributed into 6 linkage groups. The length of the genetic linkage map was 283.6 cM and the mean distance between the markers was 8.1 cM. QTL affecting body weight in three different growth periods detected on linkage groups LG1, LG4, LG6, and LG14. A QTL associated with weight in early growth stages (290–306 days post-hatching) was also identified on LG3. QTL analysis confirmed the existence of QTL affecting cortisol levels, on LG3 and LG14. Moreover, new QTL affecting only cortisol and glucose levels were detected on LG1 and LG23. No QTL affecting hormonal or biochemical marks was found on LG4 and LG6. Heritability of cortisol, lysozyme levels, and mortality were high (0.36, 0.55, and 0.38, respectively). |
Nousias, Orestis; Tsakogiannis, Alexandros; Duncan, Neil; Villa, Javier; Tzokas, Kostas; Estevez, Alicia; Chatziplis, Dimitrios; Tsigenopoulos, Costas S Parentage assignment, estimates of heritability and genetic correlation for growth-related traits in meagre Argyrosomus regius Journal Article Aquaculture, 518 , pp. 734663, 2020, ISSN: 00448486. @article{nousias_parentage_2020, title = {Parentage assignment, estimates of heritability and genetic correlation for growth-related traits in meagre Argyrosomus regius}, author = {Orestis Nousias and Alexandros Tsakogiannis and Neil Duncan and Javier Villa and Kostas Tzokas and Alicia Estevez and Dimitrios Chatziplis and Costas S Tsigenopoulos}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848619314346}, doi = {10.1016/j.aquaculture.2019.734663}, issn = {00448486}, year = {2020}, date = {2020-03-01}, urldate = {2020-08-18}, journal = {Aquaculture}, volume = {518}, pages = {734663}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Koutsouveli, Vasiliki; Manousaki, Tereza; Riesgo, Ana; Lagnel, Jacques; Kollias, Spyros; Tsigenopoulos, Costas S; Arvanitidis, Christos; Dounas, Costas; Magoulas, Antonios; Dailianis, Thanos Frontiers in Marine Science, 6 , pp. 786, 2020, ISSN: 2296-7745. @article{koutsouveli_gearing_2020, title = {Gearing Up for Warmer Times: Transcriptomic Response of Spongia officinalis to Elevated Temperatures Reveals Recruited Mechanisms and Potential for Resilience}, author = {Vasiliki Koutsouveli and Tereza Manousaki and Ana Riesgo and Jacques Lagnel and Spyros Kollias and Costas S Tsigenopoulos and Christos Arvanitidis and Costas Dounas and Antonios Magoulas and Thanos Dailianis}, url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00786/full}, doi = {10.3389/fmars.2019.00786}, issn = {2296-7745}, year = {2020}, date = {2020-01-01}, urldate = {2020-08-06}, journal = {Frontiers in Marine Science}, volume = {6}, pages = {786}, abstract = {The emblematic sponge Spongia officinalis is currently threatened by recurrent mortality incidents in its native habitats. Elevated temperature has been indicated as a major triggering factor, but the molecular mechanisms recruited for the organism’s response to thermal shifts are yet unknown. Here, we experimentally tested the effect of exposure to temperatures of varying intensity and span on its gene expression profile, replicating gradients encountered in the species’ native habitat. Analysis revealed major shifts in the organism’s transcriptomic profile induced by temperatures corresponding to the standard seasonal maximum, triggering processes related to signal transduction, inflammation, and apoptotic pathway. Further elevation of temperature corresponding to local extremes activated further the immune response of the sponge along with protein ubiquitination. Following prolonged exposure, activation of endoplasmic reticulum stress related to accumulation of misfolded proteins and signs of resilience were observed. In the latter condition, categories such as cellular response to stress, wound repair, and diminution of pathological inflammation as also genes related to cell regeneration and cell growth were upregulated. Our results highlight the acknowledged sensitivity of S. officinalis to environmental shifts, providing an insight into the molecular mechanisms involved in the process. Furthermore, they suggest innate capacity for resilience at the current thermal extremes, implying a combination of factors and not temperature per se as the lethal agent. This sheds light on the mechanisms of pressure induced by the ongoing ocean warming trend to coastal sessile invertebrates.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The emblematic sponge Spongia officinalis is currently threatened by recurrent mortality incidents in its native habitats. Elevated temperature has been indicated as a major triggering factor, but the molecular mechanisms recruited for the organism’s response to thermal shifts are yet unknown. Here, we experimentally tested the effect of exposure to temperatures of varying intensity and span on its gene expression profile, replicating gradients encountered in the species’ native habitat. Analysis revealed major shifts in the organism’s transcriptomic profile induced by temperatures corresponding to the standard seasonal maximum, triggering processes related to signal transduction, inflammation, and apoptotic pathway. Further elevation of temperature corresponding to local extremes activated further the immune response of the sponge along with protein ubiquitination. Following prolonged exposure, activation of endoplasmic reticulum stress related to accumulation of misfolded proteins and signs of resilience were observed. In the latter condition, categories such as cellular response to stress, wound repair, and diminution of pathological inflammation as also genes related to cell regeneration and cell growth were upregulated. Our results highlight the acknowledged sensitivity of S. officinalis to environmental shifts, providing an insight into the molecular mechanisms involved in the process. Furthermore, they suggest innate capacity for resilience at the current thermal extremes, implying a combination of factors and not temperature per se as the lethal agent. This sheds light on the mechanisms of pressure induced by the ongoing ocean warming trend to coastal sessile invertebrates. |
Aslam, Muhammad Luqman; Carraro, Roberta; Sonesson, Anna Kristina; Meuwissen, Theodorus; Tsigenopoulos, Costas S; Rigos, George; Bargelloni, Luca; Tzokas, Konstantinos Genetic Variation, GWAS and Accuracy of Prediction for Host Resistance to Sparicotyle chrysophrii in Farmed Gilthead Sea Bream (Sparus aurata) Journal Article Frontiers in Genetics, 11 , pp. 594770, 2020, ISSN: 1664-8021. @article{aslam_genetic_2020, title = {Genetic Variation, GWAS and Accuracy of Prediction for Host Resistance to Sparicotyle chrysophrii in Farmed Gilthead Sea Bream (Sparus aurata)}, author = {Muhammad Luqman Aslam and Roberta Carraro and Anna Kristina Sonesson and Theodorus Meuwissen and Costas S Tsigenopoulos and George Rigos and Luca Bargelloni and Konstantinos Tzokas}, url = {https://www.frontiersin.org/articles/10.3389/fgene.2020.594770/full https://imbbc.hcmr.gr/wp-content/uploads/2020/12/2020-Aslam-Frontiers-inGen-55.pdf}, doi = {10.3389/fgene.2020.594770}, issn = {1664-8021}, year = {2020}, date = {2020-01-01}, urldate = {2020-12-29}, journal = {Frontiers in Genetics}, volume = {11}, pages = {594770}, abstract = {Gilthead sea bream ( Sparus aurata ) belongs to a group of teleost which has high importance in Mediterranean aquaculture industry. However, industrial production is increasingly compromised by an elevated outbreak of diseases in sea cages, especially a disease caused by monogeneans parasite Sparicotyle chrysophrii. This parasite mainly colonizes gill tissues of host and causes considerable economical losses with mortality and reduction in growth. The aim of current study was to explore the genetics of host resistance against S. chrysophrii and investigate the potential for genomic selection to possibly accelerate genetic progress. To achieve the desired goals, a test population derived from the breeding nucleus of Andromeda Group was produced. This experimental population was established by crossing of parents mated in partial factorial crosses of ∼8 × 8 using 58 sires and 62 dams. The progeny obtained from this mating design was challenged with S. chrysophrii using a controllable cohabitation infection model. At the end of the challenge, fish were recorded for parasite count, and all the recorded fish were tissue sampled for genotyping by sequencing using 2b-RAD methodology. The initial (before challenge test) and the final body weight (after challenge test) of the fish were also recorded. The results obtained through the analysis of phenotypic records ( n = 615) and the genotypic data ( n = 841, 724 offspring and 117 parents) revealed that the resistance against this parasite is lowly heritable ( h 2 = 0.147 with pedigree and 0.137 with genomic information). We observed moderately favorable genetic correlation ( R g = −0.549 to −0.807) between production traits (i.e., body weight and specific growth rate) and parasite count, which signals a possibility of indirect selection. A locus at linkage group 17 was identified that surpassed chromosome-wide Bonferroni threshold which explained 22.68% of the total genetic variance, and might be playing role in producing genetic variation. The accuracy of prediction was improved by 8% with genomic information compared to pedigree.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Gilthead sea bream ( Sparus aurata ) belongs to a group of teleost which has high importance in Mediterranean aquaculture industry. However, industrial production is increasingly compromised by an elevated outbreak of diseases in sea cages, especially a disease caused by monogeneans parasite Sparicotyle chrysophrii. This parasite mainly colonizes gill tissues of host and causes considerable economical losses with mortality and reduction in growth. The aim of current study was to explore the genetics of host resistance against S. chrysophrii and investigate the potential for genomic selection to possibly accelerate genetic progress. To achieve the desired goals, a test population derived from the breeding nucleus of Andromeda Group was produced. This experimental population was established by crossing of parents mated in partial factorial crosses of ∼8 × 8 using 58 sires and 62 dams. The progeny obtained from this mating design was challenged with S. chrysophrii using a controllable cohabitation infection model. At the end of the challenge, fish were recorded for parasite count, and all the recorded fish were tissue sampled for genotyping by sequencing using 2b-RAD methodology. The initial (before challenge test) and the final body weight (after challenge test) of the fish were also recorded. The results obtained through the analysis of phenotypic records ( n = 615) and the genotypic data ( n = 841, 724 offspring and 117 parents) revealed that the resistance against this parasite is lowly heritable ( h 2 = 0.147 with pedigree and 0.137 with genomic information). We observed moderately favorable genetic correlation ( R g = −0.549 to −0.807) between production traits (i.e., body weight and specific growth rate) and parasite count, which signals a possibility of indirect selection. A locus at linkage group 17 was identified that surpassed chromosome-wide Bonferroni threshold which explained 22.68% of the total genetic variance, and might be playing role in producing genetic variation. The accuracy of prediction was improved by 8% with genomic information compared to pedigree. |
Polovina, Eirini-Slavka; Kourkouni, Evelina; Tsigenopoulos, Costas S; Sanchez-Jerez, Pablo; Ladoukakis, Emmanuel D Aquatic Living Resources, 33 , pp. 7, 2020, ISSN: 1765-2952. @article{polovina_genetic_2020, title = {Genetic structuring in farmed and wild Gilthead seabream and European seabass in the Mediterranean Sea: implementations for detection of escapees}, author = {Eirini-Slavka Polovina and Evelina Kourkouni and Costas S Tsigenopoulos and Pablo Sanchez-Jerez and Emmanuel D Ladoukakis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2020-Polovina-SciRep.pdf https://www.alr-journal.org/10.1051/alr/2020007}, doi = {10.1051/alr/2020007}, issn = {1765-2952}, year = {2020}, date = {2020-01-01}, urldate = {2020-08-31}, journal = {Aquatic Living Resources}, volume = {33}, pages = {7}, abstract = {Microsatellite markers were used to investigate the genetic structure of the two most important cultured fish in the Mediterranean Sea, the gilthead seabream ( Sparus aurata ) and the European seabass ( Dicentrarchus labrax ), from two (one wild and one farmed) populations in Western Mediterranean (Spain) and from two (one wild and one farmed) populations Eastern Mediterranean (Greece). All populations were in Hardy-Weinberg disequilibrium. Interestingly, wild and farmed populations for both species from Greece were genetically differentiated and could be distinguished from each other. We used Bayesian methods for cluster analysis of farmed and wild populations. Our analysis has implications for the identification of escapees from fish farms to the wild.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Microsatellite markers were used to investigate the genetic structure of the two most important cultured fish in the Mediterranean Sea, the gilthead seabream ( Sparus aurata ) and the European seabass ( Dicentrarchus labrax ), from two (one wild and one farmed) populations in Western Mediterranean (Spain) and from two (one wild and one farmed) populations Eastern Mediterranean (Greece). All populations were in Hardy-Weinberg disequilibrium. Interestingly, wild and farmed populations for both species from Greece were genetically differentiated and could be distinguished from each other. We used Bayesian methods for cluster analysis of farmed and wild populations. Our analysis has implications for the identification of escapees from fish farms to the wild. |
2019 |
Manousaki, Tereza; Koutsouveli, Vasiliki; Lagnel, Jacques; Kollias, Spyridon; Tsigenopoulos, Costas S; Arvanitidis, Christos; Magoulas, Antonios; Dounas, Costas; Dailianis, Thanos A de novo transcriptome assembly for the bath sponge Spongia officinalis, adjusting for microsymbionts Journal Article BMC Research Notes, 12 (1), pp. 813, 2019, ISSN: 1756-0500. @article{manousaki_novo_2019, title = {A de novo transcriptome assembly for the bath sponge Spongia officinalis, adjusting for microsymbionts}, author = {Tereza Manousaki and Vasiliki Koutsouveli and Jacques Lagnel and Spyridon Kollias and Costas S Tsigenopoulos and Christos Arvanitidis and Antonios Magoulas and Costas Dounas and Thanos Dailianis}, url = {https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4843-6}, doi = {10.1186/s13104-019-4843-6}, issn = {1756-0500}, year = {2019}, date = {2019-12-01}, urldate = {2020-08-06}, journal = {BMC Research Notes}, volume = {12}, number = {1}, pages = {813}, abstract = {Objectives We report a transcriptome acquisition for the bath sponge Spongia officinalis, a non-model marine organism that hosts rich symbiotic microbial communities. To this end, a pipeline was developed to efficiently separate between bacterial expressed genes from those of eukaryotic origin. The transcriptome was produced to support the assessment of gene expression and, thus, the response of the sponge, to elevated temperatures, replicating conditions currently occurring in its native habitat. Data description We describe the assembled transcriptome along with the bioinformatic pipeline used to discriminate between signals of metazoan and prokaryotic origin. The pipeline involves standard read pre-processing steps and incorporates extra analyses to identify and filter prokaryotic reads out of the analysis. The proposed pipeline can be followed to overcome the technical RNASeq problems characteristic for symbiont-rich metazoan organisms with low or non-existent tissue differentiation, such as sponges and cnidarians. At the same time, it can be valuable towards the development of approaches for parallel transcriptomic studies of symbiotic communities and the host.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Objectives We report a transcriptome acquisition for the bath sponge Spongia officinalis, a non-model marine organism that hosts rich symbiotic microbial communities. To this end, a pipeline was developed to efficiently separate between bacterial expressed genes from those of eukaryotic origin. The transcriptome was produced to support the assessment of gene expression and, thus, the response of the sponge, to elevated temperatures, replicating conditions currently occurring in its native habitat. Data description We describe the assembled transcriptome along with the bioinformatic pipeline used to discriminate between signals of metazoan and prokaryotic origin. The pipeline involves standard read pre-processing steps and incorporates extra analyses to identify and filter prokaryotic reads out of the analysis. The proposed pipeline can be followed to overcome the technical RNASeq problems characteristic for symbiont-rich metazoan organisms with low or non-existent tissue differentiation, such as sponges and cnidarians. At the same time, it can be valuable towards the development of approaches for parallel transcriptomic studies of symbiotic communities and the host. |
Natsidis, Paschalis; Tsakogiannis, Alexandros; Pavlidis, Pavlos; Tsigenopoulos, Costas S; Manousaki, Tereza Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling Journal Article Communications Biology, 2 (1), pp. 400, 2019, ISSN: 2399-3642. @article{natsidis_phylogenomics_2019, title = {Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling}, author = {Paschalis Natsidis and Alexandros Tsakogiannis and Pavlos Pavlidis and Costas S Tsigenopoulos and Tereza Manousaki}, url = {http://www.nature.com/articles/s42003-019-0654-5}, doi = {10.1038/s42003-019-0654-5}, issn = {2399-3642}, year = {2019}, date = {2019-12-01}, urldate = {2020-08-18}, journal = {Communications Biology}, volume = {2}, number = {1}, pages = {400}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Exadactylos, Athanasios; Vafidis, Dimitrios; Tsigenopoulos, Costas; Gkafas, Georgios High Connectivity of the White Seabream (Diplodus sargus, L. 1758) in the Aegean Sea, Eastern Mediterranean Basin Journal Article Animals, 9 (11), pp. 979, 2019, ISSN: 2076-2615, (BIODIV). @article{exadactylos_high_2019, title = {High Connectivity of the White Seabream (Diplodus sargus, L. 1758) in the Aegean Sea, Eastern Mediterranean Basin}, author = {Athanasios Exadactylos and Dimitrios Vafidis and Costas Tsigenopoulos and Georgios Gkafas}, url = {https://www.mdpi.com/2076-2615/9/11/979}, doi = {10.3390/ani9110979}, issn = {2076-2615}, year = {2019}, date = {2019-11-01}, urldate = {2022-01-17}, journal = {Animals}, volume = {9}, number = {11}, pages = {979}, abstract = {Population dynamics in the marine realm can shape species’ spatial structure and genetic variability between given geographical areas. Connectivity is an important factor of species’ population structure. In this study, we examined the genetic diversity and structure of white seabream (Diplodus sargus, L. 1758) in the eastern Mediterranean basin, using a panel of four microsatellite markers. Recorded low FST values within the study area indicate little evidence of genetic differentiation among populations. Results suggest high gene flow which may imply near-panmixia between populations, indicating the possibility of a probable movement of adult migrants, or strong passive drift at sea in early life stages of the species. To this extent, bibliographically speaking, different species within the Sparidae family favor altered population dynamics patterns with respect to local populations and genetic divergence, in the context of the molecular marker used.}, note = {BIODIV}, keywords = {}, pubstate = {published}, tppubtype = {article} } Population dynamics in the marine realm can shape species’ spatial structure and genetic variability between given geographical areas. Connectivity is an important factor of species’ population structure. In this study, we examined the genetic diversity and structure of white seabream (Diplodus sargus, L. 1758) in the eastern Mediterranean basin, using a panel of four microsatellite markers. Recorded low FST values within the study area indicate little evidence of genetic differentiation among populations. Results suggest high gene flow which may imply near-panmixia between populations, indicating the possibility of a probable movement of adult migrants, or strong passive drift at sea in early life stages of the species. To this extent, bibliographically speaking, different species within the Sparidae family favor altered population dynamics patterns with respect to local populations and genetic divergence, in the context of the molecular marker used. |
Kyriakis, Dimitrios; Kanterakis, Alexandros; Manousaki, Tereza; Tsakogiannis, Alexandros; Tsagris, Michalis; Tsamardinos, Ioannis; Papaharisis, Leonidas; Chatziplis, Dimitris; Potamias, George; Tsigenopoulos, Costas S Scanning of Genetic Variants and Genetic Mapping of Phenotypic Traits in Gilthead Sea Bream Through ddRAD Sequencing Journal Article Frontiers in Genetics, 10 , pp. 675, 2019, ISSN: 1664-8021. @article{kyriakis_scanning_2019, title = {Scanning of Genetic Variants and Genetic Mapping of Phenotypic Traits in Gilthead Sea Bream Through ddRAD Sequencing}, author = {Dimitrios Kyriakis and Alexandros Kanterakis and Tereza Manousaki and Alexandros Tsakogiannis and Michalis Tsagris and Ioannis Tsamardinos and Leonidas Papaharisis and Dimitris Chatziplis and George Potamias and Costas S Tsigenopoulos}, url = {https://www.frontiersin.org/article/10.3389/fgene.2019.00675/full}, doi = {10.3389/fgene.2019.00675}, issn = {1664-8021}, year = {2019}, date = {2019-08-01}, urldate = {2020-08-18}, journal = {Frontiers in Genetics}, volume = {10}, pages = {675}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Gkafas, Georgios A; Hatziioannou, Marianthi; Malandrakis, Emmanouil E; Tsigenopoulos, Costas S; Karapanagiotidis, Ioannis T; Mente, Elena; Vafidis, Dimitrios; Exadactylos, Athanasios Heterozygosity fitness correlations and generation interval of the Norway lobster in the Aegean Sea, eastern Mediterranean Journal Article Journal of Biological Research-Thessaloniki, 26 (1), pp. 14, 2019, ISSN: 2241-5793. @article{gkafas_heterozygosity_2019, title = {Heterozygosity fitness correlations and generation interval of the Norway lobster in the Aegean Sea, eastern Mediterranean}, author = {Georgios A Gkafas and Marianthi Hatziioannou and Emmanouil E Malandrakis and Costas S Tsigenopoulos and Ioannis T Karapanagiotidis and Elena Mente and Dimitrios Vafidis and Athanasios Exadactylos}, url = {https://jbiolres.biomedcentral.com/articles/10.1186/s40709-019-0103-0}, doi = {10.1186/s40709-019-0103-0}, issn = {2241-5793}, year = {2019}, date = {2019-01-01}, urldate = {2023-03-03}, journal = {Journal of Biological Research-Thessaloniki}, volume = {26}, number = {1}, pages = {14}, abstract = {Abstract Background Comprehensively detailed information on population dynamics for benthic species is crucial since potential admixture of individuals could shift the genetic subdivision and age structure during a full breeding period. The apparent genetic impact of the potential recruitment strategy of Norway lobster Nephrops norvegicus is still under research. For this reason the present study was focused on genetic variation of the species over a given continuous year period in a semi-enclosed gulf of the Aegean Sea. Results Analyses revealed that the relative smaller size class in females and the apparent faster growth of males may represent a key-role differential strategy for the two sexes, whereas females tend to mature slower. Heterozygosity fitness correlations (HFCs) showed substantially significant associations suggesting that inbreeding depression for females and outbreeding depression for males are the proximate fitness mechanisms, respectively. Conclusions Nephrops norvegicus uniformal genetic composition (background of high gene flow), could be attributed to potential population recolonization, due to a hypothesized passive larval movement from deeper waters, which may suggest that some offspring of local residents and potential male non-breeders from other regions admixture randomly.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Background Comprehensively detailed information on population dynamics for benthic species is crucial since potential admixture of individuals could shift the genetic subdivision and age structure during a full breeding period. The apparent genetic impact of the potential recruitment strategy of Norway lobster Nephrops norvegicus is still under research. For this reason the present study was focused on genetic variation of the species over a given continuous year period in a semi-enclosed gulf of the Aegean Sea. Results Analyses revealed that the relative smaller size class in females and the apparent faster growth of males may represent a key-role differential strategy for the two sexes, whereas females tend to mature slower. Heterozygosity fitness correlations (HFCs) showed substantially significant associations suggesting that inbreeding depression for females and outbreeding depression for males are the proximate fitness mechanisms, respectively. Conclusions Nephrops norvegicus uniformal genetic composition (background of high gene flow), could be attributed to potential population recolonization, due to a hypothesized passive larval movement from deeper waters, which may suggest that some offspring of local residents and potential male non-breeders from other regions admixture randomly. |
2018 |
Pauletto, Marianna; Manousaki, Tereza; Ferraresso, Serena; Babbucci, Massimiliano; Tsakogiannis, Alexandros; Louro, Bruno; Vitulo, Nicola; Quoc, Viet Ha; Carraro, Roberta; Bertotto, Daniela; Franch, Rafaella; Maroso, Francesco; Aslam, Muhammad L; Sonesson, Anna K; Simionati, Barbara; Malacrida, Giorgio; Cestaro, Alessandro; Caberlotto, Stefano; Sarropoulou, Elena; Mylonas, Costantinos C; Power, Deborah M; Patarnello, Tomaso; Canario, Adelino V M; Tsigenopoulos, Costas; Bargelloni, Luca Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish Journal Article Communications Biology, 1 (1), pp. 119, 2018, ISSN: 2399-3642. @article{pauletto_genomic_2018, title = {Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish}, author = {Marianna Pauletto and Tereza Manousaki and Serena Ferraresso and Massimiliano Babbucci and Alexandros Tsakogiannis and Bruno Louro and Nicola Vitulo and Viet Ha Quoc and Roberta Carraro and Daniela Bertotto and Rafaella Franch and Francesco Maroso and Muhammad L Aslam and Anna K Sonesson and Barbara Simionati and Giorgio Malacrida and Alessandro Cestaro and Stefano Caberlotto and Elena Sarropoulou and Costantinos C Mylonas and Deborah M Power and Tomaso Patarnello and Adelino V M Canario and Costas Tsigenopoulos and Luca Bargelloni}, url = {http://www.nature.com/articles/s42003-018-0122-7}, doi = {10.1038/s42003-018-0122-7}, issn = {2399-3642}, year = {2018}, date = {2018-12-01}, urldate = {2020-08-21}, journal = {Communications Biology}, volume = {1}, number = {1}, pages = {119}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Tsakogiannis, Alexandros; Manousaki, Tereza; Lagnel, Jacques; Papanikolaou, Nikolaos; Papandroulakis, Nikos; Mylonas, Constantinos C; Tsigenopoulos, Costas S The gene toolkit implicated in functional sex in Sparidae hermaphrodites: inferences from comparative transcriptomics Journal Article Frontiers in Genetics, 9 , pp. 749, 2018, (Publisher: Frontiers). @article{tsakogiannis_gene_2018, title = {The gene toolkit implicated in functional sex in Sparidae hermaphrodites: inferences from comparative transcriptomics}, author = {Alexandros Tsakogiannis and Tereza Manousaki and Jacques Lagnel and Nikolaos Papanikolaou and Nikos Papandroulakis and Constantinos C Mylonas and Costas S Tsigenopoulos}, year = {2018}, date = {2018-01-01}, journal = {Frontiers in Genetics}, volume = {9}, pages = {749}, note = {Publisher: Frontiers}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Tsakogiannis, A; Manousaki, T; Lagnel, J; Sterioti, A; Pavlidis, M; Papandroulakis, N; Mylonas, CC; Tsigenopoulos, CS The transcriptomic signature of different sexes in two protogynous hermaphrodites: Insights into the molecular network underlying sex phenotype in fish Journal Article Scientific reports, 8 (1), pp. 3564, 2018, (Publisher: Nature Publishing Group). @article{tsakogiannis_transcriptomic_2018, title = {The transcriptomic signature of different sexes in two protogynous hermaphrodites: Insights into the molecular network underlying sex phenotype in fish}, author = {A Tsakogiannis and T Manousaki and J Lagnel and A Sterioti and M Pavlidis and N Papandroulakis and CC Mylonas and CS Tsigenopoulos}, year = {2018}, date = {2018-01-01}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {3564}, note = {Publisher: Nature Publishing Group}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Manousaki, T; Tsakogiannis, A; Lagnel, J; Kyriakis, D; Duncan, N; Estevez, A; Tsigenopoulos, CS Muscle and liver transcriptome characterization and genetic marker discovery in the farmed meagre, Argyrosomus regius Journal Article Marine Genomics, 39 , pp. 39–44, 2018, (Publisher: Elsevier). @article{manousaki_muscle_2018, title = {Muscle and liver transcriptome characterization and genetic marker discovery in the farmed meagre, Argyrosomus regius}, author = {T Manousaki and A Tsakogiannis and J Lagnel and D Kyriakis and N Duncan and A Estevez and CS Tsigenopoulos}, doi = {10.1016/j.margen.2018.01.002}, year = {2018}, date = {2018-01-01}, journal = {Marine Genomics}, volume = {39}, pages = {39--44}, note = {Publisher: Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Viret, A; Tsaparis, D; Tsigenopoulos, C S; Berrebi, P; Sabatini, A; Arculeo, M; Fassatoui, C; Magoulas, A; Marengo, M; Morales-Nin, B; Caill-Milly, N; Durieux, E D H PLoS ONE, 13 (9), 2018, ISSN: 19326203, (Publisher: Public Library of Science). @article{viret_absence_2018, title = {Absence of spatial genetic structure in common dentex (Dentex dentex Linnaeus, 1758) in the Mediterranean Sea as evidenced by nuclear and mitochondrial molecular markers}, author = {A Viret and D Tsaparis and C S Tsigenopoulos and P Berrebi and A Sabatini and M Arculeo and C Fassatoui and A Magoulas and M Marengo and B Morales-Nin and N Caill-Milly and E D H Durieux}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85053134390&doi=10.1371%2fjournal.pone.0203866&partnerID=40&md5=bc629c803f2e5c8490f76f3d27813b81}, doi = {10.1371/journal.pone.0203866}, issn = {19326203}, year = {2018}, date = {2018-01-01}, journal = {PLoS ONE}, volume = {13}, number = {9}, abstract = {The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterranean Sea (17 sites) with an emphasis around Corsica (5 sites), plus one Atlantic Ocean site. This provided an opportunity to examine genetic structuring at local and broader scales to provide science based data for the management of fishing stocks in the region. Two mitochondrial regions were examined (D-loop and COI) along with eight microsatellite loci. The COI data was combined with publicly available sequences and demonstrated past misidentification of common dentex. All markers indicated the absence of population genetic structure from the Bay of Biscay to the eastern Mediterranean Sea. Bayesian approaches, as well as the statistical tests performed on the allelic frequencies from microsatellite loci, indicated low differentiation between samples; there was only a slight (p = 0.05) indication of isolation by distance. Common dentex is a marine fish species with a unique panmictic population in the Mediterranean and likely in the Atlantic Ocean as well. © 2018 Viret et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.}, note = {Publisher: Public Library of Science}, keywords = {}, pubstate = {published}, tppubtype = {article} } The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterranean Sea (17 sites) with an emphasis around Corsica (5 sites), plus one Atlantic Ocean site. This provided an opportunity to examine genetic structuring at local and broader scales to provide science based data for the management of fishing stocks in the region. Two mitochondrial regions were examined (D-loop and COI) along with eight microsatellite loci. The COI data was combined with publicly available sequences and demonstrated past misidentification of common dentex. All markers indicated the absence of population genetic structure from the Bay of Biscay to the eastern Mediterranean Sea. Bayesian approaches, as well as the statistical tests performed on the allelic frequencies from microsatellite loci, indicated low differentiation between samples; there was only a slight (p = 0.05) indication of isolation by distance. Common dentex is a marine fish species with a unique panmictic population in the Mediterranean and likely in the Atlantic Ocean as well. © 2018 Viret et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
2017 |
Bodur, T; Tsigenopoulos, C; Cagatay, I T Genetic structure of wild European sea bass (Dicentrarchus labrax L, 1758) populations in aegean and levantine sea using microsatellite markers Journal Article Turkish Journal of Fisheries and Aquatic Sciences, 17 (1), 2017, ISSN: 13032712, (Publisher: Central Fisheries Research Inst). @article{bodur_genetic_2017, title = {Genetic structure of wild European sea bass (Dicentrarchus labrax L, 1758) populations in aegean and levantine sea using microsatellite markers}, author = {T Bodur and C Tsigenopoulos and I T Cagatay}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85010423795&doi=10.4194%2f1303-2712-v17_1_02&partnerID=40&md5=18149ff5cd43f0c545cb18e23bc24003}, doi = {10.4194/1303-2712-v17_1_02}, issn = {13032712}, year = {2017}, date = {2017-01-01}, journal = {Turkish Journal of Fisheries and Aquatic Sciences}, volume = {17}, number = {1}, abstract = {The aim of this study is to investigate the genetic structure of Dicentrarchus labrax populations sampled in the North- East Mediterranean. These are the main areas where the hatcheries collect their broodstock candidates from the wild in Turkey, which is the biggest European sea bass producer in Europe. Five samples collected from the Turkish Levantine and Aegean Sea coasts were analysed in addition to the Atlantic and Ionian samples (total 305 individuals) for 12 microsatellite loci. The present results revealed that the Aegean populations from Homa and Doğanbey, where the sea bass culture is mostly conducted in Turkish Aegean Sea, were closely related (FST 0.00347, P>0.01). Another close relation was found between Yumurtalık and Doğanbey (FST 0.01148, P>0.01), which might be the result of massive fry transfers from Yumurtalık (East Levantine coast) to Doğanbey till 2000 in Turkey. Obtained results also show gene flow from Greek to Turkish Aegean population which most probably was the consequence of frequent juvenile transfers from Greek hatcheries to Turkish fish farms between 2000 and 2010. © Published by Central Fisheries Research Institute (CFRI) Trabzon, Turkey.}, note = {Publisher: Central Fisheries Research Inst}, keywords = {}, pubstate = {published}, tppubtype = {article} } The aim of this study is to investigate the genetic structure of Dicentrarchus labrax populations sampled in the North- East Mediterranean. These are the main areas where the hatcheries collect their broodstock candidates from the wild in Turkey, which is the biggest European sea bass producer in Europe. Five samples collected from the Turkish Levantine and Aegean Sea coasts were analysed in addition to the Atlantic and Ionian samples (total 305 individuals) for 12 microsatellite loci. The present results revealed that the Aegean populations from Homa and Doğanbey, where the sea bass culture is mostly conducted in Turkish Aegean Sea, were closely related (FST 0.00347, P>0.01). Another close relation was found between Yumurtalık and Doğanbey (FST 0.01148, P>0.01), which might be the result of massive fry transfers from Yumurtalık (East Levantine coast) to Doğanbey till 2000 in Turkey. Obtained results also show gene flow from Greek to Turkish Aegean population which most probably was the consequence of frequent juvenile transfers from Greek hatcheries to Turkish fish farms between 2000 and 2010. © Published by Central Fisheries Research Institute (CFRI) Trabzon, Turkey. |
Fanini, L; Zampicinini, G; Tsigenopoulos, C S; Barboza, F R; Lozoya, J P; Gómez, J; Celentano, E; Lercari, D; Marchetti, G M; Defeo, O Life-history, substrate choice and Cytochrome Oxidase I variations in sandy beach peracaridans along the Rio de la Plata estuary Journal Article Estuarine, Coastal and Shelf Science, 187 , pp. 152–159, 2017, ISSN: 02727714, (Publisher: Academic Press). @article{fanini_life-history_2017, title = {Life-history, substrate choice and Cytochrome Oxidase I variations in sandy beach peracaridans along the Rio de la Plata estuary}, author = {L Fanini and G Zampicinini and C S Tsigenopoulos and F R Barboza and J P Lozoya and J Gómez and E Celentano and D Lercari and G M Marchetti and O Defeo}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85009963070&doi=10.1016%2fj.ecss.2017.01.007&partnerID=40&md5=8d3b1ff2db390339e993dcd7fb67b498}, doi = {10.1016/j.ecss.2017.01.007}, issn = {02727714}, year = {2017}, date = {2017-01-01}, journal = {Estuarine, Coastal and Shelf Science}, volume = {187}, pages = {152--159}, abstract = {Life-history, substrate choice and Cytochrome Oxidase I (COI) sequences were analysed in populations of two peracaridans, the supralittoral talitrid Atlantorchestoidea brasiliensis and the intertidal cirolanid Excirolana armata. Three populations of each species, from beaches with similar grain size and located at different points along the natural gradient generated by the Rio de la Plata estuary were analysed. Abundance of E. armata increased with distance from the estuary, while the opposite trend was observed for A. brasiliensis. The proportion of females decreased towards high salinities for both species, significantly for E. armata. A test on substrate salinity preference revealed the absence of patterns due to active choice in E. armata. By contrast, A. brasiliensis showed no preference for the population closer to the estuary, while individuals from the other two sites significantly preferred high salinity substrates. Mitochondrial COI sequences were obtained from A. brasiliensis specimens tested for behaviour. Sequence analysis showed the population from the intermediate site to differ significantly from the other two. No significant genetic differentiation was instead found between populations from the two most distant sites, nor between individuals that expressed different salinity preference. Results showed that diverse sets of traits at the population level enable sandy beach species to cope with local environmental changes: life-history and behavioural traits appear to change in response to different ecological conditions, and, in the case of A brasiliensis, independently of the population structure inferred from COI sequence variation. Information from multiple traits allowed detection of population profiles, highlighting the relevance of multidisciplinary information and the concurrent analysis of field data and laboratory experiments, to detect responses of resident biota to environmental changes. © 2017 Elsevier Ltd}, note = {Publisher: Academic Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } Life-history, substrate choice and Cytochrome Oxidase I (COI) sequences were analysed in populations of two peracaridans, the supralittoral talitrid Atlantorchestoidea brasiliensis and the intertidal cirolanid Excirolana armata. Three populations of each species, from beaches with similar grain size and located at different points along the natural gradient generated by the Rio de la Plata estuary were analysed. Abundance of E. armata increased with distance from the estuary, while the opposite trend was observed for A. brasiliensis. The proportion of females decreased towards high salinities for both species, significantly for E. armata. A test on substrate salinity preference revealed the absence of patterns due to active choice in E. armata. By contrast, A. brasiliensis showed no preference for the population closer to the estuary, while individuals from the other two sites significantly preferred high salinity substrates. Mitochondrial COI sequences were obtained from A. brasiliensis specimens tested for behaviour. Sequence analysis showed the population from the intermediate site to differ significantly from the other two. No significant genetic differentiation was instead found between populations from the two most distant sites, nor between individuals that expressed different salinity preference. Results showed that diverse sets of traits at the population level enable sandy beach species to cope with local environmental changes: life-history and behavioural traits appear to change in response to different ecological conditions, and, in the case of A brasiliensis, independently of the population structure inferred from COI sequence variation. Information from multiple traits allowed detection of population profiles, highlighting the relevance of multidisciplinary information and the concurrent analysis of field data and laboratory experiments, to detect responses of resident biota to environmental changes. © 2017 Elsevier Ltd |
2016 |
Guinand, B; Chauvel, C; Lechene, M; Tournois, J; Tsigenopoulos, C S; Darnaude, A M; McKenzie, D J; Gagnaire, P A Candidate gene variation in gilthead sea bream reveals complex spatiotemporal selection patterns between marine and lagoon habitats Journal Article Marine Ecology Progress Series, 558 , pp. 115–127, 2016, ISSN: 01718630, (Publisher: Inter-Research). @article{guinand_candidate_2016, title = {Candidate gene variation in gilthead sea bream reveals complex spatiotemporal selection patterns between marine and lagoon habitats}, author = {B Guinand and C Chauvel and M Lechene and J Tournois and C S Tsigenopoulos and A M Darnaude and D J McKenzie and P A Gagnaire}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84992490269&doi=10.3354%2fmeps11851&partnerID=40&md5=33291011e97c8e63e16a9b4feb4669d1}, doi = {10.3354/meps11851}, issn = {01718630}, year = {2016}, date = {2016-01-01}, journal = {Marine Ecology Progress Series}, volume = {558}, pages = {115--127}, abstract = {In marine fishes, the extent to which spatial patterns induced by selection remain stable across generations remains largely unknown. In the gilthead sea bream Sparus aurata, polymorphisms in the growth hormone (GH) and prolactin (Prl) genes can display high levels of differentiation between marine and lagoon habitats. These genotype-environment associations have been attributed to differential selection following larval settlement, but it remains unclear whether selective mortality during later juvenile stages further shapes genetic differences among habitats. We addressed this question by analysing differentiation patterns at GH and Prl markers together with a set of 21 putatively neutral microsatellite loci. We compared genetic variation of spring juveniles that had just settled in 3 ecologically different lagoons against older juveniles sampled from the same sites in autumn, at the onset of winter outmigration. In spring, genetic differentiation among lagoons was greater than expected from neutrality for both candidate gene markers. Surprisingly, this signal disappeared completely in the older juveniles, with no significant differentiation for either locus a few months later in autumn. We searched for signals of haplotype structure within GH and Prl genes using next-generation amplicon deep sequencing. Both genes contained 2 groups of haplotypes, but high similarities among groups indicated that signatures of selection, if any, had largely been erased by recombination. Our results are consistent with the view that differential selection operates during early juvenile life in sea bream and highlight the importance of temporal replication in studies of post-settlement selection in marine fish. © The authors, CNRS and TOTAL Foundation 2016.}, note = {Publisher: Inter-Research}, keywords = {}, pubstate = {published}, tppubtype = {article} } In marine fishes, the extent to which spatial patterns induced by selection remain stable across generations remains largely unknown. In the gilthead sea bream Sparus aurata, polymorphisms in the growth hormone (GH) and prolactin (Prl) genes can display high levels of differentiation between marine and lagoon habitats. These genotype-environment associations have been attributed to differential selection following larval settlement, but it remains unclear whether selective mortality during later juvenile stages further shapes genetic differences among habitats. We addressed this question by analysing differentiation patterns at GH and Prl markers together with a set of 21 putatively neutral microsatellite loci. We compared genetic variation of spring juveniles that had just settled in 3 ecologically different lagoons against older juveniles sampled from the same sites in autumn, at the onset of winter outmigration. In spring, genetic differentiation among lagoons was greater than expected from neutrality for both candidate gene markers. Surprisingly, this signal disappeared completely in the older juveniles, with no significant differentiation for either locus a few months later in autumn. We searched for signals of haplotype structure within GH and Prl genes using next-generation amplicon deep sequencing. Both genes contained 2 groups of haplotypes, but high similarities among groups indicated that signatures of selection, if any, had largely been erased by recombination. Our results are consistent with the view that differential selection operates during early juvenile life in sea bream and highlight the importance of temporal replication in studies of post-settlement selection in marine fish. © The authors, CNRS and TOTAL Foundation 2016. |
Manousaki, Tereza; Tsakogiannis, Alexandros; Taggart, John B; Palaiokostas, Christos; Tsaparis, Dimitris; Lagnel, Jacques; Chatziplis, Dimitrios; Magoulas, Antonios; Papandroulakis, Nikos; Mylonas, Constantinos C; TSIGENOPOULOS, C S Exploring a nonmodel teleost genome through rad sequencing—linkage mapping in Common Pandora, Pagellus erythrinus and comparative genomic analysis Journal Article G3: Genes, genomes, genetics, 6 (3), pp. 509–519, 2016, (Publisher: G3: Genes, Genomes, Genetics). @article{manousaki_exploring_2016, title = {Exploring a nonmodel teleost genome through rad sequencing—linkage mapping in Common Pandora, Pagellus erythrinus and comparative genomic analysis}, author = {Tereza Manousaki and Alexandros Tsakogiannis and John B Taggart and Christos Palaiokostas and Dimitris Tsaparis and Jacques Lagnel and Dimitrios Chatziplis and Antonios Magoulas and Nikos Papandroulakis and Constantinos C Mylonas and C. S. TSIGENOPOULOS }, year = {2016}, date = {2016-01-01}, journal = {G3: Genes, genomes, genetics}, volume = {6}, number = {3}, pages = {509--519}, note = {Publisher: G3: Genes, Genomes, Genetics}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Leese, Florian; Altermatt, Florian; Bouchez, Agnès; Ekrem, Torbjørn; Hering, Daniel; Meissner, Kristian; Mergen, Patricia; Pawlowski, Jan; Piggott, Jeremy; Rimet, Frédéric; Steinke, Dirk; Taberlet, Pierre; Weigand, Alexander; Abarenkov, Kessy; Beja, Pedro; Bervoets, Lieven; Björnsdóttir, Snaedís; Boets, Pieter; Boggero, Angela; Bones, Atle; Borja, Ángel; Bruce, Kat; Bursić, Vojislava; Carlsson, Jens; Čiampor, Fedor; Čiamporová-Zatovičová, Zuzana; Coissac, Eric; Costa, Filipe; Costache, Marieta; Creer, Simon; Csabai, Zoltán; Deiner, Kristy; DelValls, Ángel; Drakare, Stina; Duarte, Sofia; Eleršek, Tina; Fazi, Stefano; Fišer, Cene; Flot, Jean-François; Fonseca, Vera; Fontaneto, Diego; Grabowski, Michael; Graf, Wolfram; Guðbrandsson, Jóhannes; Hellström, Micaela; Hershkovitz, Yaron; Hollingsworth, Peter; Japoshvili, Bella; Jones, John; Kahlert, Maria; Stroil, Belma Kalamujic; Kasapidis, Panagiotis; Kelly, Martyn; Kelly-Quinn, Mary; Keskin, Emre; Kõljalg, Urmas; Ljubešić, Zrinka; Maček, Irena; Mächler, Elvira; Mahon, Andrew; Marečková, Marketa; Mejdandzic, Maja; Mircheva, Georgina; Montagna, Matteo; Moritz, Christian; Mulk, Vallo; Naumoski, Andreja; Navodaru, Ion; Padisák, Judit; Pálsson, Snæbjörn; Panksep, Kristel; Penev, Lyubomir; Petrusek, Adam; Pfannkuchen, Martin; Primmer, Craig; Rinkevich, Baruch; Rotter, Ana; Schmidt-Kloiber, Astrid; Segurado, Pedro; Speksnijder, Arjen; Stoev, Pavel; Strand, Malin; Šulčius, Sigitas; Sundberg, Per; Traugott, Michael; Tsigenopoulos, Costas; Turon, Xavier; Valentini, Alice; Hoorn, Berry Van Der; Várbíró, Gábor; Hadjilyra, Marlen Vasquez; Viguri, Javier; Vitonytė, Irma; Vogler, Alfried; Vrålstad, Trude; Wägele, Wolfgang; Wenne, Roman; Winding, Anne; Woodward, Guy; Zegura, Bojana; Zimmermann, Jonas DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe Journal Article Research Ideas and Outcomes, 2 , pp. e11321, 2016, ISSN: 2367-7163. @article{leese_dnaqua-net_2016, title = {DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe}, author = {Florian Leese and Florian Altermatt and Agnès Bouchez and Torbjørn Ekrem and Daniel Hering and Kristian Meissner and Patricia Mergen and Jan Pawlowski and Jeremy Piggott and Frédéric Rimet and Dirk Steinke and Pierre Taberlet and Alexander Weigand and Kessy Abarenkov and Pedro Beja and Lieven Bervoets and Snaedís Björnsdóttir and Pieter Boets and Angela Boggero and Atle Bones and Ángel Borja and Kat Bruce and Vojislava Bursić and Jens Carlsson and Fedor Čiampor and Zuzana Čiamporová-Zatovičová and Eric Coissac and Filipe Costa and Marieta Costache and Simon Creer and Zoltán Csabai and Kristy Deiner and Ángel DelValls and Stina Drakare and Sofia Duarte and Tina Eleršek and Stefano Fazi and Cene Fišer and Jean-François Flot and Vera Fonseca and Diego Fontaneto and Michael Grabowski and Wolfram Graf and Jóhannes Guðbrandsson and Micaela Hellström and Yaron Hershkovitz and Peter Hollingsworth and Bella Japoshvili and John Jones and Maria Kahlert and Belma Kalamujic Stroil and Panagiotis Kasapidis and Martyn Kelly and Mary Kelly-Quinn and Emre Keskin and Urmas Kõljalg and Zrinka Ljubešić and Irena Maček and Elvira Mächler and Andrew Mahon and Marketa Marečková and Maja Mejdandzic and Georgina Mircheva and Matteo Montagna and Christian Moritz and Vallo Mulk and Andreja Naumoski and Ion Navodaru and Judit Padisák and Snæbjörn Pálsson and Kristel Panksep and Lyubomir Penev and Adam Petrusek and Martin Pfannkuchen and Craig Primmer and Baruch Rinkevich and Ana Rotter and Astrid Schmidt-Kloiber and Pedro Segurado and Arjen Speksnijder and Pavel Stoev and Malin Strand and Sigitas Šulčius and Per Sundberg and Michael Traugott and Costas Tsigenopoulos and Xavier Turon and Alice Valentini and Berry Van Der Hoorn and Gábor Várbíró and Marlen Vasquez Hadjilyra and Javier Viguri and Irma Vitonytė and Alfried Vogler and Trude Vrålstad and Wolfgang Wägele and Roman Wenne and Anne Winding and Guy Woodward and Bojana Zegura and Jonas Zimmermann}, url = {http://riojournal.com/articles.php?id=11321}, doi = {10.3897/rio.2.e11321}, issn = {2367-7163}, year = {2016}, date = {2016-01-01}, urldate = {2023-03-03}, journal = {Research Ideas and Outcomes}, volume = {2}, pages = {e11321}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2015 |
Rigos, G; Henry, M; Tsigenopoulos, C Sparicotyle chrysophrii and gilthead sea bream - Potential experimental infection model Journal Article Bulletin of the European Association of Fish Pathologists, 35 (2), pp. 50–54, 2015, ISSN: 01080288, (Publisher: FRS Marine Laboratory). @article{rigos_sparicotyle_2015, title = {Sparicotyle chrysophrii and gilthead sea bream - Potential experimental infection model}, author = {G Rigos and M Henry and C Tsigenopoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84930162854&partnerID=40&md5=0a11a3004542dd5972bac0241c2a571e}, issn = {01080288}, year = {2015}, date = {2015-01-01}, journal = {Bulletin of the European Association of Fish Pathologists}, volume = {35}, number = {2}, pages = {50--54}, abstract = {An infection model of gilthead sea bream challenged with the monogenean Sparicotyle chrysophrii is described herein. Its design aimed to simulate the pathogenesis in situ. One thousand farmed fish (16 g) in a cement tank were heavily infected by adult parasites two weeks following the transfer of the 250 donor fish (50 g). Anorexia, lethargy and anaemia along with 15 % cumulatively mortalities were observed. A parasitological analysis carried out at end of the experiment (12 weeks) revealed that 7 % of the examined population was pathogen free and the mean intensity was 6.4 parasites/ fish. Surprisingly, growth reduction of infected fish was not correlated with the parasitic load, perhaps due to the unfavourable feeding ground for the parasite in anaemic small fish. Overall, the described infection pattern resembles the characteristics of the disease seen in the field and could be ideally adopted in controlled environments.}, note = {Publisher: FRS Marine Laboratory}, keywords = {}, pubstate = {published}, tppubtype = {article} } An infection model of gilthead sea bream challenged with the monogenean Sparicotyle chrysophrii is described herein. Its design aimed to simulate the pathogenesis in situ. One thousand farmed fish (16 g) in a cement tank were heavily infected by adult parasites two weeks following the transfer of the 250 donor fish (50 g). Anorexia, lethargy and anaemia along with 15 % cumulatively mortalities were observed. A parasitological analysis carried out at end of the experiment (12 weeks) revealed that 7 % of the examined population was pathogen free and the mean intensity was 6.4 parasites/ fish. Surprisingly, growth reduction of infected fish was not correlated with the parasitic load, perhaps due to the unfavourable feeding ground for the parasite in anaemic small fish. Overall, the described infection pattern resembles the characteristics of the disease seen in the field and could be ideally adopted in controlled environments. |
Henry, M A; Nikoloudaki, C; Tsigenopoulos, C; Rigos, G Strong effect of long-term Sparicotyle chrysophrii infection on the cellular and innate immune responses of gilthead sea bream, Sparus aurata Journal Article Developmental and Comparative Immunology, 51 (1), pp. 185–193, 2015, ISSN: 0145305X, (Publisher: Elsevier Ltd). @article{henry_strong_2015, title = {Strong effect of long-term Sparicotyle chrysophrii infection on the cellular and innate immune responses of gilthead sea bream, Sparus aurata}, author = {M A Henry and C Nikoloudaki and C Tsigenopoulos and G Rigos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84926678862&doi=10.1016%2fj.dci.2015.03.010&partnerID=40&md5=174b70c31d6b753405608c4b64bd6416}, doi = {10.1016/j.dci.2015.03.010}, issn = {0145305X}, year = {2015}, date = {2015-01-01}, journal = {Developmental and Comparative Immunology}, volume = {51}, number = {1}, pages = {185--193}, abstract = {One thousand healthy recipient gilthead sea bream, Sparus aurata, cohabited with 250 donor fish parasitized by Sparicotyle chrysophrii (Van Beneden and Hesse, 1963) (Monogenea: Polyopisthocotylea), a common parasite of the gills of this fish species. Controls consisted of 1000 healthy fish kept in a separate tank. After 10 weeks, fish were weighed and parasite load, hemoglobin concentration and immunological parameters were assessed. Rather than the absence of parasite, hemoglobin concentration was a better marker of the health status of the fish, because S. . chrysophrii had detached from the strongly anemic gills of some animals leaving fish with affected immune system but without parasites. The parasite infection seemed to trigger a cellular response of the fish immune system but to inhibit its humoral components. Thus, parasitized fish may control the parasite infection through the action of reactive oxygen species but they may become more sensitive to potential secondary bacterial or parasitical infections. This phenomenon was demonstrated not only through significant differences between recipient and control fish but also through strong correlations between those parameters and parasite load, fish weight and/or hemoglobin concentration. © 2015 Elsevier Ltd.}, note = {Publisher: Elsevier Ltd}, keywords = {}, pubstate = {published}, tppubtype = {article} } One thousand healthy recipient gilthead sea bream, Sparus aurata, cohabited with 250 donor fish parasitized by Sparicotyle chrysophrii (Van Beneden and Hesse, 1963) (Monogenea: Polyopisthocotylea), a common parasite of the gills of this fish species. Controls consisted of 1000 healthy fish kept in a separate tank. After 10 weeks, fish were weighed and parasite load, hemoglobin concentration and immunological parameters were assessed. Rather than the absence of parasite, hemoglobin concentration was a better marker of the health status of the fish, because S. . chrysophrii had detached from the strongly anemic gills of some animals leaving fish with affected immune system but without parasites. The parasite infection seemed to trigger a cellular response of the fish immune system but to inhibit its humoral components. Thus, parasitized fish may control the parasite infection through the action of reactive oxygen species but they may become more sensitive to potential secondary bacterial or parasitical infections. This phenomenon was demonstrated not only through significant differences between recipient and control fish but also through strong correlations between those parameters and parasite load, fish weight and/or hemoglobin concentration. © 2015 Elsevier Ltd. |
Kaitetzidou, E; Xiang, J; Antonopoulou, E; Tsigenopoulos, C S; Sarropoulou, E Dynamics of gene expression patterns during early development of the European seabass (Dicentrarchus labrax) Journal Article Physiological Genomics, 47 (5), pp. 158–169, 2015, ISSN: 10948341, (Publisher: American Physiological Society). @article{kaitetzidou_dynamics_2015, title = {Dynamics of gene expression patterns during early development of the European seabass (Dicentrarchus labrax)}, author = {E Kaitetzidou and J Xiang and E Antonopoulou and C S Tsigenopoulos and E Sarropoulou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84930978495&doi=10.1152%2fphysiolgenomics.00001.2015&partnerID=40&md5=ac0e811b8dd4948aca47662547595ee0}, doi = {10.1152/physiolgenomics.00001.2015}, issn = {10948341}, year = {2015}, date = {2015-01-01}, journal = {Physiological Genomics}, volume = {47}, number = {5}, pages = {158--169}, abstract = {Larval and embryonic stages are the most critical period in the life cycle of marine fish. Key developmental events occur early in development and are influenced by external parameters like stress, temperature, salinity, and photoperiodism. Any failure may cause malformations, developmental delays, poor growth, and massive mortalities. Advanced understanding of molecular processes underlying marine larval development may lead to superior larval rearing conditions. Today, the new sequencing and bioinformatic methods allow transcriptome screens comprising messenger (mRNA) and microRNA (miRNA) with the scope of detecting differential expression for any species of interest. In the present study, we applied Illumina technology to investigate the transcriptome of early developmental stages of the European seabass (Dicentrarchus labrax). The European seabass, in its natural environment, is a euryhaline species and has shown high adaptation processes in early life phases. During its embryonic and larval phases the European seabass lives in a marine environment and as a juvenile it migrates to coastal zones, estuaries, and lagoons. Investigating the dynamics of gene expression in its early development may shed light on factors promoting phenotypic plasticity and may also contribute to the improvement and advancement of rearing methods of the European seabass, a species of high economic importance in European and Mediterranean aquaculture. We present the identification, characterization, and expression of mRNA and miRNA, comprising paralogous genes and differentially spliced transcripts from early developmental stages of the European seabass. We further investigated the detection of possible interactions of miRNA with mRNA. © 2015 the American Physiological Society.}, note = {Publisher: American Physiological Society}, keywords = {}, pubstate = {published}, tppubtype = {article} } Larval and embryonic stages are the most critical period in the life cycle of marine fish. Key developmental events occur early in development and are influenced by external parameters like stress, temperature, salinity, and photoperiodism. Any failure may cause malformations, developmental delays, poor growth, and massive mortalities. Advanced understanding of molecular processes underlying marine larval development may lead to superior larval rearing conditions. Today, the new sequencing and bioinformatic methods allow transcriptome screens comprising messenger (mRNA) and microRNA (miRNA) with the scope of detecting differential expression for any species of interest. In the present study, we applied Illumina technology to investigate the transcriptome of early developmental stages of the European seabass (Dicentrarchus labrax). The European seabass, in its natural environment, is a euryhaline species and has shown high adaptation processes in early life phases. During its embryonic and larval phases the European seabass lives in a marine environment and as a juvenile it migrates to coastal zones, estuaries, and lagoons. Investigating the dynamics of gene expression in its early development may shed light on factors promoting phenotypic plasticity and may also contribute to the improvement and advancement of rearing methods of the European seabass, a species of high economic importance in European and Mediterranean aquaculture. We present the identification, characterization, and expression of mRNA and miRNA, comprising paralogous genes and differentially spliced transcripts from early developmental stages of the European seabass. We further investigated the detection of possible interactions of miRNA with mRNA. © 2015 the American Physiological Society. |
Loukovitis, D; Ioannidi, B; Chatziplis, D; Kotoulas, G; Magoulas, A; Tsigenopoulos, C S Mediterranean Marine Science, 16 (1), pp. 197–200, 2015, ISSN: 1108393X, (Publisher: Hellenic Centre for Marine Research). @article{loukovitis_loss_2015, title = {Loss of genetic variation in Greek hatchery populations of the European sea bass (Dicentrarchus labrax L.) as revealed by microsatellite DNA analysis}, author = {D Loukovitis and B Ioannidi and D Chatziplis and G Kotoulas and A Magoulas and C S Tsigenopoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84924862323&doi=10.12681%2fmms.1033&partnerID=40&md5=d6f2f3b1764f0f707f4f4015dcabe4bb}, doi = {10.12681/mms.1033}, issn = {1108393X}, year = {2015}, date = {2015-01-01}, journal = {Mediterranean Marine Science}, volume = {16}, number = {1}, pages = {197--200}, abstract = {Genetic variation in four reared stocks of European sea bass Dicentrarchus labrax L., originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of three natural populations from Greece and France. The total number of alleles per marker ranged from 8 to 22 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic richness and expected heterozygosity. The genetic differentiation of cultivated samples between them as well as from the wild origin fish was significant, as indicated by Fst analysis. All population pairwise comparisons were statistically significant, except for the pair of the two natural Greek populations. Results of microsatellite DNA analysis herein showed a 37 % reduction of the mean allele number in the hatchery samples compared to the wild ones, suggesting random genetic drift and inbreeding events operating in the hatcheries. Knowledge of the genetic variation in D. labrax cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes.}, note = {Publisher: Hellenic Centre for Marine Research}, keywords = {}, pubstate = {published}, tppubtype = {article} } Genetic variation in four reared stocks of European sea bass Dicentrarchus labrax L., originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of three natural populations from Greece and France. The total number of alleles per marker ranged from 8 to 22 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic richness and expected heterozygosity. The genetic differentiation of cultivated samples between them as well as from the wild origin fish was significant, as indicated by Fst analysis. All population pairwise comparisons were statistically significant, except for the pair of the two natural Greek populations. Results of microsatellite DNA analysis herein showed a 37 % reduction of the mean allele number in the hatchery samples compared to the wild ones, suggesting random genetic drift and inbreeding events operating in the hatcheries. Knowledge of the genetic variation in D. labrax cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes. |
Brown, C; Miltiadou, D; Tsigenopoulos, C S Prevalence and survival of escaped European seabass Dicentrarchus labrax in Cyprus identified using genetic markers Journal Article Aquaculture Environment Interactions, 7 , pp. 49–59, 2015. @article{brown_prevalence_2015, title = {Prevalence and survival of escaped European seabass Dicentrarchus labrax in Cyprus identified using genetic markers}, author = {C Brown and D Miltiadou and C S Tsigenopoulos}, doi = {10.3354/aei00135}, year = {2015}, date = {2015-01-01}, journal = {Aquaculture Environment Interactions}, volume = {7}, pages = {49--59}, abstract = {The escape of European seabass Dicentrarchus labrax (L.) from fish farms is considered to be a widespread problem in the Mediterranean area, where this species is produced in large quantities in offshore cages. Whilst estimates of the number of escaped seabass in the wild have been made previously, the actual distribution, long-term survival and the potential effects on native populations remain largely unknown. This study characterises the genetic profiles of all contemporary and some historic aquaculture sources of European seabass in Cyprus and uses these profiles to identify escaped fish in seabass collected from the wild around the island. Significant differences in the microsatellite and mitochondrial DNA marker profiles were found between farmed and wild fish. The number of escapees identified was 15% of the total number of wild-caught fish sampled. However, escapees were not equally distributed; at one location 70% of wild-caught fish were escapees while in other areas escapees only accounted for up to 4%. Escapees were present in all size classes of fish, but the majority were of commercial size (300-500 g) typical of seabass farmed in seacages. This indicates that they may have escaped recently and during normal aquaculture operations as no escape event was reported in the course of the study. Two large, egg-bearing females and some juvenile fish were also classified as escapees, which suggests that long-term survival and interbreeding with wild fish is possible in Cypriot waters.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The escape of European seabass Dicentrarchus labrax (L.) from fish farms is considered to be a widespread problem in the Mediterranean area, where this species is produced in large quantities in offshore cages. Whilst estimates of the number of escaped seabass in the wild have been made previously, the actual distribution, long-term survival and the potential effects on native populations remain largely unknown. This study characterises the genetic profiles of all contemporary and some historic aquaculture sources of European seabass in Cyprus and uses these profiles to identify escaped fish in seabass collected from the wild around the island. Significant differences in the microsatellite and mitochondrial DNA marker profiles were found between farmed and wild fish. The number of escapees identified was 15% of the total number of wild-caught fish sampled. However, escapees were not equally distributed; at one location 70% of wild-caught fish were escapees while in other areas escapees only accounted for up to 4%. Escapees were present in all size classes of fish, but the majority were of commercial size (300-500 g) typical of seabass farmed in seacages. This indicates that they may have escaped recently and during normal aquaculture operations as no escape event was reported in the course of the study. Two large, egg-bearing females and some juvenile fish were also classified as escapees, which suggests that long-term survival and interbreeding with wild fish is possible in Cypriot waters. |
Guinand, B; Quéré, N; Desmarais, E; Lagnel, J; Tsigenopoulos, C S; Bonhomme, F Marine Biology, 162 , pp. 515–538, 2015. @article{guinand_laboratory_2015, title = {From the laboratory to the wild: salinity-based genetic differentiation of the European sea bass (Dicentrarchus labrax) using gene-associated and gene-independent microsatellite markers}, author = {B Guinand and N Quéré and E Desmarais and J Lagnel and C S Tsigenopoulos and F Bonhomme}, doi = {10.1007/s00227-014-2602-8}, year = {2015}, date = {2015-01-01}, journal = {Marine Biology}, volume = {162}, pages = {515--538}, abstract = {Convincing evidence reporting adaptive variation for physiologically and/or ecologically important traits in marine taxa is often derived from studies comparing field and laboratory observations and based on candidate-gene markers, mainly allozymes, responding to habitat selection. Likewise, patterns of genetic differentiation between sea and lagoon populations of the euryhaline European sea bass (Dicentrarchus labrax) were shown to correlate with changes in allele frequencies recorded during experimental salinity challenges, suggesting potential role for local adaptation. However, there has been criticism of these past approaches, causing a need for further investigation. We reinvestigated this correlation in European sea bass using a set of 20 micro- and one minisatellite markers, some of which are associated with candidate genes. We used rigorous experimental settings to demonstrate that only one single gene-associated marker consistently reported significant genetic differentiation between fish raised in seawater compared to fish acclimated to freshwater (locus EIF3E; FST = 0.060; p = 0.007}, keywords = {}, pubstate = {published}, tppubtype = {article} } Convincing evidence reporting adaptive variation for physiologically and/or ecologically important traits in marine taxa is often derived from studies comparing field and laboratory observations and based on candidate-gene markers, mainly allozymes, responding to habitat selection. Likewise, patterns of genetic differentiation between sea and lagoon populations of the euryhaline European sea bass (Dicentrarchus labrax) were shown to correlate with changes in allele frequencies recorded during experimental salinity challenges, suggesting potential role for local adaptation. However, there has been criticism of these past approaches, causing a need for further investigation. We reinvestigated this correlation in European sea bass using a set of 20 micro- and one minisatellite markers, some of which are associated with candidate genes. We used rigorous experimental settings to demonstrate that only one single gene-associated marker consistently reported significant genetic differentiation between fish raised in seawater compared to fish acclimated to freshwater (locus EIF3E; FST = 0.060; p = 0.007 |
Ilias, A; Lagnel, J; Kapantaidaki, D E; Roditakis, E; Tsigenopoulos, C S; Vontas, J; Tsagkarakou, A BMC Genomics, 16 , pp. 939, 2015. @article{ilias_transcription_2015, title = {Transcription analysis of neonicotinoid resistance in Mediterranean (MED) populations of B. tabaci reveal novel cytochrome P450s, but no nAChR mutations associated with the phenotype}, author = {A Ilias and J Lagnel and D E Kapantaidaki and E Roditakis and C S Tsigenopoulos and J Vontas and A Tsagkarakou}, url = {http://www.biomedcentral.com/1471-2164/16/939}, doi = {10.1186/s12864-015-2161-5}, year = {2015}, date = {2015-01-01}, journal = {BMC Genomics}, volume = {16}, pages = {939}, abstract = {BACKGROUND:Bemisia tabaci is one of the most damaging agricultural pests world-wide. Although its control is based on insecticides, B. tabaci has developed resistance against almost all classes of insecticides, including neonicotinoids.RESULTS:We employed an RNA-seq approach to generate genome wide expression data and identify genes associated with neonicotinoid resistance in Mediterranean (MED) B. tabaci (Q1 biotype). Twelve libraries from insecticide resistant and susceptible whitefly populations were sequenced on an Illumina Next-generation sequencing platform, and genomic sequence information of approximately 73 Gbp was generated.A reference transcriptome was built by de novo assembly and functionally annotated. A total of 146 P450s, 18 GSTs and 23 CCEs enzymes (unigenes) potentially involved in the detoxification of xenobiotics were identified, along with 78 contigs encoding putative target proteins of six different insecticide classes. Ten unigenes encoding nicotinic Acetylcholine Receptors (nAChR), the target of neoinicotinoids, were identified and phylogenetically classified. No nAChR polymorphism potentially related with the resistant phenotypes, was observed among the studied strains.DE analysis revealed that among the 550 differentially (logFCtextgreater1) over-transcribed unigenes, 52 detoxification enzymes were over expressed including unigenes with orthologues in P450s, GSTs, CCE and UDP-glucuronosyltransferases.Eight P450 unigenes belonging to clades CYP2, CYP3 and CYP4 were highly up-regulated (logFCtextgreater2) including CYP6CM1, a gene already known to confer imidacloprid resistance in B. tabaci. Using quantitative qPCRs, a larger screening of field MED B. tabaci from Crete with known neonicotinoid phenotype was performed to associate expression levels of P450s with resistance levels. Expression levels of five P450s, including CYP6CM1, were found associated with neonicotinoid resistance. However, a significant correlation was found only in CYP303 and CYP6CX3, with imidacloprid and acetamiprid respectively.CONCLUSION:Our work has generated new toxicological data and genomic resources which will significantly enrich the available dataset and substantially facilitate the molecular studies in MED B. tabaci. No evidence of target site neonicotinoid resistance has been found. Eight P450 unigenes, including CYP6CM1, were found significantly over-expressed in resistant B. tabaci. This study suggests at least two novel P450s (CYP303 and CYP6CX3) as candidates for their functional characterization as detoxification mechanisms of neonicotinoid resistance in B. tabaci.}, keywords = {}, pubstate = {published}, tppubtype = {article} } BACKGROUND:Bemisia tabaci is one of the most damaging agricultural pests world-wide. Although its control is based on insecticides, B. tabaci has developed resistance against almost all classes of insecticides, including neonicotinoids.RESULTS:We employed an RNA-seq approach to generate genome wide expression data and identify genes associated with neonicotinoid resistance in Mediterranean (MED) B. tabaci (Q1 biotype). Twelve libraries from insecticide resistant and susceptible whitefly populations were sequenced on an Illumina Next-generation sequencing platform, and genomic sequence information of approximately 73 Gbp was generated.A reference transcriptome was built by de novo assembly and functionally annotated. A total of 146 P450s, 18 GSTs and 23 CCEs enzymes (unigenes) potentially involved in the detoxification of xenobiotics were identified, along with 78 contigs encoding putative target proteins of six different insecticide classes. Ten unigenes encoding nicotinic Acetylcholine Receptors (nAChR), the target of neoinicotinoids, were identified and phylogenetically classified. No nAChR polymorphism potentially related with the resistant phenotypes, was observed among the studied strains.DE analysis revealed that among the 550 differentially (logFCtextgreater1) over-transcribed unigenes, 52 detoxification enzymes were over expressed including unigenes with orthologues in P450s, GSTs, CCE and UDP-glucuronosyltransferases.Eight P450 unigenes belonging to clades CYP2, CYP3 and CYP4 were highly up-regulated (logFCtextgreater2) including CYP6CM1, a gene already known to confer imidacloprid resistance in B. tabaci. Using quantitative qPCRs, a larger screening of field MED B. tabaci from Crete with known neonicotinoid phenotype was performed to associate expression levels of P450s with resistance levels. Expression levels of five P450s, including CYP6CM1, were found associated with neonicotinoid resistance. However, a significant correlation was found only in CYP303 and CYP6CX3, with imidacloprid and acetamiprid respectively.CONCLUSION:Our work has generated new toxicological data and genomic resources which will significantly enrich the available dataset and substantially facilitate the molecular studies in MED B. tabaci. No evidence of target site neonicotinoid resistance has been found. Eight P450 unigenes, including CYP6CM1, were found significantly over-expressed in resistant B. tabaci. This study suggests at least two novel P450s (CYP303 and CYP6CX3) as candidates for their functional characterization as detoxification mechanisms of neonicotinoid resistance in B. tabaci. |
Manousaki, T; Tsakogiannis, A; Taggart, B J; Chatziplis, D; Mylonas, C C; Tsigenopoulos, C S Linkage mapping in common pandora, Pagellus erythrinus, using ddRAD methodology Inproceedings 11th Panhellenic Symposium on Oceanography and Fisheries, pp. 69–72, Mytilene, Lesvos island, Greece, 2015, ISBN: 978-960-9798-08-2. @inproceedings{manousaki_linkage_2015, title = {Linkage mapping in common pandora, Pagellus erythrinus, using ddRAD methodology}, author = {T Manousaki and A Tsakogiannis and B J Taggart and D Chatziplis and C C Mylonas and C S Tsigenopoulos}, isbn = {978-960-9798-08-2}, year = {2015}, date = {2015-01-01}, booktitle = {11th Panhellenic Symposium on Oceanography and Fisheries}, pages = {69--72}, address = {Mytilene, Lesvos island, Greece}, abstract = {The common pandora (Pagellus erythrinus) is a relatively new species with interest for the aquaculture industry. The success of aquaculture depends on the availability of genomic information, including markers and linkage maps. We applied ddRAD methodology on a full-sib family of common pandora, to identify SNPs widely distributed in the genome. With the use of MiSeq platform, we sampled and sequenced a large genomic fraction that led to the discovery of 920 polymorphic loci. Linkage mapping analysis led to the construction of 24 linkage groups, highly homologous to stickleback genome. Our work exhibits the possibilities of new sequencing technologies in the study of cultured species.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } The common pandora (Pagellus erythrinus) is a relatively new species with interest for the aquaculture industry. The success of aquaculture depends on the availability of genomic information, including markers and linkage maps. We applied ddRAD methodology on a full-sib family of common pandora, to identify SNPs widely distributed in the genome. With the use of MiSeq platform, we sampled and sequenced a large genomic fraction that led to the discovery of 920 polymorphic loci. Linkage mapping analysis led to the construction of 24 linkage groups, highly homologous to stickleback genome. Our work exhibits the possibilities of new sequencing technologies in the study of cultured species. |
Tsaparis, D; Kyriakis, D; Darivianakis, S; Fontaine, P; Tsigenopoulos, C S Assessing genetic diversity in domesticated pikeperch (Sander lucioperca) broodstocks Inproceedings 11th Panhellenic Symposium on Oceanography and Fisheries, pp. 261–264, Mytilene, Lesvos island, Greece, 2015, ISBN: 978-960-9798-08-2. @inproceedings{tsaparis_assessing_2015, title = {Assessing genetic diversity in domesticated pikeperch (Sander lucioperca) broodstocks}, author = {D Tsaparis and D Kyriakis and S Darivianakis and P Fontaine and C S Tsigenopoulos}, isbn = {978-960-9798-08-2}, year = {2015}, date = {2015-01-01}, booktitle = {11th Panhellenic Symposium on Oceanography and Fisheries}, pages = {261--264}, address = {Mytilene, Lesvos island, Greece}, abstract = {The pikeperch (Sander lucioperca) is a fish species with growing interest for the European aquaculture. The main objective was to develop and use highly informative multiplex panels of microsatellite loci, in order to assess the genetic variability of domesticated broodstocks in commercial farms around Europe. Two multiplexes (4plex & 7plex) were developed, optimized and finally used for genotyping of 13 populations (439 fish samples). Results indicate that most of the populations show medium to low levels of genetic diversity and some of them may be inbred. Differentiation between broodstocks was high in most cases, while lowest values were estimated for pairs of known common origin or geographic proximity.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } The pikeperch (Sander lucioperca) is a fish species with growing interest for the European aquaculture. The main objective was to develop and use highly informative multiplex panels of microsatellite loci, in order to assess the genetic variability of domesticated broodstocks in commercial farms around Europe. Two multiplexes (4plex & 7plex) were developed, optimized and finally used for genotyping of 13 populations (439 fish samples). Results indicate that most of the populations show medium to low levels of genetic diversity and some of them may be inbred. Differentiation between broodstocks was high in most cases, while lowest values were estimated for pairs of known common origin or geographic proximity. |
2014 |
Zhan, S H; Glick, L; Tsigenopoulos, C S; Otto, S P; Mayrose, I Comparative analysis reveals that polyploidy does not decelerate diversification in fish Journal Article Journal of Evolutionary Biology, 27 (2), pp. 391–403, 2014, ISSN: 1010061X. @article{zhan_comparative_2014, title = {Comparative analysis reveals that polyploidy does not decelerate diversification in fish}, author = {S H Zhan and L Glick and C S Tsigenopoulos and S P Otto and I Mayrose}, url = {http://doi.wiley.com/10.1111/jeb.12308}, doi = {10.1111/jeb.12308}, issn = {1010061X}, year = {2014}, date = {2014-02-01}, urldate = {2020-08-10}, journal = {Journal of Evolutionary Biology}, volume = {27}, number = {2}, pages = {391--403}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Tsigenopoulos, C S; Louro, B; Chatziplis, D; Lagnel, J; Vogiatzi, E; Loukovitis, D; Franch, R; Sarropoulou, E; Power, D M; Patarnello, T; Mylonas, C C; Magoulas, A; Bargelloni, L; Canario, A; Kotoulas, G Second generation genetic linkage map for the gilthead sea bream Sparus aurata L. Journal Article Marine Genomics, 18 (PA), pp. 77–82, 2014, ISSN: 18747787, (Publisher: Elsevier B.V.). @article{tsigenopoulos_second_2014, title = {Second generation genetic linkage map for the gilthead sea bream Sparus aurata L.}, author = {C S Tsigenopoulos and B Louro and D Chatziplis and J Lagnel and E Vogiatzi and D Loukovitis and R Franch and E Sarropoulou and D M Power and T Patarnello and C C Mylonas and A Magoulas and L Bargelloni and A Canario and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84922896860&doi=10.1016%2fj.margen.2014.09.008&partnerID=40&md5=c3bdc2b59c298f1c4d2cf093183db7ab}, doi = {10.1016/j.margen.2014.09.008}, issn = {18747787}, year = {2014}, date = {2014-01-01}, journal = {Marine Genomics}, volume = {18}, number = {PA}, pages = {77--82}, abstract = {An updated second linkage map was constructed for the gilthead sea bream, Sparus aurata L., a fish species of great economic importance for the Mediterranean aquaculture industry. In contrast to the first linkage map which mainly consisted of genomic microsatellites (SSRs), the new linkage map is highly enriched with SSRs found in Expressed Sequence Tags (EST-SSRs), which greatly facilitates comparative mapping with other teleosts. The new map consists of 321 genetic markers in 27 linkage groups (LGs): 232 genomic microsatellites, 85 EST-SSRs and 4 SNPs; of those, 13 markers were linked to LGs but were not ordered. Eleven markers (5 SSRs, 5 EST-SSRs and 1 SNP) are not assigned to any LG. The total length of the sex-averaged map is 1769.7. cM, 42% longer than the previously published one, and the number of markers in each LG ranges from 2 to 30. The inter-marker distance varies from 0 to 75.6. cM, with an average of 5.75. cM. The male and female maps have a length of 1349.2 and 2172.1. cM, respectively, and the average distance between markers is 4.38 and 7.05. cM, respectively. Comparative mapping with the three-spined stickleback (Gasterosteus acuulatus) chromosomes and scaffolds showed conserved synteny with 132 S. aurata markers (42.9% of those mapped) having a hit on the stickleback genome. © 2014 Elsevier B.V.}, note = {Publisher: Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } An updated second linkage map was constructed for the gilthead sea bream, Sparus aurata L., a fish species of great economic importance for the Mediterranean aquaculture industry. In contrast to the first linkage map which mainly consisted of genomic microsatellites (SSRs), the new linkage map is highly enriched with SSRs found in Expressed Sequence Tags (EST-SSRs), which greatly facilitates comparative mapping with other teleosts. The new map consists of 321 genetic markers in 27 linkage groups (LGs): 232 genomic microsatellites, 85 EST-SSRs and 4 SNPs; of those, 13 markers were linked to LGs but were not ordered. Eleven markers (5 SSRs, 5 EST-SSRs and 1 SNP) are not assigned to any LG. The total length of the sex-averaged map is 1769.7. cM, 42% longer than the previously published one, and the number of markers in each LG ranges from 2 to 30. The inter-marker distance varies from 0 to 75.6. cM, with an average of 5.75. cM. The male and female maps have a length of 1349.2 and 2172.1. cM, respectively, and the average distance between markers is 4.38 and 7.05. cM, respectively. Comparative mapping with the three-spined stickleback (Gasterosteus acuulatus) chromosomes and scaffolds showed conserved synteny with 132 S. aurata markers (42.9% of those mapped) having a hit on the stickleback genome. © 2014 Elsevier B.V. |
Manousaki, Tereza; Tsakogiannis, Alexandros; Lagnel, Jacques; Sarropoulou, Elena; Xiang, Jenny Z; Papandroulakis, Nikos; Mylonas, Constantinos C; Tsigenopoulos, Costas S The sex-specific transcriptome of the hermaphrodite sparid sharpsnout seabream (Diplodus puntazzo) Journal Article BMC genomics, 15 (1), pp. 655, 2014, (Publisher: BioMed Central). @article{manousaki_sex-specific_2014, title = {The sex-specific transcriptome of the hermaphrodite sparid sharpsnout seabream (Diplodus puntazzo)}, author = {Tereza Manousaki and Alexandros Tsakogiannis and Jacques Lagnel and Elena Sarropoulou and Jenny Z Xiang and Nikos Papandroulakis and Constantinos C Mylonas and Costas S Tsigenopoulos}, year = {2014}, date = {2014-01-01}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {655}, note = {Publisher: BioMed Central}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Berrebi, Patrick; Chenuil, Anne; Kotlík, Petr; Machordom, Annie; Tsigenopoulos, C S Disentangling the evolutionary history of the genus Barbus sensu lato, a twenty years adventure Incollection Professor Carlos Almaça (1934-2010) - Estado da Arte em Áreas Cientificas que Desenvolveu, pp. 29–55, Museu Nacional de História Natural e da Ciência, Lisboa, 2014, ISBN: 978-972-98196-6-7, (Backup Publisher: Museu Nacional de História Natural e da Ciência). @incollection{berrebi_disentangling_2014, title = {Disentangling the evolutionary history of the genus Barbus sensu lato, a twenty years adventure}, author = {Patrick Berrebi and Anne Chenuil and Petr Kotlík and Annie Machordom and C S Tsigenopoulos}, isbn = {978-972-98196-6-7}, year = {2014}, date = {2014-01-01}, booktitle = {Professor Carlos Almaça (1934-2010) - Estado da Arte em Áreas Cientificas que Desenvolveu}, pages = {29--55}, publisher = {Museu Nacional de História Natural e da Ciência}, address = {Lisboa}, edition = {Museu Nacional de História Natural e da Ciência}, abstract = {During the period 1965-1985, Professor Carlos Almaça produced a great amount of data on the Barbus group. From the end of the eighties, he joined a European consortium ("Barbus Roundtables") which aimed at developing methods and concepts, gathering numerous specialists from different fields like systematics and genetics, around Europe. At present, we may consider that the structure of Barbus sensu lato (s.l.) is relatively well known, even if some new results are still pending and other studies still needed. Barbus s.l. which was first defined on the trivial character of the presence of barbels around the mouth, has proved to include diploid, tetraploid and hexaploid lineages, themselves polyphyletic, which explains the difficulty to establish a comprehensive taxonomy. The numerous contributions published since 1990, based on karyology and molecular markers gave us a clear view of the main attributes of the evolutionary history of this complex group. First, according to taxonomy rules, the "true Barbus" (Barbus sensu stricto) are composed of tetraploid species distributed around the Mediterranean, including Danubian and Mesopotamian (Tigris and Euphrates) regions. They are composed of a north Mediterranean lineage (Barbus genus) and a south Mediterranean lineage (Luciobarbus genus). Other tetraploid Barbus s.l. are known in South Africa. Barbus s.l. includes also diploid and hexaploid lineages. Diploids are widespread and diversified, comprising Asian (mainly south-east Asia) and African species. The phylogenetic relationships between diploid and polyploid species need yet to be described. Hexaploid Barbus s.l. probably appeared after hybridization between tetraploid species (as evidenced for the genus Capoeta). A clear and homogeneous hexaploid lineage can be followed from Middle East up to South Africa. This rapid African radiation constituted the genus Labeobarbus, the "large Barbus", occupying the entire continent. The present contribution develops both the known structure of this "Chinese puzzle" and the history of its description, which is not yet finished.}, note = {Backup Publisher: Museu Nacional de História Natural e da Ciência}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } During the period 1965-1985, Professor Carlos Almaça produced a great amount of data on the Barbus group. From the end of the eighties, he joined a European consortium ("Barbus Roundtables") which aimed at developing methods and concepts, gathering numerous specialists from different fields like systematics and genetics, around Europe. At present, we may consider that the structure of Barbus sensu lato (s.l.) is relatively well known, even if some new results are still pending and other studies still needed. Barbus s.l. which was first defined on the trivial character of the presence of barbels around the mouth, has proved to include diploid, tetraploid and hexaploid lineages, themselves polyphyletic, which explains the difficulty to establish a comprehensive taxonomy. The numerous contributions published since 1990, based on karyology and molecular markers gave us a clear view of the main attributes of the evolutionary history of this complex group. First, according to taxonomy rules, the "true Barbus" (Barbus sensu stricto) are composed of tetraploid species distributed around the Mediterranean, including Danubian and Mesopotamian (Tigris and Euphrates) regions. They are composed of a north Mediterranean lineage (Barbus genus) and a south Mediterranean lineage (Luciobarbus genus). Other tetraploid Barbus s.l. are known in South Africa. Barbus s.l. includes also diploid and hexaploid lineages. Diploids are widespread and diversified, comprising Asian (mainly south-east Asia) and African species. The phylogenetic relationships between diploid and polyploid species need yet to be described. Hexaploid Barbus s.l. probably appeared after hybridization between tetraploid species (as evidenced for the genus Capoeta). A clear and homogeneous hexaploid lineage can be followed from Middle East up to South Africa. This rapid African radiation constituted the genus Labeobarbus, the "large Barbus", occupying the entire continent. The present contribution develops both the known structure of this "Chinese puzzle" and the history of its description, which is not yet finished. |
Vogiatzi, E; Kalogianni, E; Zimmerman, B; Giakoumi, S; Barbieri, R; Paschou, P; Magoulas, A; Tsaparis, D; Poulakakis, N; Tsigenopoulos, CS. Biological Journal of the Linnean Society, 111 , pp. 334–349, 2014. @article{vogiatzi_reduced_2014, title = {Reduced genetic variation and strong genetic population structure in the freshwater killifish Valencia letourneuxi (Valenciidae) based on nuclear and mitochondrial markers}, author = {E Vogiatzi and E Kalogianni and B Zimmerman and S Giakoumi and R Barbieri and P Paschou and A Magoulas and D Tsaparis and N Poulakakis and CS. Tsigenopoulos}, url = {http://dx.doi.org/10.1111/bij.12206}, doi = {10.1111/bij.12206}, year = {2014}, date = {2014-01-01}, journal = {Biological Journal of the Linnean Society}, volume = {111}, pages = {334--349}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2013 |
Gkafas, Ga; Tsigenopoulos, C; Magoulas, A; Panagiotaki, P; Vafidis, D; Mamuris, Z; Exadactylos, A Population subdivision of saddled seabream Oblada melanura in the Aegean Sea revealed by genetic and morphometric analyses Journal Article Aquatic Biology, 18 (1), pp. 69–80, 2013, ISSN: 1864-7782, 1864-7790. @article{gkafas_population_2013, title = {Population subdivision of saddled seabream Oblada melanura in the Aegean Sea revealed by genetic and morphometric analyses}, author = {Ga Gkafas and C Tsigenopoulos and A Magoulas and P Panagiotaki and D Vafidis and Z Mamuris and A Exadactylos}, url = {http://www.int-res.com/abstracts/ab/v18/n1/p69-80/}, doi = {10.3354/ab00490}, issn = {1864-7782, 1864-7790}, year = {2013}, date = {2013-02-01}, urldate = {2020-08-09}, journal = {Aquatic Biology}, volume = {18}, number = {1}, pages = {69--80}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Loukovitis, D; Batargias, C; Sarropoulou, E; Apostolidis, A P; Kotoulas, G; Magoulas, A; Tsigenopoulos, C S; Chatziplis, D Quantitative trait loci affecting morphology traits in gilthead seabream (Sparus aurata L.) Journal Article Animal Genetics, 44 (4), pp. 480–483, 2013, ISSN: 02689146. @article{loukovitis_quantitative_2013, title = {Quantitative trait loci affecting morphology traits in gilthead seabream (Sparus aurata L.)}, author = {D Loukovitis and C Batargias and E Sarropoulou and A P Apostolidis and G Kotoulas and A Magoulas and C S Tsigenopoulos and D Chatziplis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84879694158&doi=10.1111%2fage.12027&partnerID=40&md5=8646dd0a21752e42aadd08f5cc9b92b9}, doi = {10.1111/age.12027}, issn = {02689146}, year = {2013}, date = {2013-01-01}, journal = {Animal Genetics}, volume = {44}, number = {4}, pages = {480--483}, abstract = {We report a quantitative trait loci (QTL) mapping study on 18 morphometric characters in gilthead seabream based on a total of 74 informative microsatellite markers genotyped in 409 offspring coming from 10 paternal half-sib families. Statistical analysis was carried out using a linear regression approach, and various suggestive and significant morphology QTL were detected in three (9, 21 and 25) of nine linkage groups examined. Fitting body weight as a covariate reduced the significance of some QTL but revealed three new QTL in other linkage groups (LG6 and LG10). Current results combined with those obtained from previous studies underline highly significant loci affecting overall growth and morphology in S. aurata. © 2013 The Authors, Animal Genetics © 2013 Stichting International Foundation for Animal Genetics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report a quantitative trait loci (QTL) mapping study on 18 morphometric characters in gilthead seabream based on a total of 74 informative microsatellite markers genotyped in 409 offspring coming from 10 paternal half-sib families. Statistical analysis was carried out using a linear regression approach, and various suggestive and significant morphology QTL were detected in three (9, 21 and 25) of nine linkage groups examined. Fitting body weight as a covariate reduced the significance of some QTL but revealed three new QTL in other linkage groups (LG6 and LG10). Current results combined with those obtained from previous studies underline highly significant loci affecting overall growth and morphology in S. aurata. © 2013 The Authors, Animal Genetics © 2013 Stichting International Foundation for Animal Genetics. |
Somarakis, S; Pavlidis, M; Saapoglou, C; Tsigenopoulos, C S; Dempster, T Evidence for 'escape through spawning' in large gilthead sea bream Sparus aurata reared in commercial sea-cages Journal Article Aquaculture Environment Interactions, 3 (2), pp. 135–152, 2013, ISSN: 1869215X. @article{somarakis_evidence_2013, title = {Evidence for 'escape through spawning' in large gilthead sea bream Sparus aurata reared in commercial sea-cages}, author = {S Somarakis and M Pavlidis and C Saapoglou and C S Tsigenopoulos and T Dempster}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84875158258&doi=10.3354%2faei00057&partnerID=40&md5=0df6f8d4535c351f735314c0d0988c8c}, doi = {10.3354/aei00057}, issn = {1869215X}, year = {2013}, date = {2013-01-01}, journal = {Aquaculture Environment Interactions}, volume = {3}, number = {2}, pages = {135--152}, abstract = {During the last decade, farming of species that may reproduce within marine fish farms has become more common. However, knowledge of the extent and ecological effects of reproduction of farmed fish within commercial farms is sparse. We examined whether large gilthead sea bream Sparus aurata reared in farms in Greece produced fertilized eggs that survived and dispersed into surrounding waters. Extensive histological investigation of gonads sampled from 5 different farms revealed that female sea bream cultivated beyond the size of sex reversal matured, ovulated and released eggs during the normal spawning period of the species. Annual fecundities (108 000 ± 60 081 eggs kg-1 of female in farms) were low relative to commercial broodstock and decreased considerably with sex ratio (i.e. with fish size in the cage). An egg-collector experiment and site-intensive ichthyoplankton study with genetic identification of sparid eggs demonstrated that sea bream eggs were spawned in farms and released to the environment. If 5-10% of the 130 000 tons yr-1 production is fish of larger size, we estimate that 3.5 × 1011 to 7.0 × 1011 eggs yr-1 are released into the Mediterranean Sea. Whilst we documented low daily survival rates of fertilized eggs in the vicinity of sea-cages, our findings imply that the escape of eggs from sea bream farms may have ecological consequences, which likely depend on the sex ratio and intensity of farming within specific regions. To avoid potentially negative ecological and genetic con sequences of escape through spawning, farms with large fish should not be placed close to the nursery grounds of wild sea bream, such as in coastal lagoons. © Inter-Research 2013.}, keywords = {}, pubstate = {published}, tppubtype = {article} } During the last decade, farming of species that may reproduce within marine fish farms has become more common. However, knowledge of the extent and ecological effects of reproduction of farmed fish within commercial farms is sparse. We examined whether large gilthead sea bream Sparus aurata reared in farms in Greece produced fertilized eggs that survived and dispersed into surrounding waters. Extensive histological investigation of gonads sampled from 5 different farms revealed that female sea bream cultivated beyond the size of sex reversal matured, ovulated and released eggs during the normal spawning period of the species. Annual fecundities (108 000 ± 60 081 eggs kg-1 of female in farms) were low relative to commercial broodstock and decreased considerably with sex ratio (i.e. with fish size in the cage). An egg-collector experiment and site-intensive ichthyoplankton study with genetic identification of sparid eggs demonstrated that sea bream eggs were spawned in farms and released to the environment. If 5-10% of the 130 000 tons yr-1 production is fish of larger size, we estimate that 3.5 × 1011 to 7.0 × 1011 eggs yr-1 are released into the Mediterranean Sea. Whilst we documented low daily survival rates of fertilized eggs in the vicinity of sea-cages, our findings imply that the escape of eggs from sea bream farms may have ecological consequences, which likely depend on the sex ratio and intensity of farming within specific regions. To avoid potentially negative ecological and genetic con sequences of escape through spawning, farms with large fish should not be placed close to the nursery grounds of wild sea bream, such as in coastal lagoons. © Inter-Research 2013. |
2012 |
Quéré, Nolwenn; Desmarais, Erick; Tsigenopoulos, Costas S; Belkhir, Khalid; Bonhomme, François; Guinand, Bruno Gene flow at major transitional areas in sea bass (Dicentrarchus labrax) and the possible emergence of a hybrid swarm Journal Article Ecology and Evolution, 2 (12), pp. 3061–3078, 2012, ISSN: 20457758. @article{quere_gene_2012, title = {Gene flow at major transitional areas in sea bass (Dicentrarchus labrax) and the possible emergence of a hybrid swarm}, author = {Nolwenn Quéré and Erick Desmarais and Costas S Tsigenopoulos and Khalid Belkhir and François Bonhomme and Bruno Guinand}, url = {http://doi.wiley.com/10.1002/ece3.406}, doi = {10.1002/ece3.406}, issn = {20457758}, year = {2012}, date = {2012-12-01}, urldate = {2020-08-10}, journal = {Ecology and Evolution}, volume = {2}, number = {12}, pages = {3061--3078}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Boyen, C; Heip, C; Cury, P; Baisnée, P-F; Brownlee, C; Tessmar-Raible, K; Allen, I; Arvanitidis, C; Austen, M; Bolhuis, H; Bouget, F-Y; Clark, M; Coll-Montón, M; Crise, A; Dupont, S; Garcon, V; Grigorov, I; Hummel, H; Ianora, A; Kooistra, W; Mariani, P; Möllmann, C; Sköld, Nilsson H; Not, F; Olsen, J; Pinto, Souza I; Queguiner, B; Reygondeau, G; d’Alcala, Ribera M; Santos, Serrão R; Sluijs, A; Soetaert, K; Solidoro, C; Thorndyke, M; Tsigenopoulos, C S; Viard, F; Volckaert, F; textbackslash, J M Węs EuroMarine Research Strategy Report Technical Report 2012, (Publisher: EUROMARINE Project Type: Report). @techreport{boyen_euromarine_2012, title = {EuroMarine Research Strategy Report}, author = {C Boyen and C Heip and P Cury and P-F Baisnée and C Brownlee and K Tessmar-Raible and I Allen and C Arvanitidis and M Austen and H Bolhuis and F-Y Bouget and M Clark and M Coll-Montón and A Crise and S Dupont and V Garcon and I Grigorov and H Hummel and A Ianora and W Kooistra and P Mariani and C Möllmann and H Nilsson Sköld and F Not and J Olsen and I Souza Pinto and B Queguiner and G Reygondeau and M Ribera d’Alcala and R Serrão Santos and A Sluijs and K Soetaert and C Solidoro and M Thorndyke and C S Tsigenopoulos and F Viard and F Volckaert and J M Węs{textbackslash}lawski}, url = {www.euromarineconsortium.eu}, year = {2012}, date = {2012-11-01}, pages = {1--36}, abstract = {EuroMarine is a Coordination and Support Action funded by the European Commission for two years (FP7, 2011-2013). Its aim is the integration of three major European marine FP6 Networks of Excellence (NoE) (Eur-oCEanS, MarBEF and Marine genomics Europe) into one durable organization EuroMarine+, bringing together leading European marine scientists and organizations to create a major internationally competitive network that will facilitate collaboration and promote interdisciplinary approaches in the marine sciences. EuroMarine’s main responsibilities therefore lie, firstly, in the definition of the vision, the specific role and the organizational and operational modes of EuroMarine+, and secondly, in a timely launch of EuroMarine+. One key objective of EuroMarine is, founded on the achievements, conclusions and prospective from each of the three NoEs, to develop a common vision on research priorities and a common research strategy based on a shared vision for the oceans, regional seas and coasts of tomorrow, in order to create a strong marine R&D leadership for Europe based on scientific excellence.}, note = {Publisher: EUROMARINE Project Type: Report}, keywords = {}, pubstate = {published}, tppubtype = {techreport} } EuroMarine is a Coordination and Support Action funded by the European Commission for two years (FP7, 2011-2013). Its aim is the integration of three major European marine FP6 Networks of Excellence (NoE) (Eur-oCEanS, MarBEF and Marine genomics Europe) into one durable organization EuroMarine+, bringing together leading European marine scientists and organizations to create a major internationally competitive network that will facilitate collaboration and promote interdisciplinary approaches in the marine sciences. EuroMarine’s main responsibilities therefore lie, firstly, in the definition of the vision, the specific role and the organizational and operational modes of EuroMarine+, and secondly, in a timely launch of EuroMarine+. One key objective of EuroMarine is, founded on the achievements, conclusions and prospective from each of the three NoEs, to develop a common vision on research priorities and a common research strategy based on a shared vision for the oceans, regional seas and coasts of tomorrow, in order to create a strong marine R&D leadership for Europe based on scientific excellence. |
Vogiatzi, E; Hanel, R; Dailianis, Thanos; Lagnel, J; Hassan, M; Magoulas, A; Tsigenopoulos, C S Biochemical Systematics and Ecology, 44 , pp. 279 – 285, 2012. @article{vogiatzi_description_2012, title = {Description of microsatellite markers in four mullids based on the development and cross-species amplification of 18 new markers in red mullet (Mullus barbatus)}, author = {E Vogiatzi and R Hanel and Thanos Dailianis and J Lagnel and M Hassan and A Magoulas and C S Tsigenopoulos}, url = {http://www.sciencedirect.com/science/article/pii/S0305197812001184}, doi = {10.1016/j.bse.2012.06.006}, year = {2012}, date = {2012-01-01}, journal = {Biochemical Systematics and Ecology}, volume = {44}, pages = {279 -- 285}, abstract = {We investigated the transferability and characterized the genetic diversity of 18 microsatellite markers newly developed for the red mullet (Mullus barbatus) in populations of four different species of the Mullidae family: the striped red mullet (Mullus surmuletus), the golden-banded goatfish (Upeneus moluccensis), the West African goatfish (Pseudupeneus prayensis) and the yellow goatfish (Mulloidichthys martinicus). Results indicate that the loci are polymorphic to different extent in M. surmuletus (94%), U. moluccensis (83%), P. prayensis (78%), and M. martinicus (67%). The high rates of successful cross-amplification of microsatellite loci among Mullidae species will offer excellent opportunities to investigate the genetic structure of wild populations, to explore their conservation genetics and fisheries management and to study any future interaction and introgression between them. © 2012 Elsevier Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We investigated the transferability and characterized the genetic diversity of 18 microsatellite markers newly developed for the red mullet (Mullus barbatus) in populations of four different species of the Mullidae family: the striped red mullet (Mullus surmuletus), the golden-banded goatfish (Upeneus moluccensis), the West African goatfish (Pseudupeneus prayensis) and the yellow goatfish (Mulloidichthys martinicus). Results indicate that the loci are polymorphic to different extent in M. surmuletus (94%), U. moluccensis (83%), P. prayensis (78%), and M. martinicus (67%). The high rates of successful cross-amplification of microsatellite loci among Mullidae species will offer excellent opportunities to investigate the genetic structure of wild populations, to explore their conservation genetics and fisheries management and to study any future interaction and introgression between them. © 2012 Elsevier Ltd. |
Makridis, P; Ferreira, T; Kokou, F; Tsigenopoulos, C S; Divanach, P Quantitative and Qualitative Aspects of Bacterial Communities Associated with Cultures of Chlorella minutissima Journal Article Journal of the World Aquaculture Society, 43 , pp. 571 – 578, 2012. @article{makridis_quantitative_2012, title = {Quantitative and Qualitative Aspects of Bacterial Communities Associated with Cultures of Chlorella minutissima}, author = {P Makridis and T Ferreira and F Kokou and C S Tsigenopoulos and P Divanach}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84864765348&partnerID=40&md5=24dbfa072f09304f0a5ae3c91e329aab}, year = {2012}, date = {2012-01-01}, journal = {Journal of the World Aquaculture Society}, volume = {43}, pages = {571 -- 578}, abstract = {Microbiological conditions in 200 L cultures of microalgae Chlorella minutissima in polyethylene sleeves were examined. The influence of addition of antibiotic (nitrofurantoin) was studied. Samples were taken 2, 5, 9, and 14 d after inoculation and were spread on solid Zobell medium and on thiosulfate citrate bile salts sucrose agar for the enumeration of total numbers of bacteria and numbers of presumptive Vibrio bacteria, respectively. Microalgae grew well in the cultures and high numbers of culturable bacteria (about 107 bacteria/mL) were present in all microalgae cultures. Addition of antibiotic in 200-L cultures of C. minutissima did not result in a significant decrease of total counts of bacteria per unit volume (P > 0.05), while the numbers of presumptive Vibrio were higher in cultures added antibiotic compared with the control treatment (P < 0.05). The numbers of presumptive Vibrio per unit volume and the percentage of fast-growing bacteria were higher in microalgae supernatant than in noncentrifuged samples. Representative colonies were taken from all samples and in total 649 bacterial strains were isolated during this study. A range of phylotypes was identified by amplification and sequencing of the 16S rDNA gene and phylogenetic trees were constructed. Several members of the Roseobacter clade were dominant among the culturable isolates. © Copyright by the World Aquaculture Society 2012.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Microbiological conditions in 200 L cultures of microalgae Chlorella minutissima in polyethylene sleeves were examined. The influence of addition of antibiotic (nitrofurantoin) was studied. Samples were taken 2, 5, 9, and 14 d after inoculation and were spread on solid Zobell medium and on thiosulfate citrate bile salts sucrose agar for the enumeration of total numbers of bacteria and numbers of presumptive Vibrio bacteria, respectively. Microalgae grew well in the cultures and high numbers of culturable bacteria (about 107 bacteria/mL) were present in all microalgae cultures. Addition of antibiotic in 200-L cultures of C. minutissima did not result in a significant decrease of total counts of bacteria per unit volume (P > 0.05), while the numbers of presumptive Vibrio were higher in cultures added antibiotic compared with the control treatment (P < 0.05). The numbers of presumptive Vibrio per unit volume and the percentage of fast-growing bacteria were higher in microalgae supernatant than in noncentrifuged samples. Representative colonies were taken from all samples and in total 649 bacterial strains were isolated during this study. A range of phylotypes was identified by amplification and sequencing of the 16S rDNA gene and phylogenetic trees were constructed. Several members of the Roseobacter clade were dominant among the culturable isolates. © Copyright by the World Aquaculture Society 2012. |
Loukovitis, D; Sarropoulou, E; Vogiatzi, E; Tsigenopoulos, C S; Kotoulas, G; Magoulas, A; Chatziplis, D Genetic variation in farmed populations of the gilthead sea bream Sparus aurata in Greece using microsatellite DNA markers Journal Article Aquaculture Research, 43 (2), pp. 239–246, 2012, ISSN: 1355557X. @article{loukovitis_genetic_2012, title = {Genetic variation in farmed populations of the gilthead sea bream Sparus aurata in Greece using microsatellite DNA markers}, author = {D Loukovitis and E Sarropoulou and E Vogiatzi and C S Tsigenopoulos and G Kotoulas and A Magoulas and D Chatziplis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-83255167256&doi=10.1111%2fj.1365-2109.2011.02821.x&partnerID=40&md5=36672ab78be0cf614702105a4a50327f}, doi = {10.1111/j.1365-2109.2011.02821.x}, issn = {1355557X}, year = {2012}, date = {2012-01-01}, journal = {Aquaculture Research}, volume = {43}, number = {2}, pages = {239--246}, abstract = {Genetic variation in seven reared stocks of gilthead sea bream Sparus aurata, originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of two natural populations from the Ionian and the Adriatic Seas. The total number of alleles per marker ranged from 11 to 19 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic diversity and expected heterozygosity. The global genetic differentiation for the cultivated samples was significant as indicated by F st analysis, which might indicate random genetic drift and inbreeding events operating in the hatcheries. On the contrary, no significant difference was found between the two wild populations. Population pairwise tests between farmed and wild stocks were also significant, with the exception of one hatchery sample, the Central Greece 1, which was not significantly different from the two wild samples perhaps due to its recent use in aquaculture from wild-caught animals. The UPGMA tree topology grouped the wild samples together with the Central Greece 1 stock, and showed a clear division between wild and farmed sample sets for the six remaining hatchery samples. Knowledge of the genetic variation in S. aurata cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for the proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes. © 2011 Blackwell Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Genetic variation in seven reared stocks of gilthead sea bream Sparus aurata, originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of two natural populations from the Ionian and the Adriatic Seas. The total number of alleles per marker ranged from 11 to 19 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic diversity and expected heterozygosity. The global genetic differentiation for the cultivated samples was significant as indicated by F st analysis, which might indicate random genetic drift and inbreeding events operating in the hatcheries. On the contrary, no significant difference was found between the two wild populations. Population pairwise tests between farmed and wild stocks were also significant, with the exception of one hatchery sample, the Central Greece 1, which was not significantly different from the two wild samples perhaps due to its recent use in aquaculture from wild-caught animals. The UPGMA tree topology grouped the wild samples together with the Central Greece 1 stock, and showed a clear division between wild and farmed sample sets for the six remaining hatchery samples. Knowledge of the genetic variation in S. aurata cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for the proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes. © 2011 Blackwell Publishing Ltd. |
Loukovitis, D; Sarropoulou, E; Batargias, C; Apostolidis, A P; Kotoulas, G; Tsigenopoulos, C S; Chatziplis, D Quantitative trait loci for body growth and sex determination in the hermaphrodite teleost fish Sparus aurata L. Journal Article Animal Genetics, 43 (6), pp. 753–759, 2012, ISSN: 02689146. @article{loukovitis_quantitative_2012, title = {Quantitative trait loci for body growth and sex determination in the hermaphrodite teleost fish Sparus aurata L.}, author = {D Loukovitis and E Sarropoulou and C Batargias and A P Apostolidis and G Kotoulas and C S Tsigenopoulos and D Chatziplis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84867582764&doi=10.1111%2fj.1365-2052.2012.02346.x&partnerID=40&md5=b7ebfa1bdacb7395e50fdd78be54840c}, doi = {10.1111/j.1365-2052.2012.02346.x}, issn = {02689146}, year = {2012}, date = {2012-01-01}, journal = {Animal Genetics}, volume = {43}, number = {6}, pages = {753--759}, abstract = {Gilthead sea bream (Sparus aurata L.) is an important marine fish in Mediterranean aquaculture. Sex determination by age and/or body weight is a critical life-history trait, the genetic basis for which is largely unknown in this sequential hermaphrodite species. Herein, we performed a partial genome scan to map quantitative trait loci (QTL) affecting body weight and sex using 74 informative microsatellite markers from 10 paternal half-sib families to construct nine linkage groups (LG). In total, four growth-related QTL (two chromosome-wide and two genome-wide) and six QTL related to sex determination (three pairs in three different LGs) were detected (two chromosome-wide and one genome-wide). The proportion of phenotypic variation explained by the body-weight QTL ranged from 9.3% to 17.2%, showing their potential for use in marker-assisted selection. The results obtained offer solid ground to investigate the structure and function of the genomic regions involved in the mechanisms of sex reversal. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Gilthead sea bream (Sparus aurata L.) is an important marine fish in Mediterranean aquaculture. Sex determination by age and/or body weight is a critical life-history trait, the genetic basis for which is largely unknown in this sequential hermaphrodite species. Herein, we performed a partial genome scan to map quantitative trait loci (QTL) affecting body weight and sex using 74 informative microsatellite markers from 10 paternal half-sib families to construct nine linkage groups (LG). In total, four growth-related QTL (two chromosome-wide and two genome-wide) and six QTL related to sex determination (three pairs in three different LGs) were detected (two chromosome-wide and one genome-wide). The proportion of phenotypic variation explained by the body-weight QTL ranged from 9.3% to 17.2%, showing their potential for use in marker-assisted selection. The results obtained offer solid ground to investigate the structure and function of the genomic regions involved in the mechanisms of sex reversal. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics. |
Chaoui, L; Gagnaire, P-A; Guinand, B; Quignard, J-P; Tsigenopoulos, C S; Kara, M H; Bonhomme, F Microsatellite length variation in candidate genes correlates with habitat in the gilthead sea bream Sparus aurata Journal Article Molecular Ecology, 21 , pp. 5497–5511, 2012. @article{chaoui_microsatellite_2012, title = {Microsatellite length variation in candidate genes correlates with habitat in the gilthead sea bream Sparus aurata}, author = {L Chaoui and P-A Gagnaire and B Guinand and J-P Quignard and C S Tsigenopoulos and M H Kara and F Bonhomme}, year = {2012}, date = {2012-01-01}, journal = {Molecular Ecology}, volume = {21}, pages = {5497--5511}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Coscia, Ilaria; Vogiatzi, Emmanouella; Kotoulas, Giorgios; Tsigenopoulos, C S; Mariani, Stefano Neutral and adaptive genetic variation in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic Journal Article Heredity, 108 , pp. 537–546, 2012. @article{coscia_neutral_2012, title = {Neutral and adaptive genetic variation in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic}, author = {Ilaria Coscia and Emmanouella Vogiatzi and Giorgios Kotoulas and C S Tsigenopoulos and Stefano Mariani}, year = {2012}, date = {2012-01-01}, journal = {Heredity}, volume = {108}, pages = {537--546}, abstract = {Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of Ireland, and genetically assayed using a suite of species-specific markers, including 15 putatively neutral microsatellites and 23 Expressed Sequence Tag-linked (ESTs) markers, as well as a portion of the mitochondrial DNA (mtDNA) Control Region. Two of the putatively neutral markers, Bld-10 and Ad-10, bore signatures of strong directional selection, particularly in the newly established Irish population, though the potential ‘surfing effect’ of rare alleles at the edge of the expansion front was also considered. Analyses after the removal of these loci suggest low but significant population structure likely affected by some degree of gene flow counteracting random genetic drift. No signal of historic divergence was detected at mtDNA. BLAST searches conducted with all 38 markers used failed to identify specific genomic regions associated to adaptive functions. However, the availability of genomic resources for this commercially valuable species is rapidly increasing, bringing us closer to the understanding of the interplay between selective and neutral evolutionary forces, shaping population divergence of an expanding species in a heterogeneous milieu.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of Ireland, and genetically assayed using a suite of species-specific markers, including 15 putatively neutral microsatellites and 23 Expressed Sequence Tag-linked (ESTs) markers, as well as a portion of the mitochondrial DNA (mtDNA) Control Region. Two of the putatively neutral markers, Bld-10 and Ad-10, bore signatures of strong directional selection, particularly in the newly established Irish population, though the potential ‘surfing effect’ of rare alleles at the edge of the expansion front was also considered. Analyses after the removal of these loci suggest low but significant population structure likely affected by some degree of gene flow counteracting random genetic drift. No signal of historic divergence was detected at mtDNA. BLAST searches conducted with all 38 markers used failed to identify specific genomic regions associated to adaptive functions. However, the availability of genomic resources for this commercially valuable species is rapidly increasing, bringing us closer to the understanding of the interplay between selective and neutral evolutionary forces, shaping population divergence of an expanding species in a heterogeneous milieu. |
Limborg, M T; Hanel, R; Debes, P V; Ring, A K; André, C; Tsigenopoulos, C S; Bekkevold, D Heredity, 109 , pp. 96 – 107, 2012. @article{limborg_imprints_2012, title = {Imprints from genetic drift and mutation imply relative divergence times across marine transition zones in a pan-European small pelagic fish (Sprattus sprattus)}, author = {M T Limborg and R Hanel and P V Debes and A K Ring and C André and C S Tsigenopoulos and D Bekkevold}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84864285409&partnerID=40&md5=345338616ad90db6404a69984576584c}, year = {2012}, date = {2012-01-01}, journal = {Heredity}, volume = {109}, pages = {96 -- 107}, abstract = {Geographic distributions of most temperate marine fishes are affected by postglacial recolonisation events, which have left complex genetic imprints on populations of marine species. This study investigated population structure and demographic history of European sprat (Sprattus sprattus L.) by combining inference from both mtDNA and microsatellite genetic markers throughout the species’ distribution. We compared effects from genetic drift and mutation for both genetic markers in shaping genetic differentiation across four transition zones. Microsatellite markers revealed significant isolation by distance and a complex population structure across the species' distribution (overall ST 0.038, P0.01). Across transition zones markers indicated larger effects of genetic drift over mutations in the northern distribution of sprat contrasting a stronger relative impact of mutation in the species’ southern distribution in the Mediterranean region. These results were interpreted to reflect more recent divergence times between northern populations in accordance with previous findings. This study demonstrates the usefulness of comparing inference from different markers and estimators of divergence for phylogeographic and population genetic studies in species with weak genetic structure, as is the case in many marine species. © 2012 Macmillan Publishers Limited All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Geographic distributions of most temperate marine fishes are affected by postglacial recolonisation events, which have left complex genetic imprints on populations of marine species. This study investigated population structure and demographic history of European sprat (Sprattus sprattus L.) by combining inference from both mtDNA and microsatellite genetic markers throughout the species’ distribution. We compared effects from genetic drift and mutation for both genetic markers in shaping genetic differentiation across four transition zones. Microsatellite markers revealed significant isolation by distance and a complex population structure across the species' distribution (overall ST 0.038, P0.01). Across transition zones markers indicated larger effects of genetic drift over mutations in the northern distribution of sprat contrasting a stronger relative impact of mutation in the species’ southern distribution in the Mediterranean region. These results were interpreted to reflect more recent divergence times between northern populations in accordance with previous findings. This study demonstrates the usefulness of comparing inference from different markers and estimators of divergence for phylogeographic and population genetic studies in species with weak genetic structure, as is the case in many marine species. © 2012 Macmillan Publishers Limited All rights reserved. |
Lefkaditou, E; Tsigenopoulos, C S; Alidromiti, C; Haralabous, J On the occurrence of Alloteuthis subulata in the Eastern Ionian Sea and its distinction from the sympatric Alloteuthis media Journal Article Journal of Biological Research, 17 , pp. 169–175, 2012. @article{lefkaditou_occurrence_2012, title = {On the occurrence of Alloteuthis subulata in the Eastern Ionian Sea and its distinction from the sympatric Alloteuthis media}, author = {E Lefkaditou and C S Tsigenopoulos and C Alidromiti and J Haralabous}, year = {2012}, date = {2012-01-01}, journal = {Journal of Biological Research}, volume = {17}, pages = {169--175}, abstract = {Despite the efforts made during the last decade, the systematics of the sympatric species Alloteuthis media and Alloteuthis subulata still remains confused and the distribution of the two species in the Mediterranean Sea doubtful. The 9 male specimens identified as Alloteuthis subulata in July-August 2008, represent the first finding of this species among samples of the “International Bottom Trawl Survey in the Mediterranean” (MEDITS), which is repeatedly carried out in the eastern Ionian Sea since 1994. Morphometric data and tissue samples for mo-lecular analysis were collected from these specimens, as well as, from male and female specimens assigned to A. media from the same and near-by sampling stations. As the longer tale is the most evident characteristic to distinguish at least adult male specimen of the two species, the length of the anterior part of the mantle (from fin’s edge to mantle opening) was used as the reference length upon which indices of different body dimensions were calculated. Genetic analyses using mitochondrial DNA cytochrome oxidase I (COI) gene sequences confirmed species allocation for all individuals assigned to A. subulata, whereas for A. media samples, one female and an unsexed juvenile seemed to carry the A. subulata COI haplotype. Discriminant function analysis (DFA) of morphometric data suggested that length of arms, tentacles and tentacle clubs, all relatively smaller in A. subulata, constitute important variables allowing the distinction of the two species. However, further genetic and morphometric analyses on a larger sample covering the whole size range for both species and sexes, are needed to confirm as decisive diagnostic the value of the above mentioned characters.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Despite the efforts made during the last decade, the systematics of the sympatric species Alloteuthis media and Alloteuthis subulata still remains confused and the distribution of the two species in the Mediterranean Sea doubtful. The 9 male specimens identified as Alloteuthis subulata in July-August 2008, represent the first finding of this species among samples of the “International Bottom Trawl Survey in the Mediterranean” (MEDITS), which is repeatedly carried out in the eastern Ionian Sea since 1994. Morphometric data and tissue samples for mo-lecular analysis were collected from these specimens, as well as, from male and female specimens assigned to A. media from the same and near-by sampling stations. As the longer tale is the most evident characteristic to distinguish at least adult male specimen of the two species, the length of the anterior part of the mantle (from fin’s edge to mantle opening) was used as the reference length upon which indices of different body dimensions were calculated. Genetic analyses using mitochondrial DNA cytochrome oxidase I (COI) gene sequences confirmed species allocation for all individuals assigned to A. subulata, whereas for A. media samples, one female and an unsexed juvenile seemed to carry the A. subulata COI haplotype. Discriminant function analysis (DFA) of morphometric data suggested that length of arms, tentacles and tentacle clubs, all relatively smaller in A. subulata, constitute important variables allowing the distinction of the two species. However, further genetic and morphometric analyses on a larger sample covering the whole size range for both species and sexes, are needed to confirm as decisive diagnostic the value of the above mentioned characters. |
Vasileiadou, A; Sarropoulou, E; Tsigenopoulos, C S; Reizopoulou, S; Nikolaidou, A; Orfanidis, S; Simboura, N; Kotoulas, G; Arvanitidis, C Genetic vs community diversity patterns of macrobenthic species: preliminary results from the lagoonal ecosystem Journal Article Transitional Waters Bulletin, 6 , pp. 20–33, 2012. @article{vasileiadou_genetic_2012, title = {Genetic vs community diversity patterns of macrobenthic species: preliminary results from the lagoonal ecosystem}, author = {A Vasileiadou and E Sarropoulou and C S Tsigenopoulos and S Reizopoulou and A Nikolaidou and S Orfanidis and N Simboura and G Kotoulas and C Arvanitidis}, url = {http://siba-ese.unisalento.it/index.php/twb/article/view/12797/11396}, doi = {10.1285/i1825229Xv6n2p20}, year = {2012}, date = {2012-01-01}, journal = {Transitional Waters Bulletin}, volume = {6}, pages = {20--33}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2011 |
Hanel, Reinhold; Tsigenopoulos, Costas S Phylogeny, Evolution and Taxonomy of Sparids with Some Notes on their Ecology and Biology Incollection Pavlidis, Michail A; Mylonas, Constantinos C (Ed.): Sparidae, pp. 51–73, Wiley-Blackwell, Oxford, UK, 2011, ISBN: 978-1-4443-9221-0 978-1-4051-9772-4. @incollection{pavlidis_phylogeny_2011, title = {Phylogeny, Evolution and Taxonomy of Sparids with Some Notes on their Ecology and Biology}, author = {Reinhold Hanel and Costas S Tsigenopoulos}, editor = {Michail A Pavlidis and Constantinos C Mylonas}, url = {http://doi.wiley.com/10.1002/9781444392210.ch2}, doi = {10.1002/9781444392210.ch2}, isbn = {978-1-4443-9221-0 978-1-4051-9772-4}, year = {2011}, date = {2011-02-01}, urldate = {2020-08-10}, booktitle = {Sparidae}, pages = {51--73}, publisher = {Wiley-Blackwell}, address = {Oxford, UK}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Dailianis, T; Tsigenopoulos, C S; Dounas, C; Voultsiadou, E Molecular Ecology, 20 (18), pp. 3757–3772, 2011, ISSN: 09621083. @article{dailianis_genetic_2011, title = {Genetic diversity of the imperilled bath sponge Spongia officinalis Linnaeus, 1759 across the Mediterranean Sea: Patterns of population differentiation and implications for taxonomy and conservation}, author = {T Dailianis and C S Tsigenopoulos and C Dounas and E Voultsiadou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84860390594&doi=10.1111%2fj.1365-294X.2011.05222.x&partnerID=40&md5=69d2c113d95d39f51f769ef7d0b5b93e}, doi = {10.1111/j.1365-294X.2011.05222.x}, issn = {09621083}, year = {2011}, date = {2011-01-01}, journal = {Molecular Ecology}, volume = {20}, number = {18}, pages = {3757--3772}, abstract = {The Mediterranean bath sponge Spongia officinalis is an iconic species with high socio-economic value and precarious future owing to unregulated harvesting, mortality incidents and lack of established knowledge regarding its ecology. This study aims to assess genetic diversity and population structure of the species at different geographical scales throughout its distribution. For this purpose, 11 locations in the Eastern Mediterranean (Aegean Sea), Western Mediterranean (Provence coast) and the Strait of Gibraltar were sampled; specimens were analysed using partial mitochondrial cytochrome oxidase subunit I (COI) sequences, along with a set of eight microsatellite loci. According to our results (i) no genetic differentiation exists among the acknowledged Mediterranean morphotypes, and hence, S. officinalis can be viewed as a single, morphologically variable species; (ii) a notable divergence was recorded in the Gibraltar region, indicating the possible existence of a cryptic species; (iii) restriction to gene flow was evidenced between the Aegean Sea and Provence giving two well-defined regional clusters, thus suggesting the existence of a phylogeographic break between the two systems; (iv) low levels of genetic structure, not correlated to geographical distance, were observed inside geographical sectors, implying mechanisms (natural or anthropogenic) that enhance dispersal and gene flow have promoted population connectivity; (v) the genetic diversity of S. officinalis is maintained high in most studied locations despite pressure from harvesting and the influence of devastating epidemics. These findings provide a basis towards the effective conservation and management of the species. © 2011 Blackwell Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Mediterranean bath sponge Spongia officinalis is an iconic species with high socio-economic value and precarious future owing to unregulated harvesting, mortality incidents and lack of established knowledge regarding its ecology. This study aims to assess genetic diversity and population structure of the species at different geographical scales throughout its distribution. For this purpose, 11 locations in the Eastern Mediterranean (Aegean Sea), Western Mediterranean (Provence coast) and the Strait of Gibraltar were sampled; specimens were analysed using partial mitochondrial cytochrome oxidase subunit I (COI) sequences, along with a set of eight microsatellite loci. According to our results (i) no genetic differentiation exists among the acknowledged Mediterranean morphotypes, and hence, S. officinalis can be viewed as a single, morphologically variable species; (ii) a notable divergence was recorded in the Gibraltar region, indicating the possible existence of a cryptic species; (iii) restriction to gene flow was evidenced between the Aegean Sea and Provence giving two well-defined regional clusters, thus suggesting the existence of a phylogeographic break between the two systems; (iv) low levels of genetic structure, not correlated to geographical distance, were observed inside geographical sectors, implying mechanisms (natural or anthropogenic) that enhance dispersal and gene flow have promoted population connectivity; (v) the genetic diversity of S. officinalis is maintained high in most studied locations despite pressure from harvesting and the influence of devastating epidemics. These findings provide a basis towards the effective conservation and management of the species. © 2011 Blackwell Publishing Ltd. |
Loukovitis, D; Sarropoulou, E; Tsigenopoulos, C S; Batargias, C; Magoulas, A; Apostolidis, A P; Chatziplis, D; Kotoulas, G Quantitative Trait Loci involved in sex determination and body growth in the gilthead sea bream (Sparus aurata L.) through targeted genome scan Journal Article PLoS ONE, 6 (1), 2011, ISSN: 19326203. @article{loukovitis_quantitative_2011, title = {Quantitative Trait Loci involved in sex determination and body growth in the gilthead sea bream (Sparus aurata L.) through targeted genome scan}, author = {D Loukovitis and E Sarropoulou and C S Tsigenopoulos and C Batargias and A Magoulas and A P Apostolidis and D Chatziplis and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79551624871&doi=10.1371%2fjournal.pone.0016599&partnerID=40&md5=97db8af3b120b4907100b6c1e8c87376}, doi = {10.1371/journal.pone.0016599}, issn = {19326203}, year = {2011}, date = {2011-01-01}, journal = {PLoS ONE}, volume = {6}, number = {1}, abstract = {Among vertebrates, teleost fish exhibit a considerably wide range of sex determination patterns that may be influenced by extrinsic parameters. However even for model fish species like the zebrafish Danio rerio the precise mechanisms involved in primary sex determination have not been studied extensively. The zebrafish, a gonochoristic species, is lacking discernible sex chromosomes and the sex of juvenile fish is difficult to determine. Sequential protandrous hermaphrodite species provide distinct determination of the gender and allow studying the sex determination process by looking at the mechanism of sex reversal. This is the first attempt to understand the genetic basis of phenotypic variation for sex determination and body weight in a sequential protandrous hermaphrodite species, the gilthead sea bream (Sparus aurata). This work demonstrates a fast and efficient strategy for Quantitative Trait Loci (QTL) detection in the gilthead sea bream, a non-model but target hermaphrodite fish species. Therefore a comparative mapping approach was performed to query syntenies against two other Perciformes, the European sea bass (Dicentrarchus labrax), a gonochoristic species and the Asian sea bass (Lates calcarifer) a protandrous hermaphrodite. In this manner two significant QTLs, one QTL affecting both body weight and sex and one QTL affecting sex, were detected on the same linkage group. The co-segregation of the two QTLs provides a genomic base to the observed genetic correlation between these two traits in sea bream as well as in other teleosts. The identification of QTLs linked to sex reversal and growth, will contribute significantly to a better understanding of the complex nature of sex determination in S. aurata where most individuals reverse to the female sex at the age of two years through development and maturation of the ovarian portion of the gonad and regression of the testicular area. [Genomic sequences reported in this manuscript have been submitted to GenBank under accession numbers HQ021443- HQ021749.]. © 2011 Loukovitis et al.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Among vertebrates, teleost fish exhibit a considerably wide range of sex determination patterns that may be influenced by extrinsic parameters. However even for model fish species like the zebrafish Danio rerio the precise mechanisms involved in primary sex determination have not been studied extensively. The zebrafish, a gonochoristic species, is lacking discernible sex chromosomes and the sex of juvenile fish is difficult to determine. Sequential protandrous hermaphrodite species provide distinct determination of the gender and allow studying the sex determination process by looking at the mechanism of sex reversal. This is the first attempt to understand the genetic basis of phenotypic variation for sex determination and body weight in a sequential protandrous hermaphrodite species, the gilthead sea bream (Sparus aurata). This work demonstrates a fast and efficient strategy for Quantitative Trait Loci (QTL) detection in the gilthead sea bream, a non-model but target hermaphrodite fish species. Therefore a comparative mapping approach was performed to query syntenies against two other Perciformes, the European sea bass (Dicentrarchus labrax), a gonochoristic species and the Asian sea bass (Lates calcarifer) a protandrous hermaphrodite. In this manner two significant QTLs, one QTL affecting both body weight and sex and one QTL affecting sex, were detected on the same linkage group. The co-segregation of the two QTLs provides a genomic base to the observed genetic correlation between these two traits in sea bream as well as in other teleosts. The identification of QTLs linked to sex reversal and growth, will contribute significantly to a better understanding of the complex nature of sex determination in S. aurata where most individuals reverse to the female sex at the age of two years through development and maturation of the ovarian portion of the gonad and regression of the testicular area. [Genomic sequences reported in this manuscript have been submitted to GenBank under accession numbers HQ021443- HQ021749.]. © 2011 Loukovitis et al. |
Boulton, K; Massault, C; Houston, R D; de Koning, D J; Haley, C S; Bovenhuis, H; Batargias, C; Canario, A V M; Kotoulas, G; Tsigenopoulos, C S QTL affecting morphometric traits and stress response in the gilthead seabream (Sparus aurata) Journal Article Aquaculture, 319 (1-2), pp. 58–66, 2011, ISSN: 00448486. @article{boulton_qtl_2011, title = {QTL affecting morphometric traits and stress response in the gilthead seabream (Sparus aurata)}, author = {K Boulton and C Massault and R D Houston and D J de Koning and C S Haley and H Bovenhuis and C Batargias and A V M Canario and G Kotoulas and C S Tsigenopoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80051590556&doi=10.1016%2fj.aquaculture.2011.06.044&partnerID=40&md5=51eee2954b6d4d2f2757c520ddc3bd70}, doi = {10.1016/j.aquaculture.2011.06.044}, issn = {00448486}, year = {2011}, date = {2011-01-01}, journal = {Aquaculture}, volume = {319}, number = {1-2}, pages = {58--66}, abstract = {The gilthead seabream (Sparus aurata) is an important aquaculture species that has only been subject to an incipient selective breeding programme. This study, which examined the genetic architecture of seabream morphology and stress response to confinement, takes a step toward the use of marker assisted selection in this species. Major loci affecting these traits were mapped, using data from 460 offspring derived from seven paternal and 73 maternal half-sib families. Fish were killed following a four-hour confinement experiment to induce stress, after which 15 morphometric measurements were collected and blood was sampled for DNA extraction and plasma cortisol level determination. Heritabilities for the morphometric traits were moderate to high (0.24-0.58), with genetic and phenotypic correlations between the traits generally very high. However, the heritability of plasma cortisol level was not significantly different from zero.A population-specific genetic linkage map was built for 56 microsatellite markers, comprising 16 linkage groups (LG) and ten unlinked markers. Half-sib and variance components QTL analyses detected a single genome-wide significant QTL (SaimbcF7b), a single unlinked marker explaining 13-23% of the phenotypic variance in the majority of the morphometric traits. Several other putative QTL were identified for morphometric traits (on LG 4a, 7, 9, 18, A, C, F and I), along with two other QTL (LG10 and B) that were suggestive for stress response. Fitting body weight as a covariate for the morphometric traits resulted in three genome-wide significant QTL affecting aspects of body shape independent of overall body size. For stress response we only identified suggestive evidence for QTL. These findings contribute to understanding the genetic regulation of important economic traits in seabream. © 2011.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The gilthead seabream (Sparus aurata) is an important aquaculture species that has only been subject to an incipient selective breeding programme. This study, which examined the genetic architecture of seabream morphology and stress response to confinement, takes a step toward the use of marker assisted selection in this species. Major loci affecting these traits were mapped, using data from 460 offspring derived from seven paternal and 73 maternal half-sib families. Fish were killed following a four-hour confinement experiment to induce stress, after which 15 morphometric measurements were collected and blood was sampled for DNA extraction and plasma cortisol level determination. Heritabilities for the morphometric traits were moderate to high (0.24-0.58), with genetic and phenotypic correlations between the traits generally very high. However, the heritability of plasma cortisol level was not significantly different from zero.A population-specific genetic linkage map was built for 56 microsatellite markers, comprising 16 linkage groups (LG) and ten unlinked markers. Half-sib and variance components QTL analyses detected a single genome-wide significant QTL (SaimbcF7b), a single unlinked marker explaining 13-23% of the phenotypic variance in the majority of the morphometric traits. Several other putative QTL were identified for morphometric traits (on LG 4a, 7, 9, 18, A, C, F and I), along with two other QTL (LG10 and B) that were suggestive for stress response. Fitting body weight as a covariate for the morphometric traits resulted in three genome-wide significant QTL affecting aspects of body shape independent of overall body size. For stress response we only identified suggestive evidence for QTL. These findings contribute to understanding the genetic regulation of important economic traits in seabream. © 2011. |
Vogiatzi, E; Lagnel, J; Pakaki, V; Louro, B; Canario, A V M; Reinhardt, R; Kotoulas, G; Magoulas, A; Tsigenopoulos, C S Marine Genomics, 4 (2), pp. 83–91, 2011, ISSN: 18747787. @article{vogiatzi_silico_2011, title = {In silico mining and characterization of simple sequence repeats from gilthead sea bream (Sparus aurata) expressed sequence tags (EST-SSRs); PCR amplification, polymorphism evaluation and multiplexing and cross-species assays}, author = {E Vogiatzi and J Lagnel and V Pakaki and B Louro and A V.M. Canario and R Reinhardt and G Kotoulas and A Magoulas and C S Tsigenopoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79956354483&doi=10.1016%2fj.margen.2011.01.003&partnerID=40&md5=3775ee5dbda814501d9fd8660740563b}, doi = {10.1016/j.margen.2011.01.003}, issn = {18747787}, year = {2011}, date = {2011-01-01}, journal = {Marine Genomics}, volume = {4}, number = {2}, pages = {83--91}, abstract = {We screened for simple sequence repeats (SSRs) found in ESTs derived from an EST-database development project ('Marine Genomics Europe' Network of Excellence). Different motifs of di-, tri-, tetra-, penta- and hexanucleotide SSRs were evaluated for variation in length and position in the expressed sequences, relative abundance and distribution in gilthead sea bream (Sparus aurata). We found 899 ESTs that harbor 997 SSRs (4.94%). On average, one SSR was found per 2.95. kb of EST sequence and the dinucleotide SSRs are the most abundant accounting for 47.6% of the total number.EST-SSRs were used as template for primer design. 664 primer pairs could be successfully identified and a subset of 206 pairs of primers was synthesized, PCR-tested and visualized on ethidium bromide stained agarose gels. The main objective was to further assess the potential of EST-SSRs as informative markers and investigate their cross-species amplification in sixteen teleost fish species: seven sparid species and nine other species from different families. Approximately 78% of the primer pairs gave PCR products of expected size in gilthead sea bream, and as expected, the rate of successful amplification of sea bream EST-SSRs was higher in sparids, lower in other perciforms and even lower in species of the Clupeiform and Gadiform orders. We finally determined the polymorphism and the heterozygosity of 63 markers in a wild gilthead sea bream population; fifty-eight loci were found to be polymorphic with the expected heterozygosity and the number of alleles ranging from 0.089 to 0.946 and from 2 to 27, respectively. These tools and markers are expected to enhance the available genetic linkage map in gilthead sea bream, to assist comparative mapping and genome analyses for this species and further with other model fish species and finally to help advance genetic analysis for cultivated and wild populations and accelerate breeding programs. © 2011 Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We screened for simple sequence repeats (SSRs) found in ESTs derived from an EST-database development project ('Marine Genomics Europe' Network of Excellence). Different motifs of di-, tri-, tetra-, penta- and hexanucleotide SSRs were evaluated for variation in length and position in the expressed sequences, relative abundance and distribution in gilthead sea bream (Sparus aurata). We found 899 ESTs that harbor 997 SSRs (4.94%). On average, one SSR was found per 2.95. kb of EST sequence and the dinucleotide SSRs are the most abundant accounting for 47.6% of the total number.EST-SSRs were used as template for primer design. 664 primer pairs could be successfully identified and a subset of 206 pairs of primers was synthesized, PCR-tested and visualized on ethidium bromide stained agarose gels. The main objective was to further assess the potential of EST-SSRs as informative markers and investigate their cross-species amplification in sixteen teleost fish species: seven sparid species and nine other species from different families. Approximately 78% of the primer pairs gave PCR products of expected size in gilthead sea bream, and as expected, the rate of successful amplification of sea bream EST-SSRs was higher in sparids, lower in other perciforms and even lower in species of the Clupeiform and Gadiform orders. We finally determined the polymorphism and the heterozygosity of 63 markers in a wild gilthead sea bream population; fifty-eight loci were found to be polymorphic with the expected heterozygosity and the number of alleles ranging from 0.089 to 0.946 and from 2 to 27, respectively. These tools and markers are expected to enhance the available genetic linkage map in gilthead sea bream, to assist comparative mapping and genome analyses for this species and further with other model fish species and finally to help advance genetic analysis for cultivated and wild populations and accelerate breeding programs. © 2011 Elsevier B.V. |
Rabaoui, Lotfi; Mejri, Randa; Tlig-Zouari, Sabiha; Bahri, Lilia; Hassine, Oum Kalthoum Ben; Tsigenopoulos, C S Genetic differentiation among populations of the endangered fan mussel Pinna nobilis (Mollusca) along the Tunisian coastline Journal Article Hydrobiologia, 678 , pp. 99–111, 2011. @article{rabaoui_genetic_2011, title = {Genetic differentiation among populations of the endangered fan mussel Pinna nobilis (Mollusca) along the Tunisian coastline}, author = {Lotfi Rabaoui and Randa Mejri and Sabiha Tlig-Zouari and Lilia Bahri and Oum Kalthoum Ben Hassine and C S Tsigenopoulos}, doi = {10.1007/s10750-011-0827-9}, year = {2011}, date = {2011-01-01}, journal = {Hydrobiologia}, volume = {678}, pages = {99--111}, abstract = {The Mediterranean fan mussel Pinna nobilis is an endangered invertebrate due to overexploitation and habitat deterioration. In this species, two distinctive morphs, the “combed” and “straight and wide” forms, have been recorded and it is not known whether this morphometric variability is attributed to genetic or environmental factors. In the present study, we used mitochondrial COI sequences to describe the genetic variability of five Pinna nobilis populations sampled along the northern, eastern and southern Tunisian coastline, and to examine whether there is a genetic differentiation between the two forms of this species. DNA sequences of 675 bp from the mitochondrial COI gene have revealed ten different haplotypes among forty-nine examined specimens. Haplotype diversity was high, ranging between 0.40441 and 0.80952, and showed a decreasing North-East gradient, which seems to be explained by the hydrogeography of the study area. The mitochondrial COI marker did not suggest a genetic distinctiveness between the two Pinna nobilis shell forms, “combed” and “straight and wide”. Although the morphometric plasticity of the fan mussel could be due to the influence of environmental factors, further genetic studies using nuclear markers are envisaged to investigate whether this differentiation is associated to gene flow restrictions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Mediterranean fan mussel Pinna nobilis is an endangered invertebrate due to overexploitation and habitat deterioration. In this species, two distinctive morphs, the “combed” and “straight and wide” forms, have been recorded and it is not known whether this morphometric variability is attributed to genetic or environmental factors. In the present study, we used mitochondrial COI sequences to describe the genetic variability of five Pinna nobilis populations sampled along the northern, eastern and southern Tunisian coastline, and to examine whether there is a genetic differentiation between the two forms of this species. DNA sequences of 675 bp from the mitochondrial COI gene have revealed ten different haplotypes among forty-nine examined specimens. Haplotype diversity was high, ranging between 0.40441 and 0.80952, and showed a decreasing North-East gradient, which seems to be explained by the hydrogeography of the study area. The mitochondrial COI marker did not suggest a genetic distinctiveness between the two Pinna nobilis shell forms, “combed” and “straight and wide”. Although the morphometric plasticity of the fan mussel could be due to the influence of environmental factors, further genetic studies using nuclear markers are envisaged to investigate whether this differentiation is associated to gene flow restrictions. |
2010 |
Katharios, P; Tsigenopoulos, C S First report of nodavirus outbreak in cultured juvenile shi drum, Umbrina cirrosa L., in Greece Journal Article Aquaculture Research, 42 , pp. 147–152, 2010, ISSN: 1355557X. @article{katharios_first_2010, title = {First report of nodavirus outbreak in cultured juvenile shi drum, Umbrina cirrosa L., in Greece}, author = {P Katharios and C S Tsigenopoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78650132503&doi=10.1111%2fj.1365-2109.2010.02532.x&partnerID=40&md5=9fb2484d5ca280c83fd3574d9a935e71}, doi = {10.1111/j.1365-2109.2010.02532.x}, issn = {1355557X}, year = {2010}, date = {2010-01-01}, journal = {Aquaculture Research}, volume = {42}, pages = {147--152}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Tsigenopoulos, C S; Kasapidis, P; Berrebi, P Phylogenetic relationships of hexaploid large-sized barbs (genus Labeobarbus, Cyprinidae) based on mtDNA data Journal Article Molecular Phylogenetics and Evolution, 56 (2), pp. 851–856, 2010, ISSN: 10557903. @article{tsigenopoulos_phylogenetic_2010, title = {Phylogenetic relationships of hexaploid large-sized barbs (genus Labeobarbus, Cyprinidae) based on mtDNA data}, author = {C S Tsigenopoulos and P Kasapidis and P Berrebi}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77953126705&doi=10.1016%2fj.ympev.2010.02.006&partnerID=40&md5=3ac6c3b5564b3f5548c45c2972bc3f84}, doi = {10.1016/j.ympev.2010.02.006}, issn = {10557903}, year = {2010}, date = {2010-01-01}, journal = {Molecular Phylogenetics and Evolution}, volume = {56}, number = {2}, pages = {851--856}, abstract = {The phylogenetic relationships among species of the Labeobarbus genus (Teleostei, Cyprinidae) which comprises large body-sized hexaploid taxa were inferred using complete cytochrome b mitochondrial gene sequences. Molecular data suggest two main evolutionary groups which roughly correspond to a Northern (Middle East and Northwest Africa) and a sub-Saharan lineage. The splitting of the African hexaploids from their Asian ancestors and their subsequent diversification on the African continent occurred in the Late Miocene, a period in which other cyprinins also invaded Africa and radiated in the Mediterranean region. Finally, systematic implications of these results to the taxonomic validity of genera or subgenera such as Varicorhinus, Kosswigobarbus, Carasobarbus and Capoeta are further discussed. © 2010 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The phylogenetic relationships among species of the Labeobarbus genus (Teleostei, Cyprinidae) which comprises large body-sized hexaploid taxa were inferred using complete cytochrome b mitochondrial gene sequences. Molecular data suggest two main evolutionary groups which roughly correspond to a Northern (Middle East and Northwest Africa) and a sub-Saharan lineage. The splitting of the African hexaploids from their Asian ancestors and their subsequent diversification on the African continent occurred in the Late Miocene, a period in which other cyprinins also invaded Africa and radiated in the Mediterranean region. Finally, systematic implications of these results to the taxonomic validity of genera or subgenera such as Varicorhinus, Kosswigobarbus, Carasobarbus and Capoeta are further discussed. © 2010 Elsevier Inc. All rights reserved. |
Dailianis, Thanos; Tsigenopoulos, C S Characterization of polymorphic microsatellite markers for the endangered Mediterranean bath sponge Spongia officinalis L Journal Article Conservation Genetics, 11 (3), pp. 1155–1158, 2010. @article{dailianis_characterization_2010, title = {Characterization of polymorphic microsatellite markers for the endangered Mediterranean bath sponge Spongia officinalis L}, author = {Thanos Dailianis and C S Tsigenopoulos}, url = {http://dx.doi.org/10.1007/s10592-009-9906-0}, doi = {10.1007/s10592-009-9906-0}, year = {2010}, date = {2010-01-01}, journal = {Conservation Genetics}, volume = {11}, number = {3}, pages = {1155--1158}, abstract = {Ten polymorphic microsatellite markers are described for the Mediterranean bath sponge Spongia officinalis. Loci were isolated from a genomic library enriched for AC repeats. Microsatellite markers were evaluated on a Cretan population of 28 individuals; the allelic richness ranged from 5 to 34 with an average of 17, while expected and observed heterozygosities varied from 0.505 to 0.964 and 0.444 to 0.963, respectively. In a species whose populations in the eastern Mediterranean basin have been substantially declined due to recurring mass mortality incidents and intensive harvesting, these markers are expected to assist studies of genetic structure and differentiation between populations.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Ten polymorphic microsatellite markers are described for the Mediterranean bath sponge Spongia officinalis. Loci were isolated from a genomic library enriched for AC repeats. Microsatellite markers were evaluated on a Cretan population of 28 individuals; the allelic richness ranged from 5 to 34 with an average of 17, while expected and observed heterozygosities varied from 0.505 to 0.964 and 0.444 to 0.963, respectively. In a species whose populations in the eastern Mediterranean basin have been substantially declined due to recurring mass mortality incidents and intensive harvesting, these markers are expected to assist studies of genetic structure and differentiation between populations. |
Louro, B; Passos, Ana Lúcia S; Souche, Erika L; Tsigenopoulos, C S; Beck, Alfred; Lagnel, J; Bonhomme, F; Cancela, Leonor; Cerdà, Joan; Clark, Melody S; Lubzens, Esther; A, Magoulas; Planas, Josep V; Volckaert, F A; Reinhardt, Richard; Canario, Adelino V M Marine Genomics, 3 (3-4), pp. 179–191, 2010, (ISBN: 1874-7787). @article{louro_gilthead_2010, title = {Gilthead sea bream (Sparus auratus) and European sea bass (Dicentrarchus labrax) expressed sequence tags: Characterization, tissue-specific expression and gene markers}, author = {B Louro and Ana Lúcia S Passos and Erika L Souche and C S Tsigenopoulos and Alfred Beck and J Lagnel and F Bonhomme and Leonor Cancela and Joan Cerdà and Melody S Clark and Esther Lubzens and Magoulas A and Josep V Planas and F A Volckaert and Richard Reinhardt and Adelino V M Canario}, url = {http://www.sciencedirect.com/science/article/B8JG7-5166W0F-1/2/a82e89b3bb9d10e05933287d876117af}, year = {2010}, date = {2010-01-01}, journal = {Marine Genomics}, volume = {3}, number = {3-4}, pages = {179--191}, abstract = {The gilthead sea bream, Sparus auratus, and the European sea bass, Dicentrarchus labrax, are two of the most important marine species cultivated in Southern Europe. This study aimed at increasing genomic resources for the two species and produced and annotated two sets of 30,000 expressed sequence tags (EST) each from 14 normalized tissue-specific cDNA libraries from sea bream and sea bass. Clustering and assembly of the ESTs formed 5268 contigs and 12,928 singletons for sea bream and 4573 contigs and 13,143 singletons for sea bass, representing 18,196 and 17,716 putative unigenes, respectively. Assuming a similar number of genes in sea bass, sea bream and in the model fish Gasterosteus aculeatus genomes, it was estimated that approximately two thirds of the sea bream and the sea bass transcriptomes were covered by the unigene collections. BLAST sequence similarity searches (using a cut off of e-value textless 10-5) against fully the curated SwissProt (and TrEMBL) databases produced matches of 28%(37%) and 43%(53%) of the sea bream and sea bass unigene datasets respectively, allowing some putative designation of function. A comparative approach is described using human Ensembl peptide ID homolog’s for functional annotation, which increased the number of unigenes with GO terms assigned and resulted in more GO terms assigned per unigene. This allowed the identification of tissue-specific genes using enrichment analysis for GO pathways and protein domains. The comparative annotation approach represents a good strategy for transferring more relevant biological information from highly studied species to genomic resource poorer species. It was possible to confirm by interspecies mRNA-to-genomic alignments 25 and 21 alternative splice events in sea bream and sea bass genes, respectively. Even using normalized cDNA from relatively few pooled individuals it was possible to identify 1145 SNPs and 1748 microsatellites loci for genetic marker development. The EST data are being applied to a range of projects, including the development microarrays, genetic and radiation hybrid maps and QTL genome scans. This highlights the important role of ESTs for generating genetic and genomic resources of aquaculture species.}, note = {ISBN: 1874-7787}, keywords = {}, pubstate = {published}, tppubtype = {article} } The gilthead sea bream, Sparus auratus, and the European sea bass, Dicentrarchus labrax, are two of the most important marine species cultivated in Southern Europe. This study aimed at increasing genomic resources for the two species and produced and annotated two sets of 30,000 expressed sequence tags (EST) each from 14 normalized tissue-specific cDNA libraries from sea bream and sea bass. Clustering and assembly of the ESTs formed 5268 contigs and 12,928 singletons for sea bream and 4573 contigs and 13,143 singletons for sea bass, representing 18,196 and 17,716 putative unigenes, respectively. Assuming a similar number of genes in sea bass, sea bream and in the model fish Gasterosteus aculeatus genomes, it was estimated that approximately two thirds of the sea bream and the sea bass transcriptomes were covered by the unigene collections. BLAST sequence similarity searches (using a cut off of e-value textless 10-5) against fully the curated SwissProt (and TrEMBL) databases produced matches of 28%(37%) and 43%(53%) of the sea bream and sea bass unigene datasets respectively, allowing some putative designation of function. A comparative approach is described using human Ensembl peptide ID homolog’s for functional annotation, which increased the number of unigenes with GO terms assigned and resulted in more GO terms assigned per unigene. This allowed the identification of tissue-specific genes using enrichment analysis for GO pathways and protein domains. The comparative annotation approach represents a good strategy for transferring more relevant biological information from highly studied species to genomic resource poorer species. It was possible to confirm by interspecies mRNA-to-genomic alignments 25 and 21 alternative splice events in sea bream and sea bass genes, respectively. Even using normalized cDNA from relatively few pooled individuals it was possible to identify 1145 SNPs and 1748 microsatellites loci for genetic marker development. The EST data are being applied to a range of projects, including the development microarrays, genetic and radiation hybrid maps and QTL genome scans. This highlights the important role of ESTs for generating genetic and genomic resources of aquaculture species. |
2009 |
Lagnel, J; Tsigenopoulos, C S; Iliopoulos, I NOBLAST and JAMBLAST: New options for BLAST and a Java application manager for BLAST results Journal Article Bioinformatics, 25 , pp. 824 – 826, 2009. @article{lagnel_noblast_2009, title = {NOBLAST and JAMBLAST: New options for BLAST and a Java application manager for BLAST results}, author = {J Lagnel and C S Tsigenopoulos and I Iliopoulos}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-62549119131&partnerID=40&md5=ae30471cc66e4a36b1ffd5f8c1e317d8}, year = {2009}, date = {2009-01-01}, journal = {Bioinformatics}, volume = {25}, pages = {824 -- 826}, abstract = {NOBLAST (New Options for BLAST) is an open source program that provides a new user-friendly tabular output format for various NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn, Tblastx, Mega BLAST and Psi BLAST) without any use of a parser and provides E-value correction in case of use of segmented BLAST database. JAMBLAST using the NOBLAST output allows the user to manage, view and filter the BLAST hits using a number of selection criteria. © The Author 2009. Published by Oxford University Press. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } NOBLAST (New Options for BLAST) is an open source program that provides a new user-friendly tabular output format for various NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn, Tblastx, Mega BLAST and Psi BLAST) without any use of a parser and provides E-value correction in case of use of segmented BLAST database. JAMBLAST using the NOBLAST output allows the user to manage, view and filter the BLAST hits using a number of selection criteria. © The Author 2009. Published by Oxford University Press. All rights reserved. |
Vogiatzi, E; Kalogianni, E; Giakoumi, S; Magoulas, A; Tsigenopoulos, C S Conservation Genetics Resources, 1 (1), pp. 27–30, 2009, ISSN: 18777252. @article{vogiatzi_characterization_2009, title = {Characterization of polymorphic microsatellite markers in valencia letourneuxi (Valenciidae) and cross-amplification in two other cyprinodontiform species}, author = {E Vogiatzi and E Kalogianni and S Giakoumi and A Magoulas and C S Tsigenopoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84859960931&doi=10.1007%2fs12686-009-9006-y&partnerID=40&md5=96676b3d404c991ab4b0a8a6952ba535}, doi = {10.1007/s12686-009-9006-y}, issn = {18777252}, year = {2009}, date = {2009-01-01}, journal = {Conservation Genetics Resources}, volume = {1}, number = {1}, pages = {27--30}, abstract = {Fourteen microsatellite loci were isolated from the critically endangered Corfu toothcarp Valencia letourneuxi using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC) probe. Nine of these loci were polymorphic in a V. letourneuxi population of 20 individuals (Vlychos stream) with mean number of alleles per locus = 2.55 and mean observed heterozygosity = 0.3447. Moreover, some of these 9 microsatellite markers and the remaining five loci, monomorphic in V. letourneuxi, were found to be polymorphic in the Spanish samaruc Valencia hispanica and the Mediterranean toothcarp Aphanius fasciatus. These microsatellite loci are expected to be used for population genetic analysis as well as studying the genetic diversity of this endangered species. © Springer Science+Business Media B.V. 2009.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fourteen microsatellite loci were isolated from the critically endangered Corfu toothcarp Valencia letourneuxi using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC) probe. Nine of these loci were polymorphic in a V. letourneuxi population of 20 individuals (Vlychos stream) with mean number of alleles per locus = 2.55 and mean observed heterozygosity = 0.3447. Moreover, some of these 9 microsatellite markers and the remaining five loci, monomorphic in V. letourneuxi, were found to be polymorphic in the Spanish samaruc Valencia hispanica and the Mediterranean toothcarp Aphanius fasciatus. These microsatellite loci are expected to be used for population genetic analysis as well as studying the genetic diversity of this endangered species. © Springer Science+Business Media B.V. 2009. |
2008 |
Apostolidis, Apostolos P; Loukovitis, Demetrios; Tsigenopoulos, Costas S Genetic characterization of brown trout (Salmo trutta) populations from the Southern Balkans using mtDNA sequencing and RFLP analysis Journal Article Hydrobiologia, 600 (1), pp. 169–176, 2008, ISSN: 0018-8158, 1573-5117. @article{apostolidis_genetic_2008, title = {Genetic characterization of brown trout (Salmo trutta) populations from the Southern Balkans using mtDNA sequencing and RFLP analysis}, author = {Apostolos P Apostolidis and Demetrios Loukovitis and Costas S Tsigenopoulos}, url = {http://link.springer.com/10.1007/s10750-007-9229-4}, doi = {10.1007/s10750-007-9229-4}, issn = {0018-8158, 1573-5117}, year = {2008}, date = {2008-03-01}, urldate = {2020-08-10}, journal = {Hydrobiologia}, volume = {600}, number = {1}, pages = {169--176}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dailianis, Thanos; Limborg, M; Hanel, R; Bekkevold, D; Lagnel, J; A, Magoulas; Tsigenopoulos, C S Characterization of nine polymorphic microsatellite markers in sprat (Sprattus sprattus L.) Journal Article Molecular Ecology Resources, 8 (4), pp. 861–863, 2008, (ISBN: 1755-0998). @article{dailianis_characterization_2008, title = {Characterization of nine polymorphic microsatellite markers in sprat (Sprattus sprattus L.)}, author = {Thanos Dailianis and M Limborg and R Hanel and D Bekkevold and J Lagnel and Magoulas A and C S Tsigenopoulos}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1755-0998.2008.02091.x}, doi = {10.1111/j.1755-0998.2008.02091.x}, year = {2008}, date = {2008-01-01}, journal = {Molecular Ecology Resources}, volume = {8}, number = {4}, pages = {861--863}, abstract = {Nine polymorphic microsatellites were isolated from sprat (Sprattus sprattus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)12 probe. The loci showed different variation patterns in a Baltic Sea population (44 individuals) with mean number of alleles at 12.7 and mean observed heterozygosity at 0.78. These microsatellite loci are expected to be used for taxonomic considerations in sprat, stock differentiation and population genetic analysis.}, note = {ISBN: 1755-0998}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nine polymorphic microsatellites were isolated from sprat (Sprattus sprattus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)12 probe. The loci showed different variation patterns in a Baltic Sea population (44 individuals) with mean number of alleles at 12.7 and mean observed heterozygosity at 0.78. These microsatellite loci are expected to be used for taxonomic considerations in sprat, stock differentiation and population genetic analysis. |
Kyriazi, P; Poulakakis, N; Parmakelis, A; Crochet, P A; Moravec, J; Rastegar-Pouyani, N; Tsigenopoulos, C S; Magoulas, A; Mylonas, M; Lymberakis, P Mitochondrial DNA reveals the genealogical history of the snake-eyed lizards (Ophisops elegans and O. occidentalis) (Sauria: Lacertidae) Journal Article Molecular Phylogenetics and Evolution, 49 , pp. 795 – 805, 2008. @article{kyriazi_mitochondrial_2008, title = {Mitochondrial DNA reveals the genealogical history of the snake-eyed lizards (Ophisops elegans and O. occidentalis) (Sauria: Lacertidae)}, author = {P Kyriazi and N Poulakakis and A Parmakelis and P A Crochet and J Moravec and N Rastegar-Pouyani and C S Tsigenopoulos and A Magoulas and M Mylonas and P Lymberakis}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-56749105770&partnerID=40&md5=c1a7d994264c6871db3860528ab105bf}, year = {2008}, date = {2008-01-01}, journal = {Molecular Phylogenetics and Evolution}, volume = {49}, pages = {795 -- 805}, abstract = {The snake-eyed lizards of the genus Ophisops (Lacertidae) have been through a series of taxonomical revisions, but still their phylogenetic relationships remain uncertain. In the present study we estimate the phylogeographic structure of O. elegans across its distributional range and we evaluate the relationships between O. elegans and the sympatric, in North Africa, species O. occidentalis, using partial mtDNA sequences (16S rRNA, COI, and cyt b). All phylogenetic analyses produced topologically identical trees where extant populations of O. elegans and O. occidentalis were found polyphyletic. Taking into account all the potential causes of polyphyly (introgressive hybridization, incomplete lineage sorting, and imperfect taxonomy) we suggest the inaccurate taxonomy as the most likely explanation for the observed pattern. Our results stress the need for re-evaluation of the current taxonomical status of these species and their subspecies. Furthermore, our biogeographic analyses and the estimated time of divergences suggest a late Miocene diversification within these species, where the present distribution of O. elegans and O. occidentalis was the result of several dispersal and vicariant events, which are associated with climatic oscillations (the late Miocene aridification of Asia and northern Africa) and paleogeographic barriers of late Miocene and Pliocene period. © 2008.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The snake-eyed lizards of the genus Ophisops (Lacertidae) have been through a series of taxonomical revisions, but still their phylogenetic relationships remain uncertain. In the present study we estimate the phylogeographic structure of O. elegans across its distributional range and we evaluate the relationships between O. elegans and the sympatric, in North Africa, species O. occidentalis, using partial mtDNA sequences (16S rRNA, COI, and cyt b). All phylogenetic analyses produced topologically identical trees where extant populations of O. elegans and O. occidentalis were found polyphyletic. Taking into account all the potential causes of polyphyly (introgressive hybridization, incomplete lineage sorting, and imperfect taxonomy) we suggest the inaccurate taxonomy as the most likely explanation for the observed pattern. Our results stress the need for re-evaluation of the current taxonomical status of these species and their subspecies. Furthermore, our biogeographic analyses and the estimated time of divergences suggest a late Miocene diversification within these species, where the present distribution of O. elegans and O. occidentalis was the result of several dispersal and vicariant events, which are associated with climatic oscillations (the late Miocene aridification of Asia and northern Africa) and paleogeographic barriers of late Miocene and Pliocene period. © 2008. |
Tsagkarakou, A; Tsigenopoulos, C S; Gorman, K; Kristoffersen, JB; Lagnel, J; Bedford, D Biotype monitoring and genetic relationships of Bemisia tabaci in Greece: Mitochondrial DNA and microsatellite polymorphism Journal Article Journal of Insect Science, 8 , pp. 48–48, 2008, (ISBN: 1536-2442). @article{tsagkarakou_biotype_2008, title = {Biotype monitoring and genetic relationships of Bemisia tabaci in Greece: Mitochondrial DNA and microsatellite polymorphism}, author = {A Tsagkarakou and C S Tsigenopoulos and K Gorman and JB Kristoffersen and J Lagnel and D Bedford}, url = {<Go to ISI>://000253056900096}, year = {2008}, date = {2008-01-01}, journal = {Journal of Insect Science}, volume = {8}, pages = {48--48}, note = {ISBN: 1536-2442}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Volckaert, F A; Batargias, C; Canário, A; Chatziplis, D; Chistiakov, D A; Haley, C S; Libertini, A; Tsigenopoulos, C S The European sea bass (Dicentrarchus labrax L.) and its genomic resources Incollection Kocher, T D; Chittaranjan, K (Ed.): Genome Mapping and Genomics in Fishes and Aquatic Animals, 2 , pp. 117–133, Springer Verlag, 2008, (Backup Publisher: Springer Verlag). @incollection{volckaert_european_2008, title = {The European sea bass (Dicentrarchus labrax L.) and its genomic resources}, author = {F A Volckaert and C Batargias and A Canário and D Chatziplis and D A Chistiakov and C S Haley and A Libertini and C S Tsigenopoulos}, editor = {T D Kocher and K Chittaranjan}, year = {2008}, date = {2008-01-01}, booktitle = {Genome Mapping and Genomics in Fishes and Aquatic Animals}, volume = {2}, pages = {117--133}, publisher = {Springer Verlag}, series = {Genome Mapping and Genomics in Animals}, abstract = {Aquaculture of European sea bass (textitDicentrarchus labrax L.) has taken off in the coastal regions of the Mediterranean Sea and southeastern Atlantic Ocean over the past 25 years, and increased to 71,649 metric tons in 2004. Genetic support for this industry was initially limited to cytogenetics and population genetics, but with time it has been complemented with selective breeding, as well as functional and comparative genomics. The haploid genome of sea bass consists of 24 chromosomes, weighing 0.78 pg and containing approximately 1,525 Mb. A number of different types of genetic markers are available. A first-generation linkage map based on 174 microsatellite markers covers 25 linkage groups (815 cM). A draft of an updated linkage map, including 369 microsatellite and AFLP markers, is now available. EST resources based on at least 17 cDNA tissue libraries and surpassing 30,000 sequence traces have been generated. A large insert BAC library has a 13x genomic coverage. Breeding goals have been established and heritability values of various traits measured. Functional genomic analysis in relation to the reproductive biology and stress physiology are in progress. A pilot analysis has detected a QTL for body length on the terminal end of linkage group 1. All these resources bring European sea bass into the group of the top ten genome resource-rich fish species. Additional genomic resources such as EST sequences, macro- and micro-arrays, a second-generation linkage map, and physical maps based on BAC fingerprints and radiation hybrids, will become available in the near future. Selective breeding of this species is expected to direct it progressively toward complete domestication}, note = {Backup Publisher: Springer Verlag}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } Aquaculture of European sea bass (textitDicentrarchus labrax L.) has taken off in the coastal regions of the Mediterranean Sea and southeastern Atlantic Ocean over the past 25 years, and increased to 71,649 metric tons in 2004. Genetic support for this industry was initially limited to cytogenetics and population genetics, but with time it has been complemented with selective breeding, as well as functional and comparative genomics. The haploid genome of sea bass consists of 24 chromosomes, weighing 0.78 pg and containing approximately 1,525 Mb. A number of different types of genetic markers are available. A first-generation linkage map based on 174 microsatellite markers covers 25 linkage groups (815 cM). A draft of an updated linkage map, including 369 microsatellite and AFLP markers, is now available. EST resources based on at least 17 cDNA tissue libraries and surpassing 30,000 sequence traces have been generated. A large insert BAC library has a 13x genomic coverage. Breeding goals have been established and heritability values of various traits measured. Functional genomic analysis in relation to the reproductive biology and stress physiology are in progress. A pilot analysis has detected a QTL for body length on the terminal end of linkage group 1. All these resources bring European sea bass into the group of the top ten genome resource-rich fish species. Additional genomic resources such as EST sequences, macro- and micro-arrays, a second-generation linkage map, and physical maps based on BAC fingerprints and radiation hybrids, will become available in the near future. Selective breeding of this species is expected to direct it progressively toward complete domestication |
Chistiakov, D A; Tsigenopoulos, C S; Lagnel, J; Guo, Y -M; Hellemans, B; Haley, C S; Volckaert, F A M; Kotoulas, G A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bass Dicentrarchus labrax L. Journal Article Animal Genetics, 39 (6), pp. 623–634, 2008, ISSN: 02689146. @article{chistiakov_combined_2008, title = {A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bass Dicentrarchus labrax L.}, author = {D A Chistiakov and C S Tsigenopoulos and J Lagnel and Y -M Guo and B Hellemans and C S Haley and F A M Volckaert and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-55949121630&doi=10.1111%2fj.1365-2052.2008.01786.x&partnerID=40&md5=02380f0e77a85dcbee993dc81962661e}, doi = {10.1111/j.1365-2052.2008.01786.x}, issn = {02689146}, year = {2008}, date = {2008-01-01}, journal = {Animal Genetics}, volume = {39}, number = {6}, pages = {623--634}, abstract = {European sea bass (Dicentrarchus labrax L., Moronidae, Teleostei) sustains a regional fishery and is commonly farmed in the Mediterranean basin, but has not undergone much long-term genetic improvement. An updated genetic linkage map of the European sea bass was constructed using 190 microsatellites, 176 amplified fragment length polymorphisms and two single nucleotide polymorphisms. From the 45 new microsatellite markers (including 31 type I markers) reported in this study, 28 were mapped. A total of 368 markers were assembled into 35 linkage groups. Among these markers, 28 represented type I (coding) markers, including those located within the peptide Y, SOX10, PXN1, ERA and TCRB genes (linkage groups 1, 7, 16, 17 and 27 respectively). The sex-averaged map spanned 1373.1 centimorgans (cM) of the genome. The female map measured 1380.0 cM, whereas the male map measured 1046.9 cM, leading to a female-to-male (F:M) recombination rate ratio of 1.32:1. The intermarker spacing of the second-generation linkage map of the European sea bass was 3.67 cM, which is smaller than that of the first-generation linkage map (5.03 cM). Comparative mapping of microsatellite flanking regions was performed with five model teleosts and this revealed a high percentage (33.6%) of evolutionarily conserved regions with the three-spined stickleback. © 2008 The Authors.}, keywords = {}, pubstate = {published}, tppubtype = {article} } European sea bass (Dicentrarchus labrax L., Moronidae, Teleostei) sustains a regional fishery and is commonly farmed in the Mediterranean basin, but has not undergone much long-term genetic improvement. An updated genetic linkage map of the European sea bass was constructed using 190 microsatellites, 176 amplified fragment length polymorphisms and two single nucleotide polymorphisms. From the 45 new microsatellite markers (including 31 type I markers) reported in this study, 28 were mapped. A total of 368 markers were assembled into 35 linkage groups. Among these markers, 28 represented type I (coding) markers, including those located within the peptide Y, SOX10, PXN1, ERA and TCRB genes (linkage groups 1, 7, 16, 17 and 27 respectively). The sex-averaged map spanned 1373.1 centimorgans (cM) of the genome. The female map measured 1380.0 cM, whereas the male map measured 1046.9 cM, leading to a female-to-male (F:M) recombination rate ratio of 1.32:1. The intermarker spacing of the second-generation linkage map of the European sea bass was 3.67 cM, which is smaller than that of the first-generation linkage map (5.03 cM). Comparative mapping of microsatellite flanking regions was performed with five model teleosts and this revealed a high percentage (33.6%) of evolutionarily conserved regions with the three-spined stickleback. © 2008 The Authors. |
Volckaert, F A M; Batargias, C; Canario, A; Chatziplis, D; Chistiakov, D; Haley, C; Libertini, A; Tsigenopoulos, C European Sea Bass Incollection Kocher, Thomas; Kole, Chittaranjan (Ed.): Genome Mapping and Genomics in Fishes and Aquatic Animals, 2 , pp. 117–133, Springer Berlin Heidelberg, Berlin, Heidelberg, 2008, ISBN: 978-3-540-73836-7 978-3-540-73837-4, (Series Title: Genome Mapping Genomics Animals). @incollection{kocher_european_2008, title = {European Sea Bass}, author = {F A M Volckaert and C Batargias and A Canario and D Chatziplis and D Chistiakov and C Haley and A Libertini and C Tsigenopoulos}, editor = {Thomas Kocher and Chittaranjan Kole}, url = {http://link.springer.com/10.1007/978-3-540-73837-4_5}, doi = {10.1007/978-3-540-73837-4_5}, isbn = {978-3-540-73836-7 978-3-540-73837-4}, year = {2008}, date = {2008-01-01}, urldate = {2020-08-10}, booktitle = {Genome Mapping and Genomics in Fishes and Aquatic Animals}, volume = {2}, pages = {117--133}, publisher = {Springer Berlin Heidelberg}, address = {Berlin, Heidelberg}, note = {Series Title: Genome Mapping Genomics Animals}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Guinand, Bruno; Dujardin, Emilie; Dufour, Vincent; Tsigenopoulos, Costas S Characterisation of genetic structure of Dicentrarchus labrax larvae in two nurseries of the Gulf of Lions (NW Mediterranean) Journal Article Aquatic Living Resources, 21 (1), pp. 81–87, 2008, ISSN: 0990-7440, 1765-2952. @article{guinand_characterisation_2008, title = {Characterisation of genetic structure of Dicentrarchus labrax larvae in two nurseries of the Gulf of Lions (NW Mediterranean)}, author = {Bruno Guinand and Emilie Dujardin and Vincent Dufour and Costas S Tsigenopoulos}, url = {http://www.alr-journal.org/10.1051/alr:2008020}, doi = {10.1051/alr:2008020}, issn = {0990-7440, 1765-2952}, year = {2008}, date = {2008-01-01}, urldate = {2020-08-10}, journal = {Aquatic Living Resources}, volume = {21}, number = {1}, pages = {81--87}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2007 |
Tsagkarakou, A; Tsigenopoulos, C S; Gorman, K; Lagnel, J; Bedford, I D Biotype status and genetic polymorphism of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) in Greece: mitochondrial DNA and microsatellites Journal Article Bulletin of Entomological Research, 97 (1), pp. 29–40, 2007, ISSN: 0007-4853, 1475-2670. @article{tsagkarakou_biotype_2007, title = {Biotype status and genetic polymorphism of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) in Greece: mitochondrial DNA and microsatellites}, author = {A Tsagkarakou and C S Tsigenopoulos and K Gorman and J Lagnel and I D Bedford}, url = {https://www.cambridge.org/core/product/identifier/S000748530700466X/type/journal_article}, doi = {10.1017/S000748530700466X}, issn = {0007-4853, 1475-2670}, year = {2007}, date = {2007-02-01}, urldate = {2020-08-10}, journal = {Bulletin of Entomological Research}, volume = {97}, number = {1}, pages = {29--40}, abstract = {Abstract The genetic polymorphism and the biotype identity of the tobacco whitefly Bemisia tabaci (Gennadius) have been studied in population samples taken from different localities within Greece from cultivated plants growing in greenhouses or in open environments and from non-cultivated plants. Two different approaches were used: sequencing of the mitochondrial cytochrome oxidase I (mtCOI) gene and genotyping using microsatellite markers. Analyses of the mtCOI sequences revealed a high homogeneity between the Greek samples which clustered together with Q biotype samples that had been collected from other countries. When genetic polymorphism was examined using six microsatellite markers, the Greek samples, which were all characterized as Q biotype were significantly differentiated from each other and clustered into at least two distinct genetic populations. Moreover, based on the fixed differences revealed by the mtCOI comparison of known B. tabaci biotype sequences, two diagnostic tests for discriminating between Q and B and non-Q/non-B biotypes were developed. Implementation of these diagnostic tools allowed an absence of the B biotype and presence of the Q biotype in the Greek samples to be determined.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract The genetic polymorphism and the biotype identity of the tobacco whitefly Bemisia tabaci (Gennadius) have been studied in population samples taken from different localities within Greece from cultivated plants growing in greenhouses or in open environments and from non-cultivated plants. Two different approaches were used: sequencing of the mitochondrial cytochrome oxidase I (mtCOI) gene and genotyping using microsatellite markers. Analyses of the mtCOI sequences revealed a high homogeneity between the Greek samples which clustered together with Q biotype samples that had been collected from other countries. When genetic polymorphism was examined using six microsatellite markers, the Greek samples, which were all characterized as Q biotype were significantly differentiated from each other and clustered into at least two distinct genetic populations. Moreover, based on the fixed differences revealed by the mtCOI comparison of known B. tabaci biotype sequences, two diagnostic tests for discriminating between Q and B and non-Q/non-B biotypes were developed. Implementation of these diagnostic tools allowed an absence of the B biotype and presence of the Q biotype in the Greek samples to be determined. |
Chatziplis, D; Batargias, C; Tsigenopoulos, C S; Magoulas, A; Kollias, S; Kotoulas, G; Volckaert, F A M; Haley, C S Mapping quantitative trait loci in European sea bass (Dicentrarchus labrax): The BASSMAP pilot study Journal Article Aquaculture, 272 (SUPPL. 1), pp. S172–S182, 2007, ISSN: 00448486. @article{chatziplis_mapping_2007, title = {Mapping quantitative trait loci in European sea bass (Dicentrarchus labrax): The BASSMAP pilot study}, author = {D Chatziplis and C Batargias and C S Tsigenopoulos and A Magoulas and S Kollias and G Kotoulas and F A M Volckaert and C S Haley}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-36448952022&doi=10.1016%2fj.aquaculture.2007.08.022&partnerID=40&md5=f7a9a7535621e9b63de89635c3dcf961}, doi = {10.1016/j.aquaculture.2007.08.022}, issn = {00448486}, year = {2007}, date = {2007-01-01}, journal = {Aquaculture}, volume = {272}, number = {SUPPL. 1}, pages = {S172--S182}, abstract = {There are great opportunities for genetic improvement in recently domesticated aquaculture species. However, the lack of appropriate tools limits the application of advanced techniques including the mapping of quantitative trait loci (QTL) and marker-assisted selection (MAS). The recent development of a genetic linkage map for the European sea bass allows the application of such methods for the first time in this species. We report a pilot trial of QTL mapping in a commercial sea bass population as a precursor to the application of MAS. Fertilized eggs collected on a single spawning day produced a population composed of a few large families. Fish were grown under commercial conditions, slaughtered at approximately 470 g and measurements were taken for several traits. Parentage analysis showed that the population consisted of 26 full sib families, with a common dam and several sires. Seven microsatellite markers spanning the largest linkage group (LG1) were then genotyped in 27 parents and their 422 progeny, in order to perform a QTL scan using half-sib interval mapping approaches. Significant QTL affecting six morphometric traits including length and depth, are reported. The success of the procedure demonstrates that QTL analysis can be applied in this species and will contribute to the study and future improvement of traits associated with production, profitability and sustainability. © 2007 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } There are great opportunities for genetic improvement in recently domesticated aquaculture species. However, the lack of appropriate tools limits the application of advanced techniques including the mapping of quantitative trait loci (QTL) and marker-assisted selection (MAS). The recent development of a genetic linkage map for the European sea bass allows the application of such methods for the first time in this species. We report a pilot trial of QTL mapping in a commercial sea bass population as a precursor to the application of MAS. Fertilized eggs collected on a single spawning day produced a population composed of a few large families. Fish were grown under commercial conditions, slaughtered at approximately 470 g and measurements were taken for several traits. Parentage analysis showed that the population consisted of 26 full sib families, with a common dam and several sires. Seven microsatellite markers spanning the largest linkage group (LG1) were then genotyped in 27 parents and their 422 progeny, in order to perform a QTL scan using half-sib interval mapping approaches. Significant QTL affecting six morphometric traits including length and depth, are reported. The success of the procedure demonstrates that QTL analysis can be applied in this species and will contribute to the study and future improvement of traits associated with production, profitability and sustainability. © 2007 Elsevier B.V. All rights reserved. |
Lymberakis, P; Poulakakis, N; Manthalou, G; Tsigenopoulos, C S; Magoulas, A; Mylonas, M Mitochondrial phylogeography of Rana (Pelophylax) populations in the Eastern Mediterranean region Journal Article Molecular Phylogenetics and Evolution, 44 , pp. 115 – 125, 2007. @article{lymberakis_mitochondrial_2007, title = {Mitochondrial phylogeography of Rana (Pelophylax) populations in the Eastern Mediterranean region}, author = {P Lymberakis and N Poulakakis and G Manthalou and C S Tsigenopoulos and A Magoulas and M Mylonas}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-34249792357&partnerID=40&md5=4e1dbe1f34604b4421ce71c49b66606e}, year = {2007}, date = {2007-01-01}, journal = {Molecular Phylogenetics and Evolution}, volume = {44}, pages = {115 -- 125}, abstract = {Phylogenetic relationships in the western fraction of Rana (Pelophylax) have not been resolved till now, even though several works have been devoted to the subject. Here, we infer phylogenetic relationships among the species distributed in the area of the Eastern Mediterranean, comparing partial mitochondrial DNA sequences for the cytochrome b and 16S rRNA genes. The obtained molecular data clearly indicate that Western Palearctic water frogs underwent a basal radiation into at least 3 major lineages (the perezi, the lessonae, and the rindibunda/bedriagae lineages) advocating an upper Miocene speciation. Moreover, we consider that within the rindibunda/bedriagae lineage, R. (P.) ridibunda, R. (P.) epeirotica, R. (P.) cretensis, R. (P.) bedriagae, R. (P.) cerigensis and R. (P.) kurtmuelleri were differentiated from a common ancestor through a series of vicariant and dispersal events, during the last ∼5 Mya, even though the specific rank of some taxa may be questionable, such as R. cerigensis in respect with R. bedriagae and R. kurtmuelleri in respect with R. ridibunda. © 2007 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Phylogenetic relationships in the western fraction of Rana (Pelophylax) have not been resolved till now, even though several works have been devoted to the subject. Here, we infer phylogenetic relationships among the species distributed in the area of the Eastern Mediterranean, comparing partial mitochondrial DNA sequences for the cytochrome b and 16S rRNA genes. The obtained molecular data clearly indicate that Western Palearctic water frogs underwent a basal radiation into at least 3 major lineages (the perezi, the lessonae, and the rindibunda/bedriagae lineages) advocating an upper Miocene speciation. Moreover, we consider that within the rindibunda/bedriagae lineage, R. (P.) ridibunda, R. (P.) epeirotica, R. (P.) cretensis, R. (P.) bedriagae, R. (P.) cerigensis and R. (P.) kurtmuelleri were differentiated from a common ancestor through a series of vicariant and dispersal events, during the last ∼5 Mya, even though the specific rank of some taxa may be questionable, such as R. cerigensis in respect with R. bedriagae and R. kurtmuelleri in respect with R. ridibunda. © 2007 Elsevier Inc. All rights reserved. |
Volckaert, F A M J; Batargias, C; Bonhomme, F; Canario, A; Chistiakov, D; Choudhuri, J V; Galibert, F; Georgoudis, A; Haley, C S; Hellemans, B; Kuhl, H; Kotoulas, G; Law, A; Libertini, A; Magoulas, A; McAndrew, B J; Reinhardt, R; Senger, F; Souche, E; Tsigenopoulos, C; Whitaker, H A Genomic resources for the aquaculture of European sea bass Journal Article Aquaculture, 272 , pp. S316–S317, 2007, ISSN: 00448486. @article{volckaert_genomic_2007, title = {Genomic resources for the aquaculture of European sea bass}, author = {F A M J Volckaert and C Batargias and F Bonhomme and A Canario and D Chistiakov and J V Choudhuri and F Galibert and A Georgoudis and C S Haley and B Hellemans and H Kuhl and G Kotoulas and A Law and A Libertini and A Magoulas and B J McAndrew and R Reinhardt and F Senger and E Souche and C Tsigenopoulos and H A Whitaker}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848607007831}, doi = {10.1016/j.aquaculture.2007.07.199}, issn = {00448486}, year = {2007}, date = {2007-01-01}, urldate = {2020-08-09}, journal = {Aquaculture}, volume = {272}, pages = {S316--S317}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2006 |
Franch, R; Louro, B; Tsalavouta, M; Chatziplis, D; Tsigenopoulos, C S; Sarropoulou, E; Antonello, J; Magoulas, A; Mylonas, C C; Babbucci, M; Patarnello, T; Power, D M; Kotoulas, G; Bargelloni, L A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L. Journal Article Genetics, 174 (2), pp. 851–861, 2006, ISSN: 00166731. @article{franch_genetic_2006, title = {A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L.}, author = {R Franch and B Louro and M Tsalavouta and D Chatziplis and C S Tsigenopoulos and E Sarropoulou and J Antonello and A Magoulas and C C Mylonas and M Babbucci and T Patarnello and D M Power and G Kotoulas and L Bargelloni}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33750471928&doi=10.1534%2fgenetics.106.059014&partnerID=40&md5=5223c21cec86860a04d8be5eff57e24c}, doi = {10.1534/genetics.106.059014}, issn = {00166731}, year = {2006}, date = {2006-01-01}, journal = {Genetics}, volume = {174}, number = {2}, pages = {851--861}, abstract = {The gilthead sea bream (Sparus aurata L.) is a marine fish of great importance for fisheries and aquaculture. It has also a peculiar sex-determination system, being a protandrous hermaphrodite. Here we report the construction of a first-generation genetic linkage map for S. aurata, based on 204 microsatellite markers. Twenty-six linkage groups (LG) were found. The total map length was 1241.9 cM. The ratio between sex-specific map lengths was 1:1.2 (male:female). Comparison with a preliminary radiation hybrid (RH) map reveals a good concordance, as all markers located in a single LG are located in a single RH group, except for Ad-25 and CId-31. Comparison with the Tetraodon nigroviridis genome revealed a considerable number of evolutionary conserved regions (ECRs) between the two species. The mean size of ECRs was 182 bp (sequence identity 60-90%). Forty-one ECRs have a known chromosomal location in the pufferfish genome. Despite the limited number of anchoring points, significant syntenic relationships were found. The linkage map presented here provides a robust comparative framework for QTL analysis in S. aurata and is a step toward the identification of genetic loci involved both in the determination of economically important traits and in the individual timing of sex reversal. Copyright © 2006 by the Genetics Society of America.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The gilthead sea bream (Sparus aurata L.) is a marine fish of great importance for fisheries and aquaculture. It has also a peculiar sex-determination system, being a protandrous hermaphrodite. Here we report the construction of a first-generation genetic linkage map for S. aurata, based on 204 microsatellite markers. Twenty-six linkage groups (LG) were found. The total map length was 1241.9 cM. The ratio between sex-specific map lengths was 1:1.2 (male:female). Comparison with a preliminary radiation hybrid (RH) map reveals a good concordance, as all markers located in a single LG are located in a single RH group, except for Ad-25 and CId-31. Comparison with the Tetraodon nigroviridis genome revealed a considerable number of evolutionary conserved regions (ECRs) between the two species. The mean size of ECRs was 182 bp (sequence identity 60-90%). Forty-one ECRs have a known chromosomal location in the pufferfish genome. Despite the limited number of anchoring points, significant syntenic relationships were found. The linkage map presented here provides a robust comparative framework for QTL analysis in S. aurata and is a step toward the identification of genetic loci involved both in the determination of economically important traits and in the individual timing of sex reversal. Copyright © 2006 by the Genetics Society of America. |
2005 |
Mantziou, G; Antoniou, A; Poulakakis, N; Goulielmos, G; Tsigenopoulos, C S; Pinou, T; Mylonas, M Isolation and characterization of six polymorphic microsatellite markers in the freshwater turtle Mauremys rivulata (Testudines: Geoemydidae) Journal Article Molecular Ecology Notes, 5 (4), pp. 727–729, 2005. @article{mantziou_isolation_2005, title = {Isolation and characterization of six polymorphic microsatellite markers in the freshwater turtle Mauremys rivulata (Testudines: Geoemydidae)}, author = {G Mantziou and A Antoniou and N Poulakakis and G Goulielmos and C S Tsigenopoulos and T Pinou and M Mylonas}, url = {http://www.blackwell-synergy.com/doi/abs/10.1111/j.1471-8286.2005.01046.x}, doi = {10.1111/j.1471-8286.2005.01046.x}, year = {2005}, date = {2005-01-01}, journal = {Molecular Ecology Notes}, volume = {5}, number = {4}, pages = {727--729}, abstract = {Abstract Six polymorphic microsatellite loci containing dinucleotide repeats were developed for the freshwater turtle Mauremys rivulata. The number of alleles ranged from five to 18. The observed and expected heterozygosities ranged from 0.19 to 0.79 and 0.46 to 0.90, respectively. These markers may serve as a valuable tool for population genetics analyses and provide information on the evolutionary history of the species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Six polymorphic microsatellite loci containing dinucleotide repeats were developed for the freshwater turtle Mauremys rivulata. The number of alleles ranged from five to 18. The observed and expected heterozygosities ranged from 0.19 to 0.79 and 0.46 to 0.90, respectively. These markers may serve as a valuable tool for population genetics analyses and provide information on the evolutionary history of the species. |
Poulakakis, N; Lymberakis, P; Tsigenopoulos, C S; Magoulas, A; Mylonas, M Phylogenetic relationships and evolutionary history of snake-eyed skink Ablepharus kitaibelii (Sauria: Scincidae) Journal Article Molecular Phylogenetics and Evolution, 34 , pp. 245 – 256, 2005. @article{poulakakis_phylogenetic_2005, title = {Phylogenetic relationships and evolutionary history of snake-eyed skink Ablepharus kitaibelii (Sauria: Scincidae)}, author = {N Poulakakis and P Lymberakis and C S Tsigenopoulos and A Magoulas and M Mylonas}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-11144266691&partnerID=40&md5=9ec5b39f41ecfb4a0f8fdb0d7b315756}, year = {2005}, date = {2005-01-01}, journal = {Molecular Phylogenetics and Evolution}, volume = {34}, pages = {245 -- 256}, abstract = {Sequence data derived from two mitochondrial markers, 16S rRNA and cytochrome b genes, were used to infer the phylogenetic relationships of 38 populations of the snake-eyed skinks of the genus Ablepharus with emphasis on A. kitaibelii from Greece and Turkey. The partition-homogeneity tests indicated that the combined data set was homogeneous, and maximum-parsimony, maximum-likelihood, and Bayesian analyses produced topologically identical trees that revealed a well-resolved phylogeny. All species except A. kitaibelii form monophyletic units. The latter species appears paraphyletic with respect to A. budaki and A. chernovi with populations clustering into two distinct clades. A. chernovi and A. budaki, which have recently been raised to species status, were confirmed as genetically distinct forms. We used sequence divergence and paleogeographic history of the Aegean region to reconstruct a biogeographic evolutionary scenario for A. kitaibelii. © 2004 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Sequence data derived from two mitochondrial markers, 16S rRNA and cytochrome b genes, were used to infer the phylogenetic relationships of 38 populations of the snake-eyed skinks of the genus Ablepharus with emphasis on A. kitaibelii from Greece and Turkey. The partition-homogeneity tests indicated that the combined data set was homogeneous, and maximum-parsimony, maximum-likelihood, and Bayesian analyses produced topologically identical trees that revealed a well-resolved phylogeny. All species except A. kitaibelii form monophyletic units. The latter species appears paraphyletic with respect to A. budaki and A. chernovi with populations clustering into two distinct clades. A. chernovi and A. budaki, which have recently been raised to species status, were confirmed as genetically distinct forms. We used sequence divergence and paleogeographic history of the Aegean region to reconstruct a biogeographic evolutionary scenario for A. kitaibelii. © 2004 Elsevier Inc. All rights reserved. |
Chistiakov, D A; Hellemans, B; Haley, C S; Law, A S; Tsigenopoulos, C S; Kotoulas, G; Bertotto, D; Libertini, A; Volckaert, F A M A microsatellite linkage map of the European sea bass Dicentrarchus labrax L. Journal Article Genetics, 170 (4), pp. 1821–1826, 2005, ISSN: 00166731. @article{chistiakov_microsatellite_2005, title = {A microsatellite linkage map of the European sea bass Dicentrarchus labrax L.}, author = {D A Chistiakov and B Hellemans and C S Haley and A S Law and C S Tsigenopoulos and G Kotoulas and D Bertotto and A Libertini and F A M Volckaert}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-25444490899&doi=10.1534%2fgenetics.104.039719&partnerID=40&md5=8dfc95ab2fdb751d0c70b2f5f1342b11}, doi = {10.1534/genetics.104.039719}, issn = {00166731}, year = {2005}, date = {2005-01-01}, journal = {Genetics}, volume = {170}, number = {4}, pages = {1821--1826}, abstract = {A genetic linkage map of the European sea bass (Dicentrarchus labrax) was constructed from 174 microsatellite markers, including 145 new markers reported in this study. The mapping panel was derived from farmed sea bass from the North Adriatic Sea and consisted of a single family including both parents and 50 full-sib progeny (biparental diploids). A total of 162 microsatellites were mapped in 25 linkage groups. Eleven loci represent type I (coding) markers; 2 loci are located within the peptide Y (linkage group 1) and cytochrome P450 aromatase (linkage group 6) genes. The sex-averaged map spans 814.5 cM of the sea bass genome. The female map covers 905.9 cM, whereas the male map covers only 567.4 cM. The constructed map represents the first linkage map of European sea bass, one of the most important aquaculture species in Europe. Copyright © 2005 by the Genetics Society of America.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A genetic linkage map of the European sea bass (Dicentrarchus labrax) was constructed from 174 microsatellite markers, including 145 new markers reported in this study. The mapping panel was derived from farmed sea bass from the North Adriatic Sea and consisted of a single family including both parents and 50 full-sib progeny (biparental diploids). A total of 162 microsatellites were mapped in 25 linkage groups. Eleven loci represent type I (coding) markers; 2 loci are located within the peptide Y (linkage group 1) and cytochrome P450 aromatase (linkage group 6) genes. The sex-averaged map spans 814.5 cM of the sea bass genome. The female map covers 905.9 cM, whereas the male map covers only 567.4 cM. The constructed map represents the first linkage map of European sea bass, one of the most important aquaculture species in Europe. Copyright © 2005 by the Genetics Society of America. |
2004 |
Chistiakov, D A; Hellemans, B; Tsigenopoulos, C S; Law, A S; Bartley, N; Bertotto, D; Libertini, A; Kotoulas, G; Haley, C S; Volckaert, F A M Development and linkage relationships for new microsatellite markers of the sea bass (Dicentrarchus labrax L.) Journal Article Animal Genetics, 35 (1), pp. 53–57, 2004, ISSN: 02689146. @article{chistiakov_development_2004, title = {Development and linkage relationships for new microsatellite markers of the sea bass (Dicentrarchus labrax L.)}, author = {D A Chistiakov and B Hellemans and C S Tsigenopoulos and A S Law and N Bartley and D Bertotto and A Libertini and G Kotoulas and C S Haley and F A M Volckaert}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-10744228402&doi=10.1046%2fj.1365-2052.2003.01076.x&partnerID=40&md5=04f787b68dff2aecc25e57226b021721}, doi = {10.1046/j.1365-2052.2003.01076.x}, issn = {02689146}, year = {2004}, date = {2004-01-01}, journal = {Animal Genetics}, volume = {35}, number = {1}, pages = {53--57}, abstract = {Twenty-eight polymorphic microsatellites were isolated from the sea bass, Dicentrarchus labrax, using a microsatellite enrichment protocol and selective hybridization with oligonucleotide probes. Analysis for these markers and 11 recently described microsatellites of D. labrax found linkage between 26 loci and revealed eight linkage groups.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Twenty-eight polymorphic microsatellites were isolated from the sea bass, Dicentrarchus labrax, using a microsatellite enrichment protocol and selective hybridization with oligonucleotide probes. Analysis for these markers and 11 recently described microsatellites of D. labrax found linkage between 26 loci and revealed eight linkage groups. |
2003 |
Tsigenopoulos, C S; Hellemans, B; Chistiakov, D A; Libertini, A; Kotoulas, G; Volckaert, F Eleven new microsatellites of the sea bass (Dicentrarchus labrax L.) Journal Article Molecular Ecology Notes, 3 (3), pp. 352–354, 2003, ISSN: 14718278. @article{tsigenopoulos_eleven_2003, title = {Eleven new microsatellites of the sea bass (Dicentrarchus labrax L.)}, author = {C S Tsigenopoulos and B Hellemans and D A Chistiakov and A Libertini and G Kotoulas and F Volckaert}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0041874880&doi=10.1046%2fj.1471-8286.2003.00447.x&partnerID=40&md5=821b63e875e1041a9f4dd3f9e973c928}, doi = {10.1046/j.1471-8286.2003.00447.x}, issn = {14718278}, year = {2003}, date = {2003-01-01}, journal = {Molecular Ecology Notes}, volume = {3}, number = {3}, pages = {352--354}, abstract = {Eleven polymorphic microsatellites were isolated from the sea bass, Dicentrarchus labrax, using a microsatellite enrichment protocol and selective hybridization with an (AC)12 probe. The loci showed different variation patterns in 21 unrelated sea bass individuals, with a mean number of alleles of 8.6 and a mean observed heterozygosity of 0.68. These microsatellite markers should be useful for population genetic analysis and biodiversity studies of sea bass.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Eleven polymorphic microsatellites were isolated from the sea bass, Dicentrarchus labrax, using a microsatellite enrichment protocol and selective hybridization with an (AC)12 probe. The loci showed different variation patterns in 21 unrelated sea bass individuals, with a mean number of alleles of 8.6 and a mean observed heterozygosity of 0.68. These microsatellite markers should be useful for population genetic analysis and biodiversity studies of sea bass. |
Berrebi, P; Tsigenopoulos, C S Phylogenetic organization of the genus Barbus sensu stricto: A review based on data using molecular markers Incollection Banarescu, P; Bogutskaya, N G (Ed.): The Freshwater Fishes of Europe, Vol. 5/II: Cyprinidae, Part II: Barbus, pp. 11–22, AULA-Verlag, 2003, (Backup Publisher: AULA-Verlag). @incollection{berrebi_phylogenetic_2003, title = {Phylogenetic organization of the genus Barbus sensu stricto: A review based on data using molecular markers}, author = {P Berrebi and C S Tsigenopoulos}, editor = {P Banarescu and N G Bogutskaya}, year = {2003}, date = {2003-01-01}, booktitle = {The Freshwater Fishes of Europe, Vol. 5/II: Cyprinidae, Part II: Barbus}, pages = {11--22}, publisher = {AULA-Verlag}, abstract = {In this review, we are providing all available information on the molecular phylogeny of the genus textitBarbus sensu lato. The number of chromosomes indicates whether each species originated as diploid (50), tetraploid (100), or hexaploid (150) fishes. This is considered the primary parameter of classification. Only the "true barbs," which are the European, West Asian, and North African tetraploids, are discussed in the text species by species. Special care is taken to provide an accurate phylogeny of the European species. The main conclusion reached through the molecular studies is that it is necessary to limit the genus textitBarbus to the "true barbs" and to give different generic names to all other taxa originally included in textitBarbus sensu lato}, note = {Backup Publisher: AULA-Verlag}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } In this review, we are providing all available information on the molecular phylogeny of the genus textitBarbus sensu lato. The number of chromosomes indicates whether each species originated as diploid (50), tetraploid (100), or hexaploid (150) fishes. This is considered the primary parameter of classification. Only the "true barbs," which are the European, West Asian, and North African tetraploids, are discussed in the text species by species. Special care is taken to provide an accurate phylogeny of the European species. The main conclusion reached through the molecular studies is that it is necessary to limit the genus textitBarbus to the "true barbs" and to give different generic names to all other taxa originally included in textitBarbus sensu lato |
Tsigenopoulos, C S; Durand, J D; Ünlü, E; Berrebi, P Biological Journal of the Linnean Society, 80 , pp. 207 – 222, 2003. @article{tsigenopoulos_rapid_2003, title = {Rapid radiation of the Mediterranean Luciobarbus species (Cyprinidae) after the Messinian salinity crisis of the Mediterranean Sea, inferred from mitochondrial phylogenetic analysis}, author = {C S Tsigenopoulos and J D Durand and E Ünlü and P Berrebi}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0142095131&partnerID=40&md5=b366bb24a4425150565d56b1f334c4ee}, year = {2003}, date = {2003-01-01}, journal = {Biological Journal of the Linnean Society}, volume = {80}, pages = {207 -- 222}, abstract = {Phylogenetic relationships of 64 freshwater Barbus s.s. species distributed in basins around the Mediterranean Sea were assessed using cytochrome b sequences. Our results are in concordance with previous morphological and genetic studies, which proposed that these species belong to two major lineages (or subgenera): Barbus and Luciobarbus. We were particularly interested in phylogenetic relationships among species of the Luciobarbus lineage that are primarily found in the southern Mediterranean region from the Iberian Peninsula to the Middle East. In the Luciobarbus lineage, species that were previously attributed to the Capoeta genus were clustered. In this study, we observed short internodes between monophyletic groups having a geographical agreement around the Mediterranean. However, groups from the opposite sides of the Mediterranean Sea (Iberian Peninsula-Capoeta, north-western Africa-Middle East) seem to be phylogenetically close. We therefore infer that rapid radiation of Luciobarbus species in the Late Miocene better fits our data rather than gradual founder events in the southern Mediterranean. We propose that the biogeographical event along an east-west route, responsible for the present distribution of Luciobarbus species, was the ’Lago Mare’ phase of the Mediterranean Sea that provided a rapid dispersal route over extensive distances. This provides new insights into the speciation pattern of this group, and may be of general use in the study of freshwater species in these regions. © 2003 The Linnean Society of London.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Phylogenetic relationships of 64 freshwater Barbus s.s. species distributed in basins around the Mediterranean Sea were assessed using cytochrome b sequences. Our results are in concordance with previous morphological and genetic studies, which proposed that these species belong to two major lineages (or subgenera): Barbus and Luciobarbus. We were particularly interested in phylogenetic relationships among species of the Luciobarbus lineage that are primarily found in the southern Mediterranean region from the Iberian Peninsula to the Middle East. In the Luciobarbus lineage, species that were previously attributed to the Capoeta genus were clustered. In this study, we observed short internodes between monophyletic groups having a geographical agreement around the Mediterranean. However, groups from the opposite sides of the Mediterranean Sea (Iberian Peninsula-Capoeta, north-western Africa-Middle East) seem to be phylogenetically close. We therefore infer that rapid radiation of Luciobarbus species in the Late Miocene better fits our data rather than gradual founder events in the southern Mediterranean. We propose that the biogeographical event along an east-west route, responsible for the present distribution of Luciobarbus species, was the ’Lago Mare’ phase of the Mediterranean Sea that provided a rapid dispersal route over extensive distances. This provides new insights into the speciation pattern of this group, and may be of general use in the study of freshwater species in these regions. © 2003 The Linnean Society of London. |
2002 |
Tsigenopoulos, Costas S; Kotlík, Petr; Berrebi, Patrick Biological Journal of the Linnean Society, 75 (1), pp. 83–99, 2002, ISSN: 00244066, 10958312. @article{tsigenopoulos_biogeography_2002, title = {Biogeography and pattern of gene flow among Barbus species (Teleostei: Cyprinidae) inhabiting the Italian Peninsula and neighbouring Adriatic drainages as revealed by allozyme and mitochondrial sequence data}, author = {Costas S Tsigenopoulos and Petr Kotlík and Patrick Berrebi}, url = {https://academic.oup.com/biolinnean/article-lookup/doi/10.1046/j.1095-8312.2002.00007.x}, doi = {10.1046/j.1095-8312.2002.00007.x}, issn = {00244066, 10958312}, year = {2002}, date = {2002-03-01}, urldate = {2020-08-10}, journal = {Biological Journal of the Linnean Society}, volume = {75}, number = {1}, pages = {83--99}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Berrebi, P; Tsigenopoulos, C S Contribution des sequences mitochondriales a l’eclatement phylogenetique du genre polyploide Barbus (Teleosteen Cyprinides). Implications biogeographiques Inproceedings Journées Annuelles de la Société Française de Systématique (SFS) ’Systématique et biogéographie’, pp. 49–56, Biosystema, Paris, France, 2002, (Backup Publisher: Biosystema). @inproceedings{berrebi_contribution_2002, title = {Contribution des sequences mitochondriales a l’eclatement phylogenetique du genre polyploide Barbus (Teleosteen Cyprinides). Implications biogeographiques}, author = {P Berrebi and C S Tsigenopoulos}, year = {2002}, date = {2002-01-01}, booktitle = {Journées Annuelles de la Société Française de Systématique (SFS) ’Systématique et biogéographie’}, volume = {20}, pages = {49--56}, publisher = {Biosystema}, address = {Paris, France}, note = {Backup Publisher: Biosystema}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Durand, J -D; Tsigenopoulos, C S; Ünlü, E; Berrebi, P Phylogeny and biogeography of the family cyprinidae in the Middle East inferred from cytochrome b DNA - Evolutionary significance of this region Journal Article Molecular Phylogenetics and Evolution, 22 , pp. 91 – 100, 2002. @article{durand_phylogeny_2002, title = {Phylogeny and biogeography of the family cyprinidae in the Middle East inferred from cytochrome b DNA - Evolutionary significance of this region}, author = {J -D Durand and C S Tsigenopoulos and E Ünlü and P Berrebi}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0036367829&partnerID=40&md5=baef71440c137fcb1a598cc09e6c17c5}, year = {2002}, date = {2002-01-01}, journal = {Molecular Phylogenetics and Evolution}, volume = {22}, pages = {91 -- 100}, abstract = {The phylogenetic relationships of cyprinid species from the Middle East and neighboring biogeographical areas were investigated using cytochrome b sequence variation in order to test hypotheses that consider the Middle Eastern area as an important interchange area or a center of speciation for the freshwater fauna. A total of 62 cyprinid species were analyzed over the complete cytochrome b fragment (1140 bp); 28 belong to the Leuciscinae subfamily and 34 to the Cyprininae. All the Leuciscinae lineage fish recorded in the Middle East are also found in Europe, which was interpreted as an important Palearctic influence in the Middle Eastern ichthyofauna consistent with the Lago Mare dispersion. However, it has also been suggested that several Danube species have their origins in the Middle East. In contrast, the Cyprininae subfamily showed three highly divergent lineages, one shared with the Euro-Mediterranean area (Barbus/Luciobarbus genus) relict of the Lago Mare dispersion, one shared with Africa (Carasobarbus/Varicorhinus subgenus), and the third shared with Asia (Garra genus). Furthermore, clades observed in the phylogenetic reconstructions are not consistent with morphometric or karyological data and disagree with previous taxonomic assumptions. Lastly, the dispersion history in the Middle East of this subfamily appears much more complicated and ancient than that of the Leuciscinae. However, taking into account Cyprininae and Leuciscinae distribution, the Middle East appears more like an important interchange area for the freshwater ichtyofauna than a center of speciation. © 2002 Elsevier Science.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The phylogenetic relationships of cyprinid species from the Middle East and neighboring biogeographical areas were investigated using cytochrome b sequence variation in order to test hypotheses that consider the Middle Eastern area as an important interchange area or a center of speciation for the freshwater fauna. A total of 62 cyprinid species were analyzed over the complete cytochrome b fragment (1140 bp); 28 belong to the Leuciscinae subfamily and 34 to the Cyprininae. All the Leuciscinae lineage fish recorded in the Middle East are also found in Europe, which was interpreted as an important Palearctic influence in the Middle Eastern ichthyofauna consistent with the Lago Mare dispersion. However, it has also been suggested that several Danube species have their origins in the Middle East. In contrast, the Cyprininae subfamily showed three highly divergent lineages, one shared with the Euro-Mediterranean area (Barbus/Luciobarbus genus) relict of the Lago Mare dispersion, one shared with Africa (Carasobarbus/Varicorhinus subgenus), and the third shared with Asia (Garra genus). Furthermore, clades observed in the phylogenetic reconstructions are not consistent with morphometric or karyological data and disagree with previous taxonomic assumptions. Lastly, the dispersion history in the Middle East of this subfamily appears much more complicated and ancient than that of the Leuciscinae. However, taking into account Cyprininae and Leuciscinae distribution, the Middle East appears more like an important interchange area for the freshwater ichtyofauna than a center of speciation. © 2002 Elsevier Science. |
Kotlik, P; Tsigenopoulos, C S; Rab, P; Berrebi, P Two new Barbus species from the Danube River basin, with redescription of B. petenyi (Teleostei: Cyprinidae) Journal Article Folia Zoologica, 51 (3), pp. 227–240, 2002. @article{kotlik_two_2002, title = {Two new Barbus species from the Danube River basin, with redescription of B. petenyi (Teleostei: Cyprinidae)}, author = {P Kotlik and C S Tsigenopoulos and P Rab and P Berrebi}, year = {2002}, date = {2002-01-01}, journal = {Folia Zoologica}, volume = {51}, number = {3}, pages = {227--240}, abstract = {Three rheophilic species of western Palaearctic textitBarbus are recognised in the Danube River basin, each diagnosed by a set of unique mitochondrial DNA alleles. The three species are parapatrically distributed and morphologically similar to each other. The redescribed textitB. petenyi, from the Eastern and Southern Carpathians and Stara Planina Mts., is distinguished by a short, sharply pointed snout. textitBarbus carpathicus, new species, from the Western and Eastern Carpathians, is distinguished by a long, sharply pointed snout. textitBarbus balcanicus, new species, from the Dinaric Mts. and Western Stara Planina Mts., is distinguished by a short, bluntly pointed snout, and a unique body and fin colour pattern..}, keywords = {}, pubstate = {published}, tppubtype = {article} } Three rheophilic species of western Palaearctic textitBarbus are recognised in the Danube River basin, each diagnosed by a set of unique mitochondrial DNA alleles. The three species are parapatrically distributed and morphologically similar to each other. The redescribed textitB. petenyi, from the Eastern and Southern Carpathians and Stara Planina Mts., is distinguished by a short, sharply pointed snout. textitBarbus carpathicus, new species, from the Western and Eastern Carpathians, is distinguished by a long, sharply pointed snout. textitBarbus balcanicus, new species, from the Dinaric Mts. and Western Stara Planina Mts., is distinguished by a short, bluntly pointed snout, and a unique body and fin colour pattern.. |
Tsigenopoulos, C S; Ráb, P; Naran, D; Berrebi, P Multiple origins of polyploidy in the phylogeny of southern African barbs (Cyprinidae) as inferred from mtDNA markers Journal Article Heredity, 88 , pp. 466 – 473, 2002. @article{tsigenopoulos_multiple_2002, title = {Multiple origins of polyploidy in the phylogeny of southern African barbs (Cyprinidae) as inferred from mtDNA markers}, author = {C S Tsigenopoulos and P Ráb and D Naran and P Berrebi}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0035988371&partnerID=40&md5=987e5b01eed62d1567a0a38697c6be52}, year = {2002}, date = {2002-01-01}, journal = {Heredity}, volume = {88}, pages = {466 -- 473}, abstract = {The cyprinid genus Barbus, with more than 800 nominal species, is an apparently polyphyletic assemblage to which a number of unrelated species, groups and/or assemblages have been assigned. It includes species that exhibit three different ploidy levels: diploid, tetraploid and hexaploid. Several lineages of the family Cyprinidae constitute a major component of the African freshwater ichthyofauna, having about 500 species, and fishes assigned to the genus ’Barbus’ have the most species on the continent. We used complete sequences of the mitochondrial cytochrome b gene in order to infer phylogenetic relationships between diploid, tetraploid and hexaploid species of ’Barbus’ occurring in southern Africa, the only region where representatives of all of the three ploidy levels occur. The results indicate that most of the lineages are incorrectly classified in the genus ’Barbus’. The southern African tetraploids probably originated from southern African diploids. They constitute a monophyletic group distinct from tetraptoids occurring in the Euro-Mediterranean region (Barbus sensu stricto). The ’small’ African diploid species seem to be paraphyletic, while the ’large’ African hexaploid barbs species are of a single, recent origin and form a monophyletic group. The evidence of multiple, independent origins of polyptoidy occurring in the African cyprinine cyprinids thus provides a significant contribution to the knowledge on the systematic diversity of these fishes, and warrants a thorough taxonomic reorganization of the genus.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The cyprinid genus Barbus, with more than 800 nominal species, is an apparently polyphyletic assemblage to which a number of unrelated species, groups and/or assemblages have been assigned. It includes species that exhibit three different ploidy levels: diploid, tetraploid and hexaploid. Several lineages of the family Cyprinidae constitute a major component of the African freshwater ichthyofauna, having about 500 species, and fishes assigned to the genus ’Barbus’ have the most species on the continent. We used complete sequences of the mitochondrial cytochrome b gene in order to infer phylogenetic relationships between diploid, tetraploid and hexaploid species of ’Barbus’ occurring in southern Africa, the only region where representatives of all of the three ploidy levels occur. The results indicate that most of the lineages are incorrectly classified in the genus ’Barbus’. The southern African tetraploids probably originated from southern African diploids. They constitute a monophyletic group distinct from tetraptoids occurring in the Euro-Mediterranean region (Barbus sensu stricto). The ’small’ African diploid species seem to be paraphyletic, while the ’large’ African hexaploid barbs species are of a single, recent origin and form a monophyletic group. The evidence of multiple, independent origins of polyptoidy occurring in the African cyprinine cyprinids thus provides a significant contribution to the knowledge on the systematic diversity of these fishes, and warrants a thorough taxonomic reorganization of the genus. |
2000 |
Tsigenopoulos, C S; Berrebi, P Molecular Phylogenetics and Evolution, 14 , pp. 165 – 179, 2000. @article{tsigenopoulos_molecular_2000, title = {Molecular phylogeny of north Mediterranean freshwater barbs (genus Barbus: Cyprinidae) inferred from cytochrome b sequences: Biogeographic and systematic implications}, author = {C S Tsigenopoulos and P Berrebi}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0034029971&partnerID=40&md5=ace051f20e05e83cd39f80b54a10d813}, year = {2000}, date = {2000-01-01}, journal = {Molecular Phylogenetics and Evolution}, volume = {14}, pages = {165 -- 179}, abstract = {We investigated phylogenetic relationships among north Mediterranean species of the genus Barbus using sequences of the cytochrome b gene. Our results indicate that the species belong to two major clades that are consistent with those previously defined from morphological features. The first clade includes species ranging from France to the Black Sea. In this clade, there is a well-supported monophyletic group of large-sized fluvio-lacustrine barbs; however, the monophyly of the small-sized rheophilic species is not clear. The second clade comprises species found in Spain, Greece, and Asia Minor and probably represents the oldest group present in the north Mediterranean rivers. In general, there is good concordance between geography and phylogenetic relationships. These results are compared to those from previous morphological- and allozyme-based studies and demonstrate widespread discordance and polyphyly in the traditional taxonomy of the genus Barbus. This study is one of the first reporting the phylogenetic and biogeographic relationships of a genus that is widely distributed in European rivers and contains species that are a major component of the European ichthyofauna. (C) 2000 Academic Press.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We investigated phylogenetic relationships among north Mediterranean species of the genus Barbus using sequences of the cytochrome b gene. Our results indicate that the species belong to two major clades that are consistent with those previously defined from morphological features. The first clade includes species ranging from France to the Black Sea. In this clade, there is a well-supported monophyletic group of large-sized fluvio-lacustrine barbs; however, the monophyly of the small-sized rheophilic species is not clear. The second clade comprises species found in Spain, Greece, and Asia Minor and probably represents the oldest group present in the north Mediterranean rivers. In general, there is good concordance between geography and phylogenetic relationships. These results are compared to those from previous morphological- and allozyme-based studies and demonstrate widespread discordance and polyphyly in the traditional taxonomy of the genus Barbus. This study is one of the first reporting the phylogenetic and biogeographic relationships of a genus that is widely distributed in European rivers and contains species that are a major component of the European ichthyofauna. (C) 2000 Academic Press. |
1999 |
Tsigenopoulos, C S; Karakousis, Y; Berrebi, P The North Mediterranean Barbus lineage : phylogenetic hypotheses and taxonomic implications based on allozyme data Journal Article Journal of Fish Biology, 54 (2), pp. 267–286, 1999. @article{tsigenopoulos_north_1999, title = {The North Mediterranean Barbus lineage : phylogenetic hypotheses and taxonomic implications based on allozyme data}, author = {C S Tsigenopoulos and Y Karakousis and P Berrebi}, year = {1999}, date = {1999-01-01}, journal = {Journal of Fish Biology}, volume = {54}, number = {2}, pages = {267--286}, abstract = {Systematics of the European species of the genus textitBarbus is controversial for decades because of the relative similarity in general morphology between species. The use of more objective and precise characters, such as osteology, has given improved results. However, in the absence of a thorough morphological analysis of the group, genetic markers providing a promising method for obtaining more accurate phylogenies.On the basis of distinct ecological and morphological characters, the European textitBarbus taxa have been clustered in two groups : a fluvio-lacustrinetextittextless/itextgreaterand a rheophilic or strictly riverine one. These two groups (or ecophenotypes) were recognised in different parts of Europe, and formed, either a species assemblage (textlessitextgreaterBarbus barbus group) or a polytypic species (textitBarbus meridionalis). The implicit idea is that species of to the same group belong, to the same phylogenetic lineage (clade) and are the result of the same transcontinental colonisation event.The analysis, using allozyme markers, of 10 taxa of the genus textitBarbus from France, Italy, Greece, the Czech Republic and Slovakia, showed that the taxa thought to belong to the fluvio-lacustrine and the rheophilic groups are not monophyletic. We mention some alternative hypotheses, including the possibility that the allozyme markers may be inadequate. The results suggest that probably in each sub-region, the founding taxon has diverged independently to form species of two different ecophenotypes ; one occupying the upstream rivers and another found in the lowland rivers. Accordingly, textitBarbus species groups represent clusters of morphologically convergent taxa living in equivalent biotopes}, keywords = {}, pubstate = {published}, tppubtype = {article} } Systematics of the European species of the genus textitBarbus is controversial for decades because of the relative similarity in general morphology between species. The use of more objective and precise characters, such as osteology, has given improved results. However, in the absence of a thorough morphological analysis of the group, genetic markers providing a promising method for obtaining more accurate phylogenies.On the basis of distinct ecological and morphological characters, the European textitBarbus taxa have been clustered in two groups : a fluvio-lacustrinetextittextless/itextgreaterand a rheophilic or strictly riverine one. These two groups (or ecophenotypes) were recognised in different parts of Europe, and formed, either a species assemblage (textlessitextgreaterBarbus barbus group) or a polytypic species (textitBarbus meridionalis). The implicit idea is that species of to the same group belong, to the same phylogenetic lineage (clade) and are the result of the same transcontinental colonisation event.The analysis, using allozyme markers, of 10 taxa of the genus textitBarbus from France, Italy, Greece, the Czech Republic and Slovakia, showed that the taxa thought to belong to the fluvio-lacustrine and the rheophilic groups are not monophyletic. We mention some alternative hypotheses, including the possibility that the allozyme markers may be inadequate. The results suggest that probably in each sub-region, the founding taxon has diverged independently to form species of two different ecophenotypes ; one occupying the upstream rivers and another found in the lowland rivers. Accordingly, textitBarbus species groups represent clusters of morphologically convergent taxa living in equivalent biotopes |
1996 |
Tsigenopoulos, C S; Karakousis, Y Phylogenetic relationships of Leuciscus keadicus, an endemic cyprinid species from Greece, with other species of the genus Leuciscus Journal Article Folia Zoologica, 45 , pp. 87–93, 1996. @article{tsigenopoulos_phylogenetic_1996, title = {Phylogenetic relationships of Leuciscus keadicus, an endemic cyprinid species from Greece, with other species of the genus Leuciscus}, author = {C S Tsigenopoulos and Y Karakousis}, year = {1996}, date = {1996-01-01}, journal = {Folia Zoologica}, volume = {45}, pages = {87--93}, keywords = {}, pubstate = {published}, tppubtype = {article} } |