2025 |
Oikonomou, Stavroula; Tasiouli, Katerina; Tsaparis, Dimitrios; Manousaki, Tereza; Vallecillos, Antonio; Oikonomaki, Katerina; Tzokas, Konstantinos; Katribouzas, Nikolaos; Batargias, Costas; Chatziplis, Dimitrios; Tsigenopoulos, Costas S Genomic evaluation for body weight, length and growth estimates in meagre Argyrosomus regius Journal Article Aquaculture, 595 , pp. 741622, 2025, ISSN: 00448486. @article{oikonomou_genomic_2025, title = {Genomic evaluation for body weight, length and growth estimates in meagre Argyrosomus regius}, author = {Stavroula Oikonomou and Katerina Tasiouli and Dimitrios Tsaparis and Tereza Manousaki and Antonio Vallecillos and Katerina Oikonomaki and Konstantinos Tzokas and Nikolaos Katribouzas and Costas Batargias and Dimitrios Chatziplis and Costas S Tsigenopoulos}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848624010846 /wp-content/uploads/2025/01/2025-Oikonomou-AQUA-3.pdf}, doi = {10.1016/j.aquaculture.2024.741622}, issn = {00448486}, year = {2025}, date = {2025-01-24}, urldate = {2025-01-24}, journal = {Aquaculture}, volume = {595}, pages = {741622}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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. |
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 |
Theissinger, Kathrin; Fernandes, Carlos; Formenti, Giulio; Bista, Iliana; Berg, Paul R; Bleidorn, Christoph; Bombarely, Aureliano; Crottini, Angelica; Gallo, Guido R; Godoy, José A; Jentoft, Sissel; Malukiewicz, Joanna; Mouton, Alice; Oomen, Rebekah A; Paez, Sadye; Palsbøll, Per J; Pampoulie, Christophe; Ruiz-López, María J; Secomandi, Simona; Svardal, Hannes; Theofanopoulou, Constantina; Vries, Jan De; Waldvogel, Ann-Marie; Zhang, Guojie; Jarvis, Erich D; Bálint, Miklós; Ciofi, Claudio; Waterhouse, Robert M; Mazzoni, Camila J; Höglund, Jacob; Aghayan, Sargis A; Alioto, Tyler S; Almudi, Isabel; Alvarez, Nadir; Alves, Paulo C; Rosario, Isabel Amorim Do R; Antunes, Agostinho; Arribas, Paula; Baldrian, Petr; Bertorelle, Giorgio; Böhne, Astrid; Bonisoli-Alquati, Andrea; Boštjančić, Ljudevit L; Boussau, Bastien; Breton, Catherine M; Buzan, Elena; Campos, Paula F; Carreras, Carlos; Castro, FIlipe L C; Chueca, Luis J; Čiampor, Fedor; Conti, Elena; Cook-Deegan, Robert; Croll, Daniel; Cunha, Mónica V; Delsuc, Frédéric; Dennis, Alice B; Dimitrov, Dimitar; Faria, Rui; Favre, Adrien; Fedrigo, Olivier D; Fernández, Rosa; Ficetola, Gentile Francesco; Flot, Jean-François; Gabaldón, Toni; Agius, Dolores R; Giani, Alice M; Gilbert, Thomas M P; Grebenc, Tine; Guschanski, Katerina; Guyot, Romain; Hausdorf, Bernhard; Hawlitschek, Oliver; Heintzman, Peter D; Heinze, Berthold; Hiller, Michael; Husemann, Martin; Iannucci, Alessio; Irisarri, Iker; Jakobsen, Kjetill S; Klinga, Peter; Kloch, Agnieszka; Kratochwil, Claudius F; Kusche, Henrik; Layton, Kara K S; Leonard, Jennifer A; Lerat, Emmanuelle; Liti, Gianni; Manousaki, Tereza; Marques-Bonet, Tomas; Matos-Maraví, Pável; Matschiner, Michael; Maumus, Florian; Cartney, Ann Mc M; Meiri, Shai; Melo-Ferreira, José; Mengual, Ximo; Monaghan, Michael T; Montagna, Matteo; Mysłajek, Robert W; Neiber, Marco T; Nicolas, Violaine; Novo, Marta; Ozretić, Petar; Palero, Ferran; Pârvulescu, Lucian; Pascual, Marta; Paulo, Octávio S; Pavlek, Martina; Pegueroles, Cinta; Pellissier, Loïc; Pesole, Graziano; Primmer, Craig R; Riesgo, Ana; Rüber, Lukas; Rubolini, Diego; Salvi, Daniele; Seehausen, Ole; Seidel, Matthias; Studer, Bruno; Theodoridis, Spyros; Thines, Marco; Urban, Lara; Vasemägi, Anti; Vella, Adriana; Vella, Noel; Vernes, Sonja C; Vernesi, Cristiano; Vieites, David R; Wheat, Christopher W; Wörheide, Gert; Wurm, Yannick; Zammit, Gabrielle How genomics can help biodiversity conservation Journal Article Trends in Genetics, 39 (7), pp. 545–559, 2023, ISSN: 01689525. @article{theissinger_how_2023, title = {How genomics can help biodiversity conservation}, author = {Kathrin Theissinger and Carlos Fernandes and Giulio Formenti and Iliana Bista and Paul R Berg and Christoph Bleidorn and Aureliano Bombarely and Angelica Crottini and Guido R Gallo and José A Godoy and Sissel Jentoft and Joanna Malukiewicz and Alice Mouton and Rebekah A Oomen and Sadye Paez and Per J Palsbøll and Christophe Pampoulie and María J Ruiz-López and Simona Secomandi and Hannes Svardal and Constantina Theofanopoulou and Jan De Vries and Ann-Marie Waldvogel and Guojie Zhang and Erich D Jarvis and Miklós Bálint and Claudio Ciofi and Robert M Waterhouse and Camila J Mazzoni and Jacob Höglund and Sargis A Aghayan and Tyler S Alioto and Isabel Almudi and Nadir Alvarez and Paulo C Alves and Isabel R Amorim Do Rosario and Agostinho Antunes and Paula Arribas and Petr Baldrian and Giorgio Bertorelle and Astrid Böhne and Andrea Bonisoli-Alquati and Ljudevit L Boštjančić and Bastien Boussau and Catherine M Breton and Elena Buzan and Paula F Campos and Carlos Carreras and FIlipe L C Castro and Luis J Chueca and Fedor Čiampor and Elena Conti and Robert Cook-Deegan and Daniel Croll and Mónica V Cunha and Frédéric Delsuc and Alice B Dennis and Dimitar Dimitrov and Rui Faria and Adrien Favre and Olivier D Fedrigo and Rosa Fernández and Gentile Francesco Ficetola and Jean-François Flot and Toni Gabaldón and Dolores R Agius and Alice M Giani and Thomas M P Gilbert and Tine Grebenc and Katerina Guschanski and Romain Guyot and Bernhard Hausdorf and Oliver Hawlitschek and Peter D Heintzman and Berthold Heinze and Michael Hiller and Martin Husemann and Alessio Iannucci and Iker Irisarri and Kjetill S Jakobsen and Peter Klinga and Agnieszka Kloch and Claudius F Kratochwil and Henrik Kusche and Kara K S Layton and Jennifer A Leonard and Emmanuelle Lerat and Gianni Liti and Tereza Manousaki and Tomas Marques-Bonet and Pável Matos-Maraví and Michael Matschiner and Florian Maumus and Ann M Mc Cartney and Shai Meiri and José Melo-Ferreira and Ximo Mengual and Michael T Monaghan and Matteo Montagna and Robert W Mysłajek and Marco T Neiber and Violaine Nicolas and Marta Novo and Petar Ozretić and Ferran Palero and Lucian Pârvulescu and Marta Pascual and Octávio S Paulo and Martina Pavlek and Cinta Pegueroles and Loïc Pellissier and Graziano Pesole and Craig R Primmer and Ana Riesgo and Lukas Rüber and Diego Rubolini and Daniele Salvi and Ole Seehausen and Matthias Seidel and Bruno Studer and Spyros Theodoridis and Marco Thines and Lara Urban and Anti Vasemägi and Adriana Vella and Noel Vella and Sonja C Vernes and Cristiano Vernesi and David R Vieites and Christopher W Wheat and Gert Wörheide and Yannick Wurm and Gabrielle Zammit}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/09/2023-Theissinger-Trends-Genetics-44.pdf https://linkinghub.elsevier.com/retrieve/pii/S0168952523000203}, doi = {10.1016/j.tig.2023.01.005}, issn = {01689525}, year = {2023}, date = {2023-08-31}, urldate = {2023-09-01}, journal = {Trends in Genetics}, volume = {39}, number = {7}, pages = {545--559}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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. |
Formenti Giulio; Secomandi, Simona; Studer Bruno; Theodoridis Spyros; Thines Marco; Urban Lara;Theissinger Kathrin; Manousaki Tereza; Wörheide Gert; Wurm Yannick; Zammit Gabrielle... The era of reference genomes in conservation genomics Journal Article Trends in Ecology & Evolution, 37 , pp. 197-202, 2022, ISSN: 01695347. @article{FormentiGiulio2022, title = {The era of reference genomes in conservation genomics}, author = {Formenti, Giulio; Secomandi, Simona; Studer, Bruno; Theodoridis, Spyros; Thines, Marco; Urban, Lara;Theissinger, Kathrin; Manousaki, Tereza; Wörheide, Gert; Wurm, Yannick; Zammit, Gabrielle...}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Formenti-Trends-in-EE-10-1.pdf}, doi = {10.1016/j.tree.2021.11.008}, issn = {01695347}, year = {2022}, date = {2022-03-05}, journal = {Trends in Ecology & Evolution}, volume = {37}, pages = {197-202}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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} } |
2021 |
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} } |
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} } |
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 |
Tsakogiannis, Alexandros; Manousaki, Tereza; Anagnostopoulou, Vasileia; Stavroulaki, Melanthia; Apostolaki, Eugenia T The Importance of Genomics for Deciphering the Invasion Success of the Seagrass Halophila stipulacea in the Changing Mediterranean Sea Journal Article Diversity, 12 (7), 2020, ISSN: 1424-2818. @article{tsakogiannis_importance_2020, title = {The Importance of Genomics for Deciphering the Invasion Success of the Seagrass Halophila stipulacea in the Changing Mediterranean Sea}, author = {Alexandros Tsakogiannis and Tereza Manousaki and Vasileia Anagnostopoulou and Melanthia Stavroulaki and Eugenia T Apostolaki}, url = {https://www.mdpi.com/1424-2818/12/7/263}, doi = {10.3390/d12070263}, issn = {1424-2818}, year = {2020}, date = {2020-01-01}, journal = {Diversity}, volume = {12}, number = {7}, abstract = {The Mediterranean Sea is subject to pressures from biological invasion due to coastal anthropic activities and global warming, which potentially modify its biogeography. The Red Sea tropical seagrass Halophila stipulacea entered the Eastern Mediterranean over a century ago, and its occurrence is expanding towards the northwest. Here, we highlight the importance of genomics for deciphering the evolutionary and ecological procedures taking place during the invasion process of H. stipulacea and review the relatively sparse genetic information available for the species to date. We report the first draft whole-genome sequencing of a H. stipulacea individual from Greece, based on Illumina Sequencing technology. A comparison of the Internal Transcribed Spacer (ITS) regions revealed a high divergence of the herein sequenced individual compared to Mediterranean populations sequenced two decades ago, rendering further questions on the evolutionary processes taking place during H. stipulacea adaptation in the invaded Mediterranean Sea. Our work sets the baseline for a future analysis of the invasion genomic of the focal species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Mediterranean Sea is subject to pressures from biological invasion due to coastal anthropic activities and global warming, which potentially modify its biogeography. The Red Sea tropical seagrass Halophila stipulacea entered the Eastern Mediterranean over a century ago, and its occurrence is expanding towards the northwest. Here, we highlight the importance of genomics for deciphering the evolutionary and ecological procedures taking place during the invasion process of H. stipulacea and review the relatively sparse genetic information available for the species to date. We report the first draft whole-genome sequencing of a H. stipulacea individual from Greece, based on Illumina Sequencing technology. A comparison of the Internal Transcribed Spacer (ITS) regions revealed a high divergence of the herein sequenced individual compared to Mediterranean populations sequenced two decades ago, rendering further questions on the evolutionary processes taking place during H. stipulacea adaptation in the invaded Mediterranean Sea. Our work sets the baseline for a future analysis of the invasion genomic of the focal species. |
Blakeslee, April M H; Manousaki, Tereza; Vasileiadou, Katerina; Tepolt, Carolyn K An evolutionary perspective on marine invasions Journal Article Evolutionary Applications, 13 (3), pp. 479–485, 2020, (_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12906). @article{blakeslee_evolutionary_2020, title = {An evolutionary perspective on marine invasions}, author = {April M H Blakeslee and Tereza Manousaki and Katerina Vasileiadou and Carolyn K Tepolt}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.12906}, doi = {10.1111/eva.12906}, year = {2020}, date = {2020-01-01}, journal = {Evolutionary Applications}, volume = {13}, number = {3}, pages = {479--485}, abstract = {Abstract Species distributions are rapidly changing as human globalization increasingly moves organisms to novel environments. In marine systems, species introductions are the result of a number of anthropogenic mechanisms, notably shipping, aquaculture/mariculture, the pet and bait trades, and the creation of canals. Marine invasions are a global threat to human and non-human populations alike and are often listed as one of the top conservation concerns worldwide, having ecological, evolutionary, and social ramifications. Evolutionary investigations of marine invasions can provide crucial insight into an introduced species’ potential impacts in its new range, including: physiological adaptation and behavioral changes to exploit new environments; changes in resident populations, community interactions, and ecosystems; and severe reductions in genetic diversity that may limit evolutionary potential in the introduced range. This special issue focuses on current research advances in the evolutionary biology of marine invasions and can be broadly classified into a few major avenues of research: the evolutionary history of invasive populations, post-invasion reproductive changes, and the role of evolution in parasite introductions. Together, they demonstrate the value of investigating marine invasions from an evolutionary perspective, with benefits to both fundamental and applied evolutionary biology at local and broad scales.}, note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12906}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Species distributions are rapidly changing as human globalization increasingly moves organisms to novel environments. In marine systems, species introductions are the result of a number of anthropogenic mechanisms, notably shipping, aquaculture/mariculture, the pet and bait trades, and the creation of canals. Marine invasions are a global threat to human and non-human populations alike and are often listed as one of the top conservation concerns worldwide, having ecological, evolutionary, and social ramifications. Evolutionary investigations of marine invasions can provide crucial insight into an introduced species’ potential impacts in its new range, including: physiological adaptation and behavioral changes to exploit new environments; changes in resident populations, community interactions, and ecosystems; and severe reductions in genetic diversity that may limit evolutionary potential in the introduced range. This special issue focuses on current research advances in the evolutionary biology of marine invasions and can be broadly classified into a few major avenues of research: the evolutionary history of invasive populations, post-invasion reproductive changes, and the role of evolution in parasite introductions. Together, they demonstrate the value of investigating marine invasions from an evolutionary perspective, with benefits to both fundamental and applied evolutionary biology at local and broad scales. |
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. |
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} } |
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} } |
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} } |
2017 |
Lee, Hyuk Je; Schneider, Ralf F; Manousaki, Tereza; Kang, Ji Hyoun; Lein, Etienne; Franchini, Paolo; Meyer, Axel Genome biology and evolution, 9 (11), pp. 3122–3136, 2017, (Publisher: Oxford University Press). @article{lee_lateralized_2017, title = {Lateralized feeding behavior is associated with asymmetrical neuroanatomy and lateralized gene expressions in the brain in scale-eating cichlid fish}, author = {Hyuk Je Lee and Ralf F Schneider and Tereza Manousaki and Ji Hyoun Kang and Etienne Lein and Paolo Franchini and Axel Meyer}, doi = {10.1093/gbe/evx218}, year = {2017}, date = {2017-01-01}, journal = {Genome biology and evolution}, volume = {9}, number = {11}, pages = {3122--3136}, note = {Publisher: Oxford University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2016 |
Braasch, Ingo; Gehrke, Andrew R; Smith, Jeramiah J; Kawasaki, Kazuhiko; Manousaki, Tereza; Pasquier, Jeremy; Amores, Angel; Desvignes, Thomas; Batzel, Peter; Catchen, Julian; Berlin, Aaron M; Campbell, Michael S; Barrell, Daniel; Martin, Kyle J; Mulley, John F; Ravi, Vydianathan; Lee, Alison P; Nakamura, Tetsuya; Chalopin, Domitille; Fan, Shaohua; Wcisel, Dustin; Cañestro, Cristian; Sydes, Jason; Beaudry, Felix E G; Sun, Yi; Hertel, Jana; Beam, Michael J; Fasold, Mario; Ishiyama, Mikio; Johnson, Jeremy; Kehr, Steffi; Lara, Marcia; Letaw, John H; Litman, Gary W; Litman, Ronda T; Mikami, Masato; Ota, Tatsuya; Saha, Nil Ratan; Williams, Louise; Stadler, Peter F; Wang, Han; Taylor, John S; Fontenot, Quenton; Ferrara, Allyse; Searle, Stephen M J; Aken, Bronwen; Yandell, Mark; Schneider, Igor; Yoder, Jeffrey A; Volff, Jean-Nicolas; Meyer, Axel; Amemiya, Chris T; Venkatesh, Byrappa; Holland, Peter W H; Guiguen, Yann; Bobe, Julien; Shubin, Neil H; Palma, Federica Di; Alföldi, Jessica; Lindblad-Toh, Kerstin; Postlethwait, John H The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons Journal Article Nature Genetics, 48 (4), pp. 427–437, 2016, ISSN: 1061-4036, 1546-1718. @article{braasch_spotted_2016, title = {The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons}, author = {Ingo Braasch and Andrew R Gehrke and Jeramiah J Smith and Kazuhiko Kawasaki and Tereza Manousaki and Jeremy Pasquier and Angel Amores and Thomas Desvignes and Peter Batzel and Julian Catchen and Aaron M Berlin and Michael S Campbell and Daniel Barrell and Kyle J Martin and John F Mulley and Vydianathan Ravi and Alison P Lee and Tetsuya Nakamura and Domitille Chalopin and Shaohua Fan and Dustin Wcisel and Cristian Cañestro and Jason Sydes and Felix E G Beaudry and Yi Sun and Jana Hertel and Michael J Beam and Mario Fasold and Mikio Ishiyama and Jeremy Johnson and Steffi Kehr and Marcia Lara and John H Letaw and Gary W Litman and Ronda T Litman and Masato Mikami and Tatsuya Ota and Nil Ratan Saha and Louise Williams and Peter F Stadler and Han Wang and John S Taylor and Quenton Fontenot and Allyse Ferrara and Stephen M J Searle and Bronwen Aken and Mark Yandell and Igor Schneider and Jeffrey A Yoder and Jean-Nicolas Volff and Axel Meyer and Chris T Amemiya and Byrappa Venkatesh and Peter W H Holland and Yann Guiguen and Julien Bobe and Neil H Shubin and Federica Di Palma and Jessica Alföldi and Kerstin Lindblad-Toh and John H Postlethwait}, url = {http://www.nature.com/articles/ng.3526}, doi = {10.1038/ng.3526}, issn = {1061-4036, 1546-1718}, year = {2016}, date = {2016-04-01}, urldate = {2020-08-09}, journal = {Nature Genetics}, volume = {48}, number = {4}, pages = {427--437}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Manousaki, Tereza; Qiu, Huan; Noro, Miyuki; Hildebrand, Falk; Meyer, Axel; Kuraku, Shigehiro Molecular evolution in the lamprey genomes and its relevance to the timing of whole genome duplications Incollection Jawless Fishes of the World, 1 , Cambridge Scholars, 2016. @incollection{manousaki_molecular_2016, title = {Molecular evolution in the lamprey genomes and its relevance to the timing of whole genome duplications}, author = {Tereza Manousaki and Huan Qiu and Miyuki Noro and Falk Hildebrand and Axel Meyer and Shigehiro Kuraku}, year = {2016}, date = {2016-01-01}, booktitle = {Jawless Fishes of the World}, volume = {1}, publisher = {Cambridge Scholars}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
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} } |
2015 |
Kang, Ji Hyoun; Manousaki, Tereza; Franchini, Paolo; Kneitz, Susanne; Schartl, Manfred; Meyer, Axel Ecology and Evolution, 5 (4), pp. 848–864, 2015, ISSN: 20457758. @article{kang_transcriptomics_2015, title = {Transcriptomics of two evolutionary novelties: how to make a sperm-transfer organ out of an anal fin and a sexually selected “sword” out of a caudal fin}, author = {Ji Hyoun Kang and Tereza Manousaki and Paolo Franchini and Susanne Kneitz and Manfred Schartl and Axel Meyer}, url = {http://doi.wiley.com/10.1002/ece3.1390}, doi = {10.1002/ece3.1390}, issn = {20457758}, year = {2015}, date = {2015-02-01}, urldate = {2020-08-09}, journal = {Ecology and Evolution}, volume = {5}, number = {4}, pages = {848--864}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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. |
2014 |
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} } |
2013 |
Amemiya, Chris T; Alföldi, Jessica; Lee, Alison P; Fan, Shaohua; Philippe, Hervé; MacCallum, Iain; Braasch, Ingo; Manousaki, Tereza; Schneider, Igor; Rohner, Nicolas; Organ, Chris; Chalopin, Domitille; Smith, Jeramiah J; Robinson, Mark; Dorrington, Rosemary A; Gerdol, Marco; Aken, Bronwen; Biscotti, Maria Assunta; Barucca, Marco; Baurain, Denis; Berlin, Aaron M; Blatch, Gregory L; Buonocore, Francesco; Burmester, Thorsten; Campbell, Michael S; Canapa, Adriana; Cannon, John P; Christoffels, Alan; Moro, Gianluca De; Edkins, Adrienne L; Fan, Lin; Fausto, Anna Maria; Feiner, Nathalie; Forconi, Mariko; Gamieldien, Junaid; Gnerre, Sante; Gnirke, Andreas; Goldstone, Jared V; Haerty, Wilfried; Hahn, Mark E; Hesse, Uljana; Hoffmann, Steve; Johnson, Jeremy; Karchner, Sibel I; Kuraku, Shigehiro; Lara, Marcia; Levin, Joshua Z; Litman, Gary W; Mauceli, Evan; Miyake, Tsutomu; Mueller, Gail M; Nelson, David R; Nitsche, Anne; Olmo, Ettore; Ota, Tatsuya; Pallavicini, Alberto; Panji, Sumir; Picone, Barbara; Ponting, Chris P; Prohaska, Sonja J; Przybylski, Dariusz; Saha, Nil Ratan; Ravi, Vydianathan; Ribeiro, Filipe J; Sauka-Spengler, Tatjana; Scapigliati, Giuseppe; Searle, Stephen M J; Sharpe, Ted; Simakov, Oleg; Stadler, Peter F; Stegeman, John J; Sumiyama, Kenta; Tabbaa, Diana; Tafer, Hakim; Turner-Maier, Jason; van Heusden, Peter; White, Simon; Williams, Louise; Yandell, Mark; Brinkmann, Henner; Volff, Jean-Nicolas; Tabin, Clifford J; Shubin, Neil; Schartl, Manfred; Jaffe, David B; Postlethwait, John H; Venkatesh, Byrappa; Palma, Federica Di; Lander, Eric S; Meyer, Axel; Lindblad-Toh, Kerstin The African coelacanth genome provides insights into tetrapod evolution Journal Article Nature, 496 (7445), pp. 311–316, 2013, ISSN: 0028-0836, 1476-4687. @article{amemiya_african_2013, title = {The African coelacanth genome provides insights into tetrapod evolution}, author = {Chris T Amemiya and Jessica Alföldi and Alison P Lee and Shaohua Fan and Hervé Philippe and Iain MacCallum and Ingo Braasch and Tereza Manousaki and Igor Schneider and Nicolas Rohner and Chris Organ and Domitille Chalopin and Jeramiah J Smith and Mark Robinson and Rosemary A Dorrington and Marco Gerdol and Bronwen Aken and Maria Assunta Biscotti and Marco Barucca and Denis Baurain and Aaron M Berlin and Gregory L Blatch and Francesco Buonocore and Thorsten Burmester and Michael S Campbell and Adriana Canapa and John P Cannon and Alan Christoffels and Gianluca De Moro and Adrienne L Edkins and Lin Fan and Anna Maria Fausto and Nathalie Feiner and Mariko Forconi and Junaid Gamieldien and Sante Gnerre and Andreas Gnirke and Jared V Goldstone and Wilfried Haerty and Mark E Hahn and Uljana Hesse and Steve Hoffmann and Jeremy Johnson and Sibel I Karchner and Shigehiro Kuraku and Marcia Lara and Joshua Z Levin and Gary W Litman and Evan Mauceli and Tsutomu Miyake and Gail M Mueller and David R Nelson and Anne Nitsche and Ettore Olmo and Tatsuya Ota and Alberto Pallavicini and Sumir Panji and Barbara Picone and Chris P Ponting and Sonja J Prohaska and Dariusz Przybylski and Nil Ratan Saha and Vydianathan Ravi and Filipe J Ribeiro and Tatjana Sauka-Spengler and Giuseppe Scapigliati and Stephen M J Searle and Ted Sharpe and Oleg Simakov and Peter F Stadler and John J Stegeman and Kenta Sumiyama and Diana Tabbaa and Hakim Tafer and Jason Turner-Maier and Peter van Heusden and Simon White and Louise Williams and Mark Yandell and Henner Brinkmann and Jean-Nicolas Volff and Clifford J Tabin and Neil Shubin and Manfred Schartl and David B Jaffe and John H Postlethwait and Byrappa Venkatesh and Federica Di Palma and Eric S Lander and Axel Meyer and Kerstin Lindblad-Toh}, url = {http://www.nature.com/articles/nature12027}, doi = {10.1038/nature12027}, issn = {0028-0836, 1476-4687}, year = {2013}, date = {2013-04-01}, urldate = {2020-08-09}, journal = {Nature}, volume = {496}, number = {7445}, pages = {311--316}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Manousaki, Tereza; Hull, Pincelli M; Kusche, Henrik; Machado-Schiaffino, Gonzalo; Franchini, Paolo; Harrod, Chris; Elmer, Kathryn R; Meyer, Axel Molecular Ecology, 22 (3), pp. 650–669, 2013. @article{manousaki_parsing_2013, title = {Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped M idas cichlid fishes from N icaragua}, author = {Tereza Manousaki and Pincelli M Hull and Henrik Kusche and Gonzalo Machado-Schiaffino and Paolo Franchini and Chris Harrod and Kathryn R Elmer and Axel Meyer}, url = {https://doi.org/10.1111/mec.12034}, doi = {10.1111/mec.12034}, year = {2013}, date = {2013-01-01}, journal = {Molecular Ecology}, volume = {22}, number = {3}, pages = {650--669}, abstract = {The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex) - from two Great Lakes and two crater lakes in Nicaragua - to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips’ gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and δ15N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution. © 2012 Blackwell Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex) - from two Great Lakes and two crater lakes in Nicaragua - to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips’ gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and δ15N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution. © 2012 Blackwell Publishing Ltd. |
Smith, Jeramiah J; Kuraku, Shigehiro; Holt, Carson; Sauka-Spengler, Tatjana; Jiang, Ning; Campbell, Michael S; Yandell, Mark D; Manousaki, Tereza; Meyer, Axel; Bloom, Ona E; others, Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution Journal Article Nature Genetics, 45 (4), pp. 415–421, 2013, (Publisher: Nature Publishing Group). @article{smith_sequencing_2013, title = {Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution}, author = {Jeramiah J Smith and Shigehiro Kuraku and Carson Holt and Tatjana Sauka-Spengler and Ning Jiang and Michael S Campbell and Mark D Yandell and Tereza Manousaki and Axel Meyer and Ona E Bloom and others}, url = {https://www.nature.com/articles/ng.2568}, doi = {10.1038/ng.2568}, year = {2013}, date = {2013-01-01}, journal = {Nature Genetics}, volume = {45}, number = {4}, pages = {415--421}, note = {Publisher: Nature Publishing Group}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2011 |
Manousaki, Tereza; Feiner, Nathalie; Begemann, Gerrit; Meyer, Axel; Kuraku, Shigehiro Co-orthology of P ax4 and P ax6 to the fly eyeless gene: molecular phylogenetic, comparative genomic, and embryological analyses Journal Article Evolution & Development, 13 (5), pp. 448–459, 2011. @article{manousaki_co-orthology_2011, title = {Co-orthology of P ax4 and P ax6 to the fly eyeless gene: molecular phylogenetic, comparative genomic, and embryological analyses}, author = {Tereza Manousaki and Nathalie Feiner and Gerrit Begemann and Axel Meyer and Shigehiro Kuraku}, url = {https://doi.org/10.1111/j.1525-142X.2011.00502.x}, doi = {10.1111/j.1525-142X.2011.00502.x}, year = {2011}, date = {2011-01-01}, journal = {Evolution & Development}, volume = {13}, number = {5}, pages = {448--459}, abstract = {The functional equivalence of P ax6/eyeless genes across distantly related animal phyla has been one of central findings on which evo‐devo studies is based. In this study, we show that P ax4 , in addition to P ax6 , is a vertebrate ortholog of the fly eyeless gene (and its duplicate, twin of eyeless [toy ] gene, unique to I nsecta). Molecular phylogenetic trees published to date placed the P ax4 gene outside the P ax6 /eyeless subgroup as if the P ax4 gene originated from a gene duplication before the origin of bilaterians. However, P ax4 genes had only been reported for mammals. Our molecular phylogenetic analysis, including previously unidentified teleost fish pax4 genes, equally supported two scenarios: one with the P ax4 –P ax6 duplication early in vertebrate evolution and the other with this duplication before the bilaterian radiation. We then investigated gene compositions in the genomic regions containing P ax4 and P ax6 , and identified (1) conserved synteny between these two regions, suggesting that the P ax4 –P ax6 split was caused by a large‐scale duplication and (2) its timing within early vertebrate evolution based on the duplication timing of the members of neighboring gene families. Our results are consistent with the so‐called two‐round genome duplications in early vertebrates. Overall, the P ax6 /eyeless ortholog is merely part of a 2:2 orthology relationship between vertebrates (with P ax4 and P ax6 ) and the fly (with eyeless and toy ). In this context, evolution of transcriptional regulation associated with the P ax4 –P ax6 split is also discussed in light of the zebrafish pax4 expression pattern that is analyzed here for the first time}, keywords = {}, pubstate = {published}, tppubtype = {article} } The functional equivalence of P ax6/eyeless genes across distantly related animal phyla has been one of central findings on which evo‐devo studies is based. In this study, we show that P ax4 , in addition to P ax6 , is a vertebrate ortholog of the fly eyeless gene (and its duplicate, twin of eyeless [toy ] gene, unique to I nsecta). Molecular phylogenetic trees published to date placed the P ax4 gene outside the P ax6 /eyeless subgroup as if the P ax4 gene originated from a gene duplication before the origin of bilaterians. However, P ax4 genes had only been reported for mammals. Our molecular phylogenetic analysis, including previously unidentified teleost fish pax4 genes, equally supported two scenarios: one with the P ax4 –P ax6 duplication early in vertebrate evolution and the other with this duplication before the bilaterian radiation. We then investigated gene compositions in the genomic regions containing P ax4 and P ax6 , and identified (1) conserved synteny between these two regions, suggesting that the P ax4 –P ax6 split was caused by a large‐scale duplication and (2) its timing within early vertebrate evolution based on the duplication timing of the members of neighboring gene families. Our results are consistent with the so‐called two‐round genome duplications in early vertebrates. Overall, the P ax6 /eyeless ortholog is merely part of a 2:2 orthology relationship between vertebrates (with P ax4 and P ax6 ) and the fly (with eyeless and toy ). In this context, evolution of transcriptional regulation associated with the P ax4 –P ax6 split is also discussed in light of the zebrafish pax4 expression pattern that is analyzed here for the first time |
Dessimoz, Christophe; Zoller, Stefan; Manousaki, Tereza; Qiu, Huan; Meyer, Axel; Kuraku, Shigehiro Briefings in Bioinformatics, 12 (5), pp. 474–484, 2011, (Publisher: Oxford University Press). @article{dessimoz_comparative_2011, title = {Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes)}, author = {Christophe Dessimoz and Stefan Zoller and Tereza Manousaki and Huan Qiu and Axel Meyer and Shigehiro Kuraku}, url = {https://doi.org/10.1093/bib/bbr038}, doi = {10.1093/bib/bbr038}, year = {2011}, date = {2011-01-01}, journal = {Briefings in Bioinformatics}, volume = {12}, number = {5}, pages = {474--484}, note = {Publisher: Oxford University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } |