2024 |
Gioti, Anastasia; Theodosopoulou, Danai; Bravakos, Panos; Magoulas, Antonios; Kotoulas, Georgios The bioinformatics landscape in environmental omics: Lessons from a national ELIXIR survey Journal Article iScience, 27 (6), pp. 110062, 2024, ISSN: 25890042. @article{gioti_bioinformatics_2024, title = {The bioinformatics landscape in environmental omics: Lessons from a national ELIXIR survey}, author = {Anastasia Gioti and Danai Theodosopoulou and Panos Bravakos and Antonios Magoulas and Georgios Kotoulas}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/06/2024-Gioti-iScience-26.pdf https://linkinghub.elsevier.com/retrieve/pii/S2589004224012872}, doi = {10.1016/j.isci.2024.110062}, issn = {25890042}, year = {2024}, date = {2024-06-08}, urldate = {2024-06-10}, journal = {iScience}, volume = {27}, number = {6}, pages = {110062}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Skaraki, Katerina; Pavloudi, Christina; Dailianis, Thanos; Lagnel, Jacques; Pantazidou, Adriani; Magoulas, Antonios; Kotoulas, Georgios Microbial diversity in four Mediterranean irciniid sponges Journal Article Biodiversity Data Journal, 12 , pp. e114809, 2024, ISSN: 1314-2828, 1314-2836. @article{skaraki_microbial_2024, title = {Microbial diversity in four Mediterranean irciniid sponges}, author = {Katerina Skaraki and Christina Pavloudi and Thanos Dailianis and Jacques Lagnel and Adriani Pantazidou and Antonios Magoulas and Georgios Kotoulas}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/02/2024-Skaraki-BioDDJ-6.pdf https://bdj.pensoft.net/article/114809/}, doi = {10.3897/BDJ.12.e114809}, issn = {1314-2828, 1314-2836}, year = {2024}, date = {2024-02-01}, urldate = {2024-02-05}, journal = {Biodiversity Data Journal}, volume = {12}, pages = {e114809}, abstract = {This paper describes a dataset of microbial communities from four different sponge species: Ircinia oros (Schmidt, 1864), Ircinia variabilis (Schmidt, 1862), Sarcotragus spinosulus Schmidt, 1862 and Sarcotragus fasciculatus (Pallas, 1766). The examined sponges all belong to Demospongiae (Class); Keratosa (Subclass); Dictyoceratida (Order); Irciniidae (Family). Samples were collected by scuba diving at depths between 6-14 m from two sampling sites of rocky formations at the northern coast of Crete (Cretan Sea, eastern Mediterranean) and were subjected to metabarcoding for the V5-V6 region of the 16S rRNA gene.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This paper describes a dataset of microbial communities from four different sponge species: Ircinia oros (Schmidt, 1864), Ircinia variabilis (Schmidt, 1862), Sarcotragus spinosulus Schmidt, 1862 and Sarcotragus fasciculatus (Pallas, 1766). The examined sponges all belong to Demospongiae (Class); Keratosa (Subclass); Dictyoceratida (Order); Irciniidae (Family). Samples were collected by scuba diving at depths between 6-14 m from two sampling sites of rocky formations at the northern coast of Crete (Cretan Sea, eastern Mediterranean) and were subjected to metabarcoding for the V5-V6 region of the 16S rRNA gene. |
2023 |
Zafeiropoulos, Haris; Beracochea, Martin; Ninidakis, Stelios; Exter, Katrina; Potirakis, Antonis; De Moro, Gianluca; Richardson, Lorna; Corre, Erwan; Machado, João; Pafilis, Evangelos; Kotoulas, Georgios; Santi, Ioulia; Finn, Robert D; Cox, Cymon J; Pavloudi, Christina metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data Journal Article GigaScience, 12 , pp. giad078, 2023, ISSN: 2047-217X. @article{zafeiropoulos_metagoflow_2022, title = {metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data}, author = {Haris Zafeiropoulos and Martin Beracochea and Stelios Ninidakis and Katrina Exter and Antonis Potirakis and Gianluca De Moro and Lorna Richardson and Erwan Corre and João Machado and Evangelos Pafilis and Georgios Kotoulas and Ioulia Santi and Robert D Finn and Cymon J Cox and Christina Pavloudi}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/10/2023-Zafeiropoulos-GiGa-57.pdf https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad078/7321054}, doi = {10.1093/gigascience/giad078}, issn = {2047-217X}, year = {2023}, date = {2023-10-19}, urldate = {2023-10-23}, journal = {GigaScience}, volume = {12}, pages = {giad078}, abstract = {Abstract Background Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that conduct regular biological community samplings to generate environmental and metagenomic data of microbial communities from designated marine stations around Europe. The development of an effective workflow is essential for the analysis of the EMO BON metagenomic data in a timely and reproducible manner. Findings Based on the established MGnify resource, we developed metaGOflow. metaGOflow supports the fast inference of taxonomic profiles from GO-derived data based on ribosomal RNA genes and their functional annotation using the raw reads. Thanks to the Research Object Crate packaging, relevant metadata about the sample under study, and the details of the bioinformatics analysis it has been subjected to, are inherited to the data product while its modular implementation allows running the workflow partially. The analysis of 2 EMO BON samples and 1 Tara Oceans sample was performed as a use case. Conclusions metaGOflow is an efficient and robust workflow that scales to the needs of projects producing big metagenomic data such as EMO BON. It highlights how containerization technologies along with modern workflow languages and metadata package approaches can support the needs of researchers when dealing with ever-increasing volumes of biological data. Despite being initially oriented to address the needs of EMO BON, metaGOflow is a flexible and easy-to-use workflow that can be broadly used for one-sample-at-a-time analysis of shotgun metagenomics data.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Background Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that conduct regular biological community samplings to generate environmental and metagenomic data of microbial communities from designated marine stations around Europe. The development of an effective workflow is essential for the analysis of the EMO BON metagenomic data in a timely and reproducible manner. Findings Based on the established MGnify resource, we developed metaGOflow. metaGOflow supports the fast inference of taxonomic profiles from GO-derived data based on ribosomal RNA genes and their functional annotation using the raw reads. Thanks to the Research Object Crate packaging, relevant metadata about the sample under study, and the details of the bioinformatics analysis it has been subjected to, are inherited to the data product while its modular implementation allows running the workflow partially. The analysis of 2 EMO BON samples and 1 Tara Oceans sample was performed as a use case. Conclusions metaGOflow is an efficient and robust workflow that scales to the needs of projects producing big metagenomic data such as EMO BON. It highlights how containerization technologies along with modern workflow languages and metadata package approaches can support the needs of researchers when dealing with ever-increasing volumes of biological data. Despite being initially oriented to address the needs of EMO BON, metaGOflow is a flexible and easy-to-use workflow that can be broadly used for one-sample-at-a-time analysis of shotgun metagenomics data. |
Santi, Ioulia; Beluche, Odette; Beraud, Mélanie; Buttigieg, Pier Luigi; Casotti, Raffaella; Cox, Cymon J; Cunliffe, Michael; Davies, Neil; Cerio, Oihane Diaz De; Exter, Katrina; Kervella, Anne Emmanuelle; Kotoulas, Georgios; Lagaisse, Rune; Laroquette, Arnaud; Louro, Bruno; Not, Fabrice; Obst, Matthias; Pavloudi, Christina; Poulain, Julie; Præbel, Kim; Vanaverbeke, Jan; Pade, Nicolas European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation Journal Article Frontiers in Marine Science, 10 , pp. 1118120, 2023, ISSN: 2296-7745. @article{santi_european_2023, title = {European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation}, author = {Ioulia Santi and Odette Beluche and Mélanie Beraud and Pier Luigi Buttigieg and Raffaella Casotti and Cymon J Cox and Michael Cunliffe and Neil Davies and Oihane Diaz De Cerio and Katrina Exter and Anne Emmanuelle Kervella and Georgios Kotoulas and Rune Lagaisse and Arnaud Laroquette and Bruno Louro and Fabrice Not and Matthias Obst and Christina Pavloudi and Julie Poulain and Kim Præbel and Jan Vanaverbeke and Nicolas Pade}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Santi-Frontiers-MarSci-24.pdf https://www.frontiersin.org/articles/10.3389/fmars.2023.1118120/full}, doi = {10.3389/fmars.2023.1118120}, issn = {2296-7745}, year = {2023}, date = {2023-05-29}, urldate = {2023-06-06}, journal = {Frontiers in Marine Science}, volume = {10}, pages = {1118120}, abstract = {Marine ecosystems, ranging from coastal seas and wetlands to the open ocean, accommodate a wealth of biological diversity from small microorganisms to large mammals. This biodiversity and its associated ecosystem function occurs across complex spatial and temporal scales and is not yet fully understood. Given the wide range of external pressures on the marine environment, this knowledge is crucial for enabling effective conservation measures and defining the limits of sustainable use. The development and application of omics-based approaches to biodiversity research has helped overcome hurdles, such as allowing the previously hidden community of microbial life to be identified, thereby enabling a holistic view of an entire ecosystem’s biodiversity and functioning. The potential of omics-based approaches for marine ecosystems observation is enormous and their added value to ecosystem monitoring, management, and conservation is widely acknowledged. Despite these encouraging prospects, most omics-based studies are short-termed and typically cover only small spatial scales which therefore fail to include the full spatio-temporal complexity and dynamics of the system. To date, few attempts have been made to establish standardised, coordinated, broad scaled, and long-term omics observation networks. Here we outline the creation of an omics-based marine observation network at the European scale, the European Marine Omics Biodiversity Observation Network (EMO BON). We illustrate how linking multiple existing individual observation efforts increases the observational power in large-scale assessments of status and change in biodiversity in the oceans. Such large-scale observation efforts have the added value of cross-border cooperation, are characterised by shared costs through economies of scale, and produce structured, comparable data. The key components required to compile reference environmental datasets and how these should be linked are major challenges that we address.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Marine ecosystems, ranging from coastal seas and wetlands to the open ocean, accommodate a wealth of biological diversity from small microorganisms to large mammals. This biodiversity and its associated ecosystem function occurs across complex spatial and temporal scales and is not yet fully understood. Given the wide range of external pressures on the marine environment, this knowledge is crucial for enabling effective conservation measures and defining the limits of sustainable use. The development and application of omics-based approaches to biodiversity research has helped overcome hurdles, such as allowing the previously hidden community of microbial life to be identified, thereby enabling a holistic view of an entire ecosystem’s biodiversity and functioning. The potential of omics-based approaches for marine ecosystems observation is enormous and their added value to ecosystem monitoring, management, and conservation is widely acknowledged. Despite these encouraging prospects, most omics-based studies are short-termed and typically cover only small spatial scales which therefore fail to include the full spatio-temporal complexity and dynamics of the system. To date, few attempts have been made to establish standardised, coordinated, broad scaled, and long-term omics observation networks. Here we outline the creation of an omics-based marine observation network at the European scale, the European Marine Omics Biodiversity Observation Network (EMO BON). We illustrate how linking multiple existing individual observation efforts increases the observational power in large-scale assessments of status and change in biodiversity in the oceans. Such large-scale observation efforts have the added value of cross-border cooperation, are characterised by shared costs through economies of scale, and produce structured, comparable data. The key components required to compile reference environmental datasets and how these should be linked are major challenges that we address. |
2021 |
Bravakos, Panos; Mandalakis, Manolis; Nomikou, Paraskevi; Anastasiou, Thekla I; Kristoffersen, Jon Bent; Stavroulaki, Melanthia; Kilias, Stephanos; Kotoulas, Georgios; Magoulas, Antonios; Polymenakou, Paraskevi N Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece Journal Article Sci Rep, 11 (1), pp. 1336, 2021, ISSN: 2045-2322. @article{bravakos_genomic_2021, title = {Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece}, author = {Panos Bravakos and Manolis Mandalakis and Paraskevi Nomikou and Thekla I Anastasiou and Jon Bent Kristoffersen and Melanthia Stavroulaki and Stephanos Kilias and Georgios Kotoulas and Antonios Magoulas and Paraskevi N Polymenakou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021-Bravakos-SciReport-4.pdf http://www.nature.com/articles/s41598-020-79359-y}, doi = {10.1038/s41598-020-79359-y}, issn = {2045-2322}, year = {2021}, date = {2021-01-01}, urldate = {2021-02-02}, journal = {Sci Rep}, volume = {11}, number = {1}, pages = {1336}, abstract = {Abstract Although the rise of antibiotic and multidrug resistant bacteria is one of the biggest current threats to human health, our understanding of the mechanisms involved in antibiotic resistance selection remains scarce. We performed whole genome sequencing of 21 Pseudomonas strains, previously isolated from an active submarine volcano of Greece, the Kolumbo volcano. Our goal was to identify the genetic basis of the enhanced co-tolerance to antibiotics and acidity of these Pseudomonas strains. Pangenome analysis identified 10,908 Gene Clusters (GCs). It revealed that the numbers of phage-related GCs and sigma factors, which both provide the mechanisms of adaptation to environmental stressors, were much higher in the high tolerant Pseudomonas strains compared to the rest ones. All identified GCs of these strains were associated with antimicrobial and multidrug resistance. The present study provides strong evidence that the CO 2 -rich seawater of the volcano associated with low pH might be a reservoir of microorganisms carrying multidrug efflux-mediated systems and pumps. We, therefore, suggest further studies of other extreme environments (or ecosystems) and their associated physicochemical parameters (or factors) in the rise of antibiotic resistance.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Although the rise of antibiotic and multidrug resistant bacteria is one of the biggest current threats to human health, our understanding of the mechanisms involved in antibiotic resistance selection remains scarce. We performed whole genome sequencing of 21 Pseudomonas strains, previously isolated from an active submarine volcano of Greece, the Kolumbo volcano. Our goal was to identify the genetic basis of the enhanced co-tolerance to antibiotics and acidity of these Pseudomonas strains. Pangenome analysis identified 10,908 Gene Clusters (GCs). It revealed that the numbers of phage-related GCs and sigma factors, which both provide the mechanisms of adaptation to environmental stressors, were much higher in the high tolerant Pseudomonas strains compared to the rest ones. All identified GCs of these strains were associated with antimicrobial and multidrug resistance. The present study provides strong evidence that the CO 2 -rich seawater of the volcano associated with low pH might be a reservoir of microorganisms carrying multidrug efflux-mediated systems and pumps. We, therefore, suggest further studies of other extreme environments (or ecosystems) and their associated physicochemical parameters (or factors) in the rise of antibiotic resistance. |
Polymenakou, Paraskevi N; Nomikou, Paraskevi; Zafeiropoulos, Haris; Mandalakis, Manolis; Anastasiou, Thekla I; Kilias, Stephanos; Kyrpides, Nikos C; Kotoulas, Georgios; Magoulas, Antoniοs The Santorini Volcanic Complex as a Valuable Source of Enzymes for Bioenergy Journal Article Energies, 14 (5), pp. 1414, 2021, ISSN: 1996-1073. @article{polymenakou_santorini_2021, title = {The Santorini Volcanic Complex as a Valuable Source of Enzymes for Bioenergy}, author = {Paraskevi N Polymenakou and Paraskevi Nomikou and Haris Zafeiropoulos and Manolis Mandalakis and Thekla I Anastasiou and Stephanos Kilias and Nikos C Kyrpides and Georgios Kotoulas and Antoniοs Magoulas}, url = {https://www.mdpi.com/1996-1073/14/5/1414 https://imbbc.hcmr.gr/wp-content/uploads/2021/03/2021-Polymenakou-ENERGIES-24.pdf}, doi = {10.3390/en14051414}, issn = {1996-1073}, year = {2021}, date = {2021-01-01}, urldate = {2021-03-17}, journal = {Energies}, volume = {14}, number = {5}, pages = {1414}, abstract = {Marine microbial communities are an untapped reservoir of genetic and metabolic diversity and a valuable source for the discovery of new natural products of biotechnological interest. The newly discovered hydrothermal vent field of Santorini volcanic complex located in the Aegean Sea is gaining increasing interest for potential biotechnological exploitation. The conditions in these environments, i.e., high temperatures, low pH values and high concentration of heavy metals, often resemble harsh industrial settings. Thus, these environments may serve as pools of enzymes of enhanced catalytic properties that may provide benefits to biotechnology. Here, we screened 11 metagenomic libraries previously constructed from microbial mat samples covering the seafloor and the polymetallic chimneys of Kolumbo volcano as well as mat samples from Santorini caldera, to mine, in silico, genes associated with bioenergy applications. We particularly focused on genes encoding biomass hydrolysis enzymes such as cellulases, hemicellulases and lignin-degrading enzymes. A total of 10,417 genes were found for three specific groups of enzymes—i.e., the endoglucanases, the three different beta-glucosidases BGL, bglX and bglB, and the alpha-galactosidases melA, and rafA. Overall, we concluded that the Santorini–Kolumbo volcanic ecosystems constitute a significant resource of novel genes with potential applications in bioenergy that deserve further investigation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Marine microbial communities are an untapped reservoir of genetic and metabolic diversity and a valuable source for the discovery of new natural products of biotechnological interest. The newly discovered hydrothermal vent field of Santorini volcanic complex located in the Aegean Sea is gaining increasing interest for potential biotechnological exploitation. The conditions in these environments, i.e., high temperatures, low pH values and high concentration of heavy metals, often resemble harsh industrial settings. Thus, these environments may serve as pools of enzymes of enhanced catalytic properties that may provide benefits to biotechnology. Here, we screened 11 metagenomic libraries previously constructed from microbial mat samples covering the seafloor and the polymetallic chimneys of Kolumbo volcano as well as mat samples from Santorini caldera, to mine, in silico, genes associated with bioenergy applications. We particularly focused on genes encoding biomass hydrolysis enzymes such as cellulases, hemicellulases and lignin-degrading enzymes. A total of 10,417 genes were found for three specific groups of enzymes—i.e., the endoglucanases, the three different beta-glucosidases BGL, bglX and bglB, and the alpha-galactosidases melA, and rafA. Overall, we concluded that the Santorini–Kolumbo volcanic ecosystems constitute a significant resource of novel genes with potential applications in bioenergy that deserve further investigation. |
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 |
Obst, Matthias; Exter, Katrina; Allcock, Louise A; Arvanitidis, Christos; Axberg, Alizz; Bustamante, Maria; Cancio, Ibon; Carreira-Flores, Diego; Chatzinikolaou, Eva; Chatzigeorgiou, Giorgos; Chrismas, Nathan; Clark, Melody S; Comtet, Thierry; Dailianis, Thanos; Davies, Neil; Deneudt, Klaas; de Cerio, Oihane Diaz; Fortič, Ana; Gerovasileiou, Vasilis; Hablützel, Pascal I; Keklikoglou, Kleoniki; Kotoulas, Georgios; Lasota, Rafal; Leite, Barbara R; Loisel, Stéphane; Lévêque, Laurent; Levy, Liraz; Malachowicz, Magdalena; Mavrič, Borut; Meyer, Christopher; Mortelmans, Jonas; Norkko, Joanna; Pade, Nicolas; Power, Anne Marie; Ramšak, Andreja; Reiss, Henning; Solbakken, Jostein; Staehr, Peter A; Sundberg, Per; Thyrring, Jakob; Troncoso, Jesus S; Viard, Frédérique; Wenne, Roman; Yperifanou, Eleni Ioanna; Zbawicka, Malgorzata; Pavloudi, Christina A Marine Biodiversity Observation Network for Genetic Monitoring of Hard-Bottom Communities (ARMS-MBON) Journal Article Frontiers in Marine Science, 7 , pp. 572680, 2020, ISSN: 2296-7745. @article{obst_marine_2020, title = {A Marine Biodiversity Observation Network for Genetic Monitoring of Hard-Bottom Communities (ARMS-MBON)}, author = {Matthias Obst and Katrina Exter and Louise A Allcock and Christos Arvanitidis and Alizz Axberg and Maria Bustamante and Ibon Cancio and Diego Carreira-Flores and Eva Chatzinikolaou and Giorgos Chatzigeorgiou and Nathan Chrismas and Melody S Clark and Thierry Comtet and Thanos Dailianis and Neil Davies and Klaas Deneudt and Oihane Diaz de Cerio and Ana Fortič and Vasilis Gerovasileiou and Pascal I Hablützel and Kleoniki Keklikoglou and Georgios Kotoulas and Rafal Lasota and Barbara R Leite and Stéphane Loisel and Laurent Lévêque and Liraz Levy and Magdalena Malachowicz and Borut Mavrič and Christopher Meyer and Jonas Mortelmans and Joanna Norkko and Nicolas Pade and Anne Marie Power and Andreja Ramšak and Henning Reiss and Jostein Solbakken and Peter A Staehr and Per Sundberg and Jakob Thyrring and Jesus S Troncoso and Frédérique Viard and Roman Wenne and Eleni Ioanna Yperifanou and Malgorzata Zbawicka and Christina Pavloudi}, url = {https://www.frontiersin.org/articles/10.3389/fmars.2020.572680/full}, doi = {10.3389/fmars.2020.572680}, issn = {2296-7745}, year = {2020}, date = {2020-11-01}, urldate = {2020-12-08}, journal = {Frontiers in Marine Science}, volume = {7}, pages = {572680}, abstract = {Marine hard-bottom communities are undergoing severe change under the influence of multiple drivers, notably climate change, extraction of natural resources, pollution and eutrophication, habitat degradation, and invasive species. Monitoring marine biodiversity in such habitats is, however, challenging as it typically involves expensive, non-standardized, and often destructive sampling methods that limit its scalability. Differences in monitoring approaches furthermore hinders inter-comparison among monitoring programs. Here, we announce a Marine Biodiversity Observation Network (MBON) consisting of Autonomous Reef Monitoring Structures (ARMS) with the aim to assess the status and changes in benthic fauna with genomic-based methods, notably DNA metabarcoding, in combination with image-based identifications. This article presents the results of a 30-month pilot phase in which we established an operational and geographically expansive ARMS-MBON. The network currently consists of 20 observatories distributed across European coastal waters and the polar regions, in which 134 ARMS have been deployed to date. Sampling takes place annually, either as short-term deployments during the summer or as long-term deployments starting in spring. The pilot phase was used to establish a common set of standards for field sampling, genetic analysis, data management, and legal compliance, which are presented here. We also tested the potential of ARMS for combining genetic and image-based identification methods in comparative studies of benthic diversity, as well as for detecting non-indigenous species. Results show that ARMS are suitable for monitoring hard-bottom environments as they provide genetic data that can be continuously enriched, re-analyzed, and integrated with conventional data to document benthic community composition and detect non-indigenous species. Finally, we provide guidelines to expand the network and present a sustainability plan as part of the European Marine Biological Resource Centre ( www.embrc.eu ).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Marine hard-bottom communities are undergoing severe change under the influence of multiple drivers, notably climate change, extraction of natural resources, pollution and eutrophication, habitat degradation, and invasive species. Monitoring marine biodiversity in such habitats is, however, challenging as it typically involves expensive, non-standardized, and often destructive sampling methods that limit its scalability. Differences in monitoring approaches furthermore hinders inter-comparison among monitoring programs. Here, we announce a Marine Biodiversity Observation Network (MBON) consisting of Autonomous Reef Monitoring Structures (ARMS) with the aim to assess the status and changes in benthic fauna with genomic-based methods, notably DNA metabarcoding, in combination with image-based identifications. This article presents the results of a 30-month pilot phase in which we established an operational and geographically expansive ARMS-MBON. The network currently consists of 20 observatories distributed across European coastal waters and the polar regions, in which 134 ARMS have been deployed to date. Sampling takes place annually, either as short-term deployments during the summer or as long-term deployments starting in spring. The pilot phase was used to establish a common set of standards for field sampling, genetic analysis, data management, and legal compliance, which are presented here. We also tested the potential of ARMS for combining genetic and image-based identification methods in comparative studies of benthic diversity, as well as for detecting non-indigenous species. Results show that ARMS are suitable for monitoring hard-bottom environments as they provide genetic data that can be continuously enriched, re-analyzed, and integrated with conventional data to document benthic community composition and detect non-indigenous species. Finally, we provide guidelines to expand the network and present a sustainability plan as part of the European Marine Biological Resource Centre ( www.embrc.eu ). |
Tsiola, Anastasia; Michoud, Grégoire; Fodelianakis, Stilianos; Karakassis, Ioannis; Kotoulas, Georgios; Pavlidou, Alexandra; Pavloudi, Christina; Pitta, Paraskevi; Simboura, Nomiki; Daffonchio, Daniele; Tsapakis, Manolis Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone Journal Article Viruses, 12 (8), pp. 806, 2020. @article{tsiola_viral_2020, title = {Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone}, author = {Anastasia Tsiola and Grégoire Michoud and Stilianos Fodelianakis and Ioannis Karakassis and Georgios Kotoulas and Alexandra Pavlidou and Christina Pavloudi and Paraskevi Pitta and Nomiki Simboura and Daniele Daffonchio and Manolis Tsapakis}, url = {https://www.mdpi.com/1999-4915/12/8/806}, doi = {10.3390/v12080806}, year = {2020}, date = {2020-08-01}, urldate = {2020-08-06}, journal = {Viruses}, volume = {12}, number = {8}, pages = {806}, abstract = {Viruses interfere with their host’s metabolism through the expression of auxiliary metabolic genes (AMGs) that, until now, are mostly studied under large physicochemical gradients. Here, we focus on coastal marine ecosystems and we sequence the viral metagenome (virome) of samples with discrete levels of human-driven disturbances. We aim to describe the relevance of viromics with respect to ecological quality status, defined by the classic seawater trophic index (TRIX). Neither viral (family level) nor bacterial (family level, based on 16S rRNA sequencing) community structure correlated with TRIX. AMGs involved in the Calvin and tricarboxylic acid cycles were found at stations with poor ecological quality, supporting viral lysis by modifying the host’s energy supply. AMGs involved in “non-traditional” energy-production pathways (3HP, sulfur oxidation) were found irrespective of ecological quality, highlighting the importance of recognizing the prevalent metabolic paths and their intermediate byproducts. Various AMGs explained the variability between stations with poor vs. good ecological quality. Our study confirms the pivotal role of the virome content in ecosystem functioning, acting as a “pool” of available functions that may be transferred to the hosts. Further, it suggests that AMGs could be used as an ultra-sensitive metric of energy-production pathways with relevance in the vulnerable coastal zone and its ecological quality.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Viruses interfere with their host’s metabolism through the expression of auxiliary metabolic genes (AMGs) that, until now, are mostly studied under large physicochemical gradients. Here, we focus on coastal marine ecosystems and we sequence the viral metagenome (virome) of samples with discrete levels of human-driven disturbances. We aim to describe the relevance of viromics with respect to ecological quality status, defined by the classic seawater trophic index (TRIX). Neither viral (family level) nor bacterial (family level, based on 16S rRNA sequencing) community structure correlated with TRIX. AMGs involved in the Calvin and tricarboxylic acid cycles were found at stations with poor ecological quality, supporting viral lysis by modifying the host’s energy supply. AMGs involved in “non-traditional” energy-production pathways (3HP, sulfur oxidation) were found irrespective of ecological quality, highlighting the importance of recognizing the prevalent metabolic paths and their intermediate byproducts. Various AMGs explained the variability between stations with poor vs. good ecological quality. Our study confirms the pivotal role of the virome content in ecosystem functioning, acting as a “pool” of available functions that may be transferred to the hosts. Further, it suggests that AMGs could be used as an ultra-sensitive metric of energy-production pathways with relevance in the vulnerable coastal zone and its ecological quality. |
Gioti, Anastasia; Siaperas, Romanos; Nikolaivits, Efstratios; Goff, Géraldine Le; Ouazzani, Jamal; Kotoulas, Georgios; Topakas, Evangelos Draft Genome Sequence of a Cladosporium Species Isolated from the Mesophotic Ascidian Didemnum maculosum Journal Article Microbiology Resource Announcements, 9 (18), 2020, (Publisher: American Society for Microbiology Journals _eprint: https://mra.asm.org/content/9/18/e00311-20.full.pdf). @article{gioti_draft_2020, title = {Draft Genome Sequence of a Cladosporium Species Isolated from the Mesophotic Ascidian Didemnum maculosum}, author = {Anastasia Gioti and Romanos Siaperas and Efstratios Nikolaivits and Géraldine Le Goff and Jamal Ouazzani and Georgios Kotoulas and Evangelos Topakas}, editor = {Antonis Rokas}, url = {https://mra.asm.org/content/9/18/e00311-20}, doi = {10.1128/MRA.00311-20}, year = {2020}, date = {2020-01-01}, journal = {Microbiology Resource Announcements}, volume = {9}, number = {18}, abstract = {We report the 28-Mbp draft genome sequence of the marine fungus Cladosporium sp. strain TM138. The species was isolated from the marine invertebrate Didemnum maculosum. Its genome sequence will inform future investigations into the species’ enzymatic potential for bioremediation and its evolution in marine environments.}, note = {Publisher: American Society for Microbiology Journals _eprint: https://mra.asm.org/content/9/18/e00311-20.full.pdf}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report the 28-Mbp draft genome sequence of the marine fungus Cladosporium sp. strain TM138. The species was isolated from the marine invertebrate Didemnum maculosum. Its genome sequence will inform future investigations into the species’ enzymatic potential for bioremediation and its evolution in marine environments. |
Polymenakou, Paraskevi N; Nomikou, Paraskevi; Mandalakis, Manolis; Kilias, Stephanos; Kotoulas, Giorgos; Kyrpides, Nikos C; Magoulas, Antonios Microbial Benthic Communities in the Aegean Sea Incollection Springer Berlin Heidelberg, Berlin, Heidelberg, 2020, (Series Title: The Handbook of Environmental Chemistry). @incollection{polymenakou_microbial_2020, title = {Microbial Benthic Communities in the Aegean Sea}, author = {Paraskevi N Polymenakou and Paraskevi Nomikou and Manolis Mandalakis and Stephanos Kilias and Giorgos Kotoulas and Nikos C Kyrpides and Antonios Magoulas}, url = {https://link.springer.com/10.1007/698_2020_685}, doi = {10.1007/698_2020_685}, year = {2020}, date = {2020-01-01}, urldate = {2022-02-17}, publisher = {Springer Berlin Heidelberg}, address = {Berlin, Heidelberg}, note = {Series Title: The Handbook of Environmental Chemistry}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
2019 |
Tsaparis, Dimitris; Sotiropoulos, Konstantinos; Legakis, Anastasios; Kotoulas, Georgios; Kasapidis, Panagiotis New phylogeographic insights support the distinctiveness and conservation value of the little-known Greek roe deer populations Journal Article Mammalian Biology, 96 , pp. 23–27, 2019, ISSN: 16165047. @article{tsaparis_new_2019, title = {New phylogeographic insights support the distinctiveness and conservation value of the little-known Greek roe deer populations}, author = {Dimitris Tsaparis and Konstantinos Sotiropoulos and Anastasios Legakis and Georgios Kotoulas and Panagiotis Kasapidis}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1616504718302581}, doi = {10.1016/j.mambio.2019.03.010}, issn = {16165047}, year = {2019}, date = {2019-05-01}, urldate = {2020-08-26}, journal = {Mammalian Biology}, volume = {96}, pages = {23--27}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Rizzo, Andrea Luca; Caracausi, Antonio; Chavagnac, Valérie; Nomikou, Paraskevi; Polymenakou, Paraskevi N; Mandalakis, Manolis; Kotoulas, Georgios; Magoulas, Antonios; Castillo, Alain; Lampridou, Danai; Marusczak, Nicolas; Sonke, Jeroen E Geochemistry of CO2-Rich Gases Venting From Submarine Volcanism: The Case of Kolumbo (Hellenic Volcanic Arc, Greece) Journal Article Frontiers in Earth Science, 7 , pp. 60, 2019, ISSN: 2296-6463, (BIODIV). @article{rizzo_geochemistry_2019, title = {Geochemistry of CO2-Rich Gases Venting From Submarine Volcanism: The Case of Kolumbo (Hellenic Volcanic Arc, Greece)}, author = {Andrea Luca Rizzo and Antonio Caracausi and Valérie Chavagnac and Paraskevi Nomikou and Paraskevi N Polymenakou and Manolis Mandalakis and Georgios Kotoulas and Antonios Magoulas and Alain Castillo and Danai Lampridou and Nicolas Marusczak and Jeroen E Sonke}, url = {https://www.frontiersin.org/article/10.3389/feart.2019.00060/full}, doi = {10.3389/feart.2019.00060}, issn = {2296-6463}, year = {2019}, date = {2019-04-01}, urldate = {2022-01-17}, journal = {Frontiers in Earth Science}, volume = {7}, pages = {60}, note = {BIODIV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Mandalakis, M; Gavriilidou, A; Polymenakou, P N; Christakis, C A; Nomikou, P; Medvecký, M; Kilias, S P; Kentouri, M; Kotoulas, G; Magoulas, A Microbial strains isolated from CO2-venting Kolumbo submarine volcano show enhanced co-tolerance to acidity and antibiotics Journal Article Marine Environmental Research, 2019, ISSN: 01411136, (Publisher: Elsevier Ltd). @article{mandalakis_microbial_2019, title = {Microbial strains isolated from CO2-venting Kolumbo submarine volcano show enhanced co-tolerance to acidity and antibiotics}, author = {M Mandalakis and A Gavriilidou and P N Polymenakou and C A Christakis and P Nomikou and M Medvecký and S P Kilias and M Kentouri and G Kotoulas and A Magoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85059814164&doi=10.1016%2fj.marenvres.2019.01.002&partnerID=40&md5=69e25c6daab89af12b0091a2c75b0d18}, doi = {10.1016/j.marenvres.2019.01.002}, issn = {01411136}, year = {2019}, date = {2019-01-01}, journal = {Marine Environmental Research}, abstract = {As ocean acidification intensifies, there is growing global concern about the impacts that future pH levels are likely to have on marine life and ecosystems. By analogy, a steep decrease of seawater pH with depth is encountered inside the Kolumbo submarine volcano (northeast Santorini) as a result of natural CO2 venting, making this system ideal for ocean acidification research. Here, we investigated whether the increase of acidity towards deeper layers of Kolumbo crater had any effect on relevant phenotypic traits of bacterial isolates. A total of 31 Pseudomonas strains were isolated from both surface- (SSL) and deep-seawater layers (DSL), with the latter presenting a significantly higher acid tolerance. In particular, the DSL strains were able to cope with H+ levels that were 18 times higher. Similarly, the DSL isolates exhibited a significantly higher tolerance than SSL strains against six commonly used antibiotics and As(III). More importantly, a significant positive correlation was revealed between antibiotics and acid tolerance across the entire set of SSL and DSL isolates. Our findings imply that Pseudomonas species with higher resilience to antibiotics could be favored by the prospect of acidifying oceans. Further studies are required to determine if this feature is universal across marine bacteria and to assess potential ecological impacts. © 2019 Elsevier Ltd}, note = {Publisher: Elsevier Ltd}, keywords = {}, pubstate = {published}, tppubtype = {article} } As ocean acidification intensifies, there is growing global concern about the impacts that future pH levels are likely to have on marine life and ecosystems. By analogy, a steep decrease of seawater pH with depth is encountered inside the Kolumbo submarine volcano (northeast Santorini) as a result of natural CO2 venting, making this system ideal for ocean acidification research. Here, we investigated whether the increase of acidity towards deeper layers of Kolumbo crater had any effect on relevant phenotypic traits of bacterial isolates. A total of 31 Pseudomonas strains were isolated from both surface- (SSL) and deep-seawater layers (DSL), with the latter presenting a significantly higher acid tolerance. In particular, the DSL strains were able to cope with H+ levels that were 18 times higher. Similarly, the DSL isolates exhibited a significantly higher tolerance than SSL strains against six commonly used antibiotics and As(III). More importantly, a significant positive correlation was revealed between antibiotics and acid tolerance across the entire set of SSL and DSL isolates. Our findings imply that Pseudomonas species with higher resilience to antibiotics could be favored by the prospect of acidifying oceans. Further studies are required to determine if this feature is universal across marine bacteria and to assess potential ecological impacts. © 2019 Elsevier Ltd |
2018 |
Christakis, C A; Polymenakou, P N; Mandalakis, M; Nomikou, P; Kristoffersen, J B; Lampridou, D; Kotoulas, G; Magoulas, A Microbial community differentiation between active and inactive sulfide chimneys of the Kolumbo submarine volcano, Hellenic Volcanic Arc Journal Article Extremophiles, 22 (1), pp. 13–27, 2018, ISSN: 14310651, (Publisher: Springer Tokyo). @article{christakis_microbial_2018, title = {Microbial community differentiation between active and inactive sulfide chimneys of the Kolumbo submarine volcano, Hellenic Volcanic Arc}, author = {C A Christakis and P N Polymenakou and M Mandalakis and P Nomikou and J B Kristoffersen and D Lampridou and G Kotoulas and A Magoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85032008505&doi=10.1007%2fs00792-017-0971-x&partnerID=40&md5=2258d2985b658c3f415f37d92d684597}, doi = {10.1007/s00792-017-0971-x}, issn = {14310651}, year = {2018}, date = {2018-01-01}, journal = {Extremophiles}, volume = {22}, number = {1}, pages = {13--27}, abstract = {Over the last decades, there has been growing interest about the ecological role of hydrothermal sulfide chimneys, their microbial diversity and associated biotechnological potential. Here, we performed dual-index Illumina sequencing of bacterial and archaeal communities on active and inactive sulfide chimneys collected from the Kolumbo hydrothermal field, situated on a geodynamic convergent setting. A total of 15,701 OTUs (operational taxonomic units) were assigned to 56 bacterial and 3 archaeal phyla, 133 bacterial and 16 archaeal classes. Active chimney communities were dominated by OTUs related to thermophilic members of Epsilonproteobacteria, Aquificae and Deltaproteobacteria. Inactive chimney communities were dominated by an OTU closely related to the archaeon Nitrosopumilus sp., and by members of Gammaproteobacteria, Deltaproteobacteria, Planctomycetes and Bacteroidetes. These lineages are closely related to phylotypes typically involved in iron, sulfur, nitrogen, hydrogen and methane cycling. Overall, the inactive sulfide chimneys presented highly diverse and uniform microbial communities, in contrast to the active chimney communities, which were dominated by chemolithoautotrophic and thermophilic lineages. This study represents one of the most comprehensive investigations of microbial diversity in submarine chimneys and elucidates how the dissipation of hydrothermal activity affects the structure of microbial consortia in these extreme ecological niches. © 2017, Springer Japan KK.}, note = {Publisher: Springer Tokyo}, keywords = {}, pubstate = {published}, tppubtype = {article} } Over the last decades, there has been growing interest about the ecological role of hydrothermal sulfide chimneys, their microbial diversity and associated biotechnological potential. Here, we performed dual-index Illumina sequencing of bacterial and archaeal communities on active and inactive sulfide chimneys collected from the Kolumbo hydrothermal field, situated on a geodynamic convergent setting. A total of 15,701 OTUs (operational taxonomic units) were assigned to 56 bacterial and 3 archaeal phyla, 133 bacterial and 16 archaeal classes. Active chimney communities were dominated by OTUs related to thermophilic members of Epsilonproteobacteria, Aquificae and Deltaproteobacteria. Inactive chimney communities were dominated by an OTU closely related to the archaeon Nitrosopumilus sp., and by members of Gammaproteobacteria, Deltaproteobacteria, Planctomycetes and Bacteroidetes. These lineages are closely related to phylotypes typically involved in iron, sulfur, nitrogen, hydrogen and methane cycling. Overall, the inactive sulfide chimneys presented highly diverse and uniform microbial communities, in contrast to the active chimney communities, which were dominated by chemolithoautotrophic and thermophilic lineages. This study represents one of the most comprehensive investigations of microbial diversity in submarine chimneys and elucidates how the dissipation of hydrothermal activity affects the structure of microbial consortia in these extreme ecological niches. © 2017, Springer Japan KK. |
Vasileiadou, K; Pavloudi, C; Camisa, F; Tsikopoulou, I; Fragopoulou, N; Kotoulas, G; Arvanitidis, C Genetic diversity of Nephtys hombergii (Phyllodocida, Polychaeta) associated with environmental factors in a highly fluctuating ecosystem Journal Article Journal of the Marine Biological Association of the United Kingdom, 98 (4), pp. 777–789, 2018, ISSN: 00253154, (Publisher: Cambridge University Press). @article{vasileiadou_genetic_2018, title = {Genetic diversity of Nephtys hombergii (Phyllodocida, Polychaeta) associated with environmental factors in a highly fluctuating ecosystem}, author = {K Vasileiadou and C Pavloudi and F Camisa and I Tsikopoulou and N Fragopoulou and G Kotoulas and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85009786126&doi=10.1017%2fS0025315416001910&partnerID=40&md5=8e7cb2651bd57afe644615018866185a}, doi = {10.1017/S0025315416001910}, issn = {00253154}, year = {2018}, date = {2018-01-01}, journal = {Journal of the Marine Biological Association of the United Kingdom}, volume = {98}, number = {4}, pages = {777--789}, abstract = {Genetic diversity and population distribution are influenced by environmental factors, yet information is scarce on the interrelations that define dispersal of populations. Transitional water ecosystems are hosting habitats with temporally and spatially variable conditions, which make them very useful in understanding the mechanisms affecting population establishment. For the study, seasonal samples were collected from four lagoons in the lagoonal complex of Amvrakikos Gulf (W Greece). The mitochondrial DNA (COI gene) was analysed from polychaetes of Nephtys hombergii, as it is considered an important component of these assemblages and shows great dispersal ability. The results of the genetic analysis showed intraspecific variability in all the lagoons, with genetic structuring tending to follow a seasonal pattern rather than a spatial one. The results of BIOENV analysis indicated correlation of the observed pattern with the water pH levels, the redox potential and the concentration of phosphate in the sediment. The complexity of the network suggested the enhancement of the local population with more recently established haplotypes. The findings of the study support the necessity of designing management strategies by taking into account genetic diversity and population demography approaches in addition to those based on species and habitats. © Copyright Marine Biological Association of the United Kingdom 2017.}, note = {Publisher: Cambridge University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } Genetic diversity and population distribution are influenced by environmental factors, yet information is scarce on the interrelations that define dispersal of populations. Transitional water ecosystems are hosting habitats with temporally and spatially variable conditions, which make them very useful in understanding the mechanisms affecting population establishment. For the study, seasonal samples were collected from four lagoons in the lagoonal complex of Amvrakikos Gulf (W Greece). The mitochondrial DNA (COI gene) was analysed from polychaetes of Nephtys hombergii, as it is considered an important component of these assemblages and shows great dispersal ability. The results of the genetic analysis showed intraspecific variability in all the lagoons, with genetic structuring tending to follow a seasonal pattern rather than a spatial one. The results of BIOENV analysis indicated correlation of the observed pattern with the water pH levels, the redox potential and the concentration of phosphate in the sediment. The complexity of the network suggested the enhancement of the local population with more recently established haplotypes. The findings of the study support the necessity of designing management strategies by taking into account genetic diversity and population demography approaches in addition to those based on species and habitats. © Copyright Marine Biological Association of the United Kingdom 2017. |
Tsiola, A; Toncelli, C; Fodelianakis, S; Michoud, G; Bucheli, T D; Gavriilidou, A; Kagiorgi, M; Kalantzi, I; Knauer, K; Kotoulas, G; Mylona, K; Papadopoulou, E; Psarra, S; Santi, I; Tsapakis, M; Daffonchio, D; Pergantis, S A; Pitta, P Low-dose addition of silver nanoparticles stresses marine plankton communities Journal Article Environmental Science: Nano, 5 (8), pp. 1965–1980, 2018, ISSN: 20518153, (Publisher: Royal Society of Chemistry). @article{tsiola_low-dose_2018, title = {Low-dose addition of silver nanoparticles stresses marine plankton communities}, author = {A Tsiola and C Toncelli and S Fodelianakis and G Michoud and T D Bucheli and A Gavriilidou and M Kagiorgi and I Kalantzi and K Knauer and G Kotoulas and K Mylona and E Papadopoulou and S Psarra and I Santi and M Tsapakis and D Daffonchio and S A Pergantis and P Pitta}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85051542012&doi=10.1039%2fc8en00195b&partnerID=40&md5=fbfca29c271ba8fddfd015137b66c273}, doi = {10.1039/c8en00195b}, issn = {20518153}, year = {2018}, date = {2018-01-01}, journal = {Environmental Science: Nano}, volume = {5}, number = {8}, pages = {1965--1980}, abstract = {The release of silver nanoparticles (AgNPs) is expected to rise in the near future, with possible negative effects on aquatic life and enhancement of microbial resistance against AgNPs. However, a realistic evaluation of the toxicity of AgNPs to the marine ecosystem is currently missing. Therefore, we designed a mesocosm experiment to assess the impact of AgNP exposure on natural microbial plankton community dynamics in a coastal marine site at environmentally relevant concentrations. We monitored changes in the composition of the planktonic community, from viruses to protists. Further, we analyzed the concentration and properties of AgNPs for the total time of exposure. We found that the addition of AgNPs even at a low dose affected the plankton communities. Specifically, the growth of Synechococcus was inhibited and bacterial community composition significantly changed. Additionally, the amount of a lysogeny-related gene increased and viral auxiliary metabolic genes that are involved in cyanobacterial photosynthesis decreased, revealing a damaged photosynthetic potential after AgNP exposure. Microbial plankton was significantly affected due to both increased dissolved silver ions and decreased AgNP size. Our results highlight that the release of AgNPs alters the functioning of the marine food web by hampering important viral and bacterial processes. © The Royal Society of Chemistry.}, note = {Publisher: Royal Society of Chemistry}, keywords = {}, pubstate = {published}, tppubtype = {article} } The release of silver nanoparticles (AgNPs) is expected to rise in the near future, with possible negative effects on aquatic life and enhancement of microbial resistance against AgNPs. However, a realistic evaluation of the toxicity of AgNPs to the marine ecosystem is currently missing. Therefore, we designed a mesocosm experiment to assess the impact of AgNP exposure on natural microbial plankton community dynamics in a coastal marine site at environmentally relevant concentrations. We monitored changes in the composition of the planktonic community, from viruses to protists. Further, we analyzed the concentration and properties of AgNPs for the total time of exposure. We found that the addition of AgNPs even at a low dose affected the plankton communities. Specifically, the growth of Synechococcus was inhibited and bacterial community composition significantly changed. Additionally, the amount of a lysogeny-related gene increased and viral auxiliary metabolic genes that are involved in cyanobacterial photosynthesis decreased, revealing a damaged photosynthetic potential after AgNP exposure. Microbial plankton was significantly affected due to both increased dissolved silver ions and decreased AgNP size. Our results highlight that the release of AgNPs alters the functioning of the marine food web by hampering important viral and bacterial processes. © The Royal Society of Chemistry. |
Bounas, A; Tsaparis, D; Efrat, R; Gradev, G; Gustin, M; Mikulic, K; Rodríguez, A; Sarà, M; Kotoulas, G; Sotiropoulos, K Genetic structure of a patchily distributed philopatric migrant: Implications for management and conservation Journal Article Biological Journal of the Linnean Society, 124 (4), pp. 633–644, 2018, ISSN: 00244066, (Publisher: Oxford University Press). @article{bounas_genetic_2018, title = {Genetic structure of a patchily distributed philopatric migrant: Implications for management and conservation}, author = {A Bounas and D Tsaparis and R Efrat and G Gradev and M Gustin and K Mikulic and A Rodríguez and M Sarà and G Kotoulas and K Sotiropoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85047856934&doi=10.1093%2fbiolinnean%2fbly073&partnerID=40&md5=9d0888f5ed006f4f62c6383a965fbe40}, doi = {10.1093/biolinnean/bly073}, issn = {00244066}, year = {2018}, date = {2018-01-01}, journal = {Biological Journal of the Linnean Society}, volume = {124}, number = {4}, pages = {633--644}, abstract = {Significant demographic fluctuations can have major genetic consequences in wild populations. The lesser kestrel (Falco naumanni) has suffered both population declines and range fragmentation during the second half of the 20th century. In this study we analysed multilocus microsatellite data to assess the genetic structure of the species. Our analysis revealed significant genetic structuring of lesser kestrel populations, not only at the cross-continental scale, but also regionally within the Central and Eastern (CE) Mediterranean region. We detected signs of genetic bottlenecks in some of the peripheral populations coupled with small effective population sizes. Values of genetic differentiation among the largest populations were low, albeit significant, whereas the small peripheral CE Mediterranean populations showed higher levels of differentiation from all other populations. Gene flow levels were relatively low among the discontinuously distributed populations of the CE Mediterranean region. We argue that the observed spatial genetic structure can be attributed at some level to the past demographic decline experienced by the species. Finally, we identify management units in the region, and inform the design of conservation actions aimed at the increase of population sizes and dispersal rates among peripheral populations. © 2018 The Linnean Society of London, Biological Journal of the Linnean Society.}, note = {Publisher: Oxford University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } Significant demographic fluctuations can have major genetic consequences in wild populations. The lesser kestrel (Falco naumanni) has suffered both population declines and range fragmentation during the second half of the 20th century. In this study we analysed multilocus microsatellite data to assess the genetic structure of the species. Our analysis revealed significant genetic structuring of lesser kestrel populations, not only at the cross-continental scale, but also regionally within the Central and Eastern (CE) Mediterranean region. We detected signs of genetic bottlenecks in some of the peripheral populations coupled with small effective population sizes. Values of genetic differentiation among the largest populations were low, albeit significant, whereas the small peripheral CE Mediterranean populations showed higher levels of differentiation from all other populations. Gene flow levels were relatively low among the discontinuously distributed populations of the CE Mediterranean region. We argue that the observed spatial genetic structure can be attributed at some level to the past demographic decline experienced by the species. Finally, we identify management units in the region, and inform the design of conservation actions aimed at the increase of population sizes and dispersal rates among peripheral populations. © 2018 The Linnean Society of London, Biological Journal of the Linnean Society. |
Bounas, A; Tsaparis, D; Gustin, M; Mikulic, K; Sarà, M; Kotoulas, G; Sotiropoulos, K Using genetic markers to unravel the origin of birds converging towards pre-migratory sites Journal Article Scientific Reports, 8 (1), 2018, ISSN: 20452322, (Publisher: Nature Publishing Group). @article{bounas_using_2018, title = {Using genetic markers to unravel the origin of birds converging towards pre-migratory sites}, author = {A Bounas and D Tsaparis and M Gustin and K Mikulic and M Sarà and G Kotoulas and K Sotiropoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85047852224&doi=10.1038%2fs41598-018-26669-x&partnerID=40&md5=8e2ef459ac38098f966dd8cf2ad04369}, doi = {10.1038/s41598-018-26669-x}, issn = {20452322}, year = {2018}, date = {2018-01-01}, journal = {Scientific Reports}, volume = {8}, number = {1}, abstract = {Identifying patterns of individual movements in spatial and temporal scales can provide valuable insight into the structure of populations and the dynamics of communities and ecosystems. Especially for migrating birds, that can face a variety of unfavorable conditions along their journey, resolving movements of individuals across their annual cycle is necessary in order to design better targeted conservation strategies. Here, we studied the movements of a small migratory falcon, the Lesser Kestrel (Falco naumanni), by genetically assigning feathers from individuals of unknown origin that concentrate in large roosts during the pre-migratory period. Our findings suggest that birds from multiple breeding populations in the Central and Eastern Mediterranean region move towards two pre-migratory sites in the Balkans, some of them detouring greatly from their expected flyways, travelling more than 500 km to reach these sites and prepare for the post-nuptial migration. By identifying the origin of individuals using the pre-migratory sites, not only we provide a better understanding of the possible impact of local threats at these sites on multiple breeding populations but also inform the design of effective conservation actions for the species. © 2018 The Author(s).}, note = {Publisher: Nature Publishing Group}, keywords = {}, pubstate = {published}, tppubtype = {article} } Identifying patterns of individual movements in spatial and temporal scales can provide valuable insight into the structure of populations and the dynamics of communities and ecosystems. Especially for migrating birds, that can face a variety of unfavorable conditions along their journey, resolving movements of individuals across their annual cycle is necessary in order to design better targeted conservation strategies. Here, we studied the movements of a small migratory falcon, the Lesser Kestrel (Falco naumanni), by genetically assigning feathers from individuals of unknown origin that concentrate in large roosts during the pre-migratory period. Our findings suggest that birds from multiple breeding populations in the Central and Eastern Mediterranean region move towards two pre-migratory sites in the Balkans, some of them detouring greatly from their expected flyways, travelling more than 500 km to reach these sites and prepare for the post-nuptial migration. By identifying the origin of individuals using the pre-migratory sites, not only we provide a better understanding of the possible impact of local threats at these sites on multiple breeding populations but also inform the design of effective conservation actions for the species. © 2018 The Author(s). |
2017 |
Moitinho-Silva, Lucas; Nielsen, Shaun; Amir, Amnon; Gonzalez, Antonio; Ackermann, Gail L; Cerrano, Carlo; Astudillo-Garcia, Carmen; Easson, Cole; Sipkema, Detmer; Liu, Fang; Steinert, Georg; Kotoulas, Giorgos; McCormack, Grace P; Feng, Guofang; Bell, James J; Vicente, Jan; Björk, Johannes R; Montoya, Jose M; Olson, Julie B; Reveillaud, Julie; Steindler, Laura; Pineda, Mari-Carmen; Marra, Maria V; Ilan, Micha; Taylor, Michael W; Polymenakou, Paraskevi; Erwin, Patrick M; Schupp, Peter J; Simister, Rachel L; Knight, Rob; Thacker, Robert W; Costa, Rodrigo; Hill, Russell T; Lopez-Legentil, Susanna; Dailianis, Thanos; Ravasi, Timothy; Hentschel, Ute; Li, Zhiyong; Webster, Nicole S; Thomas, Torsten The sponge microbiome project Journal Article GigaScience, 6 (10), pp. gix077, 2017, ISSN: 2047-217X. @article{moitinho-silva_sponge_2017, title = {The sponge microbiome project}, author = {Lucas Moitinho-Silva and Shaun Nielsen and Amnon Amir and Antonio Gonzalez and Gail L Ackermann and Carlo Cerrano and Carmen Astudillo-Garcia and Cole Easson and Detmer Sipkema and Fang Liu and Georg Steinert and Giorgos Kotoulas and Grace P McCormack and Guofang Feng and James J Bell and Jan Vicente and Johannes R Björk and Jose M Montoya and Julie B Olson and Julie Reveillaud and Laura Steindler and Mari-Carmen Pineda and Maria V Marra and Micha Ilan and Michael W Taylor and Paraskevi Polymenakou and Patrick M Erwin and Peter J Schupp and Rachel L Simister and Rob Knight and Robert W Thacker and Rodrigo Costa and Russell T Hill and Susanna Lopez-Legentil and Thanos Dailianis and Timothy Ravasi and Ute Hentschel and Zhiyong Li and Nicole S Webster and Torsten Thomas}, url = {https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/gix077/4082886}, doi = {10.1093/gigascience/gix077}, issn = {2047-217X}, year = {2017}, date = {2017-10-01}, urldate = {2020-08-09}, journal = {GigaScience}, volume = {6}, number = {10}, pages = {gix077}, abstract = {Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 269 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with a) a standard protocol using QIIME closed-reference picking resulting in 39,543 Operational Taxonomic Units (OTU) at 97% sequence identity, b) a de novo protocol using Mothur resulting in 518,246 OTUs, and c) a new high-resolution Deblur protocol resulting in 83,908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host-specificity, convergent evolution, environmental drivers of microbiome structure and the sponge-associated rare biosphere.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 269 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with a) a standard protocol using QIIME closed-reference picking resulting in 39,543 Operational Taxonomic Units (OTU) at 97% sequence identity, b) a de novo protocol using Mothur resulting in 518,246 OTUs, and c) a new high-resolution Deblur protocol resulting in 83,908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host-specificity, convergent evolution, environmental drivers of microbiome structure and the sponge-associated rare biosphere. |
Antoniou, A; Kasapidis, P; Kotoulas, G; Mylonas, C C; Magoulas, A Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: Insights from genome-wide SNPs and microsatellites Journal Article Journal of Biological Research-Thessaloniki, 24 (1), pp. 3, 2017. @article{antoniou_genetic_2017, title = {Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: Insights from genome-wide SNPs and microsatellites}, author = {A Antoniou and P Kasapidis and G Kotoulas and C C Mylonas and A Magoulas}, doi = {10.1186/s40709-017-0062-2}, year = {2017}, date = {2017-01-01}, journal = {Journal of Biological Research-Thessaloniki}, volume = {24}, number = {1}, pages = {3}, abstract = {© The Author(s) 2017. Background: Elucidating the patterns of the Atlantic Bluefin tuna [ABFT, Thunnus thynnus (Linnaeus, 1758)] population structure constitutes a challenging task of great importance. Most of the unique challenges stem from its biology, as well as the attributes of the marine realm in which it disperses. Accurate information is urgently needed for stock assessment, and the identification of critical features to the persistence and adaptation of populations in order to formulate and adopt effective strategies for ABFT conservation and management. Conclusions of a great number of ABFT genetic studies on the Mediterranean Sea stock structure are rather controversial and not yet conclusive. In this study, ABFT genomic diversity was investigated in the Mediterranean Sea, which is the most important area for the species' reproduction. Results: Analyzing genome-wide SNPs and microsatellites from ABFT samples collected throughout the Mediterranean Sea did not provide strong evidence of genetic structure, pointing towards the existence of a single panmictic unit. An alternative view would recognize a failure to reject the null hypothesis of a panmictic unit as an effect of the study's sampling design, the type of markers used, and the effectiveness/suitability of analysis methods in respect to the species biological characteristics or any combination of the above. Conclusions: Unravelling the drivers of ABFT population diversity would require the consideration of important aspects of the species spawning behavior for the determination of the appropriate sampling design. Novel approaches and methods of analysis that will bring together experts in genetics/-omics, ecology and oceanography are deemed necessary. Analyzing ABFT genetic data under the discipline of seascape genetics could provide the analysis framework under which major abiotic and biotic forces controlling ABFT recruitment could be identified, elucidating the complicated population dynamics of the species, while multiple and continuous fisheries monitoring should in all cases be considered as a prerequisite in order to achieve efficient and long-term ABFT conservation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } © The Author(s) 2017. Background: Elucidating the patterns of the Atlantic Bluefin tuna [ABFT, Thunnus thynnus (Linnaeus, 1758)] population structure constitutes a challenging task of great importance. Most of the unique challenges stem from its biology, as well as the attributes of the marine realm in which it disperses. Accurate information is urgently needed for stock assessment, and the identification of critical features to the persistence and adaptation of populations in order to formulate and adopt effective strategies for ABFT conservation and management. Conclusions of a great number of ABFT genetic studies on the Mediterranean Sea stock structure are rather controversial and not yet conclusive. In this study, ABFT genomic diversity was investigated in the Mediterranean Sea, which is the most important area for the species' reproduction. Results: Analyzing genome-wide SNPs and microsatellites from ABFT samples collected throughout the Mediterranean Sea did not provide strong evidence of genetic structure, pointing towards the existence of a single panmictic unit. An alternative view would recognize a failure to reject the null hypothesis of a panmictic unit as an effect of the study's sampling design, the type of markers used, and the effectiveness/suitability of analysis methods in respect to the species biological characteristics or any combination of the above. Conclusions: Unravelling the drivers of ABFT population diversity would require the consideration of important aspects of the species spawning behavior for the determination of the appropriate sampling design. Novel approaches and methods of analysis that will bring together experts in genetics/-omics, ecology and oceanography are deemed necessary. Analyzing ABFT genetic data under the discipline of seascape genetics could provide the analysis framework under which major abiotic and biotic forces controlling ABFT recruitment could be identified, elucidating the complicated population dynamics of the species, while multiple and continuous fisheries monitoring should in all cases be considered as a prerequisite in order to achieve efficient and long-term ABFT conservation. |
Pavloudi, C; Oulas, A; Vasileiadou, K; Kotoulas, G; Troch, De M; Friedrich, M W; Arvanitidis, C Aquatic Microbial Ecology, 79 (3), pp. 209–219, 2017, ISSN: 09483055, (Publisher: Inter-Research). @article{pavloudi_diversity_2017, title = {Diversity and abundance of sulfate-reducing microorganisms in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea) derived from dsrB gene}, author = {C Pavloudi and A Oulas and K Vasileiadou and G Kotoulas and M De Troch and M W Friedrich and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021092263&doi=10.3354%2fame01829&partnerID=40&md5=8be345d2d8f932cc9b640cf2072c2bb0}, doi = {10.3354/ame01829}, issn = {09483055}, year = {2017}, date = {2017-01-01}, journal = {Aquatic Microbial Ecology}, volume = {79}, number = {3}, pages = {209--219}, abstract = {Sulfate-reducing microorganisms (SRMs) are a phylogenetically and physiologically diverse group of microorganisms, responsible for the dissimilatory reduction of sulfate. SRMs thrive under anaerobic conditions with high availability of organic matter. Such conditions characterize lagoonal ecosystems which experience regular dystrophic crises. The aim of the present study was to explore the biodiversity patterns of SRMs and to examine the extent to which these patterns are associated with biogeographic and environmental factors. Sediment samples were collected from 5 lagoons in the Amvrakikos Gulf (Ionian Sea, western Greece). DNA was extracted from the sediment and was further processed through pyrosequencing of a region of the dissimilatory sulfite reductase β-subunit (dsrB). The results of this exploratory study show that the majority of the observed operational taxonomic units (OTUs) belong to the Deltaproteobacteria supercluster and more specifically, to the Desulfobacteraceae family. Salinity and ammonium ions are the environmental factors that best correlated with the SRM community pattern. Furthermore, the SRM community of the brackish lagoons is differentiated from that of the brackish-marine lagoons and the studied lagoons have distinct SRM communities. © Inter-Research 2017.}, note = {Publisher: Inter-Research}, keywords = {}, pubstate = {published}, tppubtype = {article} } Sulfate-reducing microorganisms (SRMs) are a phylogenetically and physiologically diverse group of microorganisms, responsible for the dissimilatory reduction of sulfate. SRMs thrive under anaerobic conditions with high availability of organic matter. Such conditions characterize lagoonal ecosystems which experience regular dystrophic crises. The aim of the present study was to explore the biodiversity patterns of SRMs and to examine the extent to which these patterns are associated with biogeographic and environmental factors. Sediment samples were collected from 5 lagoons in the Amvrakikos Gulf (Ionian Sea, western Greece). DNA was extracted from the sediment and was further processed through pyrosequencing of a region of the dissimilatory sulfite reductase β-subunit (dsrB). The results of this exploratory study show that the majority of the observed operational taxonomic units (OTUs) belong to the Deltaproteobacteria supercluster and more specifically, to the Desulfobacteraceae family. Salinity and ammonium ions are the environmental factors that best correlated with the SRM community pattern. Furthermore, the SRM community of the brackish lagoons is differentiated from that of the brackish-marine lagoons and the studied lagoons have distinct SRM communities. © Inter-Research 2017. |
Sarropoulou, E; Sundaram, A Y M; Kaitetzidou, E; Kotoulas, G; Gilfillan, G D; Papandroulakis, N; Mylonas, C C; Magoulas, A Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili Journal Article GigaScience, 6 (12), pp. 1–13, 2017, ISSN: 2047217X, (Publisher: Oxford University Press). @article{sarropoulou_full_2017, title = {Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili}, author = {E Sarropoulou and A Y M Sundaram and E Kaitetzidou and G Kotoulas and G D Gilfillan and N Papandroulakis and C C Mylonas and A Magoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85042364258&doi=10.1093%2fgigascience%2fgix108&partnerID=40&md5=fa6e269b1e6ff57a26c0c9c6efe45226}, doi = {10.1093/gigascience/gix108}, issn = {2047217X}, year = {2017}, date = {2017-01-01}, journal = {GigaScience}, volume = {6}, number = {12}, pages = {1--13}, abstract = {Background: Teleosts of the genus Seriola, commonly known as amberjacks, are of high commercial value in international markets due to their flesh quality and worldwide distribution. The Seriola species of interest to Mediterranean aquaculture is the greater amberjack (Seriola dumerili). This species holds great potential for the aquaculture industry, but in captivity, reproduction has proved to be challenging, and observed growth dysfunction hinders their domestication. Insights into molecular mechanisms may contribute to a better understanding of traits like growth and sex, but investigations to unravel the molecular background of amberjacks have begun only recently. Findings: Illumina HiSeq sequencing generated a high-coverage greater amberjack genome sequence comprising 45 909 scaffolds. Comparative mapping to the Japanese yellowtail (Seriola quinqueriadiata) and to the model species medaka (Oryzias latipes) allowed the generation of in silico groups. Additional gonad transcriptome sequencing identified sex-biased transcripts, including known sex-determining and differentiation genes. Investigation of the muscle transcriptome of slow-growing individuals showed that transcripts involved in oxygen and gas transport were differentially expressed compared with fast/normal-growing individuals. On the other hand, transcripts involved in muscle functions were found to be enriched in fast/normal-growing individuals. Conclusion: The present study provides the first insights into the molecular background of male and female amberjacks and of fast- and slow-growing fish. Therefore, valuable molecular resources have been generated in the form of a first draft genome and a reference transcriptome. Sex-biased genes, which may also have roles in sex determination or differentiation, and genes that may be responsible for slow growth are suggested. © The Author(s) 2017.}, note = {Publisher: Oxford University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background: Teleosts of the genus Seriola, commonly known as amberjacks, are of high commercial value in international markets due to their flesh quality and worldwide distribution. The Seriola species of interest to Mediterranean aquaculture is the greater amberjack (Seriola dumerili). This species holds great potential for the aquaculture industry, but in captivity, reproduction has proved to be challenging, and observed growth dysfunction hinders their domestication. Insights into molecular mechanisms may contribute to a better understanding of traits like growth and sex, but investigations to unravel the molecular background of amberjacks have begun only recently. Findings: Illumina HiSeq sequencing generated a high-coverage greater amberjack genome sequence comprising 45 909 scaffolds. Comparative mapping to the Japanese yellowtail (Seriola quinqueriadiata) and to the model species medaka (Oryzias latipes) allowed the generation of in silico groups. Additional gonad transcriptome sequencing identified sex-biased transcripts, including known sex-determining and differentiation genes. Investigation of the muscle transcriptome of slow-growing individuals showed that transcripts involved in oxygen and gas transport were differentially expressed compared with fast/normal-growing individuals. On the other hand, transcripts involved in muscle functions were found to be enriched in fast/normal-growing individuals. Conclusion: The present study provides the first insights into the molecular background of male and female amberjacks and of fast- and slow-growing fish. Therefore, valuable molecular resources have been generated in the form of a first draft genome and a reference transcriptome. Sex-biased genes, which may also have roles in sex determination or differentiation, and genes that may be responsible for slow growth are suggested. © The Author(s) 2017. |
2016 |
Pavloudi, C; Oulas, A; Vasileiadou, K; Sarropoulou, E; Kotoulas, G; Arvanitidis, C Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea) Journal Article Marine Genomics, 28 , pp. 71–81, 2016, ISSN: 18747787, (Publisher: Elsevier B.V.). @article{pavloudi_salinity_2016, title = {Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea)}, author = {C Pavloudi and A Oulas and K Vasileiadou and E Sarropoulou and G Kotoulas and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84955611416&doi=10.1016%2fj.margen.2016.01.005&partnerID=40&md5=a226c6872c0a3044831db4a1b5f65ca3}, doi = {10.1016/j.margen.2016.01.005}, issn = {18747787}, year = {2016}, date = {2016-01-01}, journal = {Marine Genomics}, volume = {28}, pages = {71--81}, abstract = {Lagoons are naturally enriched habitats, with unstable environmental conditions caused by their confinement, shallow depth and state of saprobity. The frequent fluctuations of the abiotic variables cause severe changes in the abundance and distribution of biota. This relationship has been studied extensively for the macrofaunal communities, but not sufficiently so for the bacterial ones. The aim of the present study was to explore the biodiversity patterns of bacterial assemblages and to examine whether these patterns are associated with biogeographic and environmental factors. For this purpose, sediment samples were collected from five lagoons located in the Amvrakikos Gulf (Ionian Sea, Western Greece). DNA was extracted from the sediment and was further processed through 16S rRNA pyrosequencing. The results of this exploratory study imply that salinity is the environmental factor best correlated with the bacterial community pattern, which has also been suggested in similar studies but for macrofaunal community patterns. In addition, the bacterial community of the brackish lagoons is differentiated from that of the brackish-marine lagoons. The findings of this study indicate that the studied lagoons have distinct bacterial communities. © 2016 Elsevier B.V.}, note = {Publisher: Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Lagoons are naturally enriched habitats, with unstable environmental conditions caused by their confinement, shallow depth and state of saprobity. The frequent fluctuations of the abiotic variables cause severe changes in the abundance and distribution of biota. This relationship has been studied extensively for the macrofaunal communities, but not sufficiently so for the bacterial ones. The aim of the present study was to explore the biodiversity patterns of bacterial assemblages and to examine whether these patterns are associated with biogeographic and environmental factors. For this purpose, sediment samples were collected from five lagoons located in the Amvrakikos Gulf (Ionian Sea, Western Greece). DNA was extracted from the sediment and was further processed through 16S rRNA pyrosequencing. The results of this exploratory study imply that salinity is the environmental factor best correlated with the bacterial community pattern, which has also been suggested in similar studies but for macrofaunal community patterns. In addition, the bacterial community of the brackish lagoons is differentiated from that of the brackish-marine lagoons. The findings of this study indicate that the studied lagoons have distinct bacterial communities. © 2016 Elsevier B.V. |
Oulas, Anastasis; Polymenakou, Paraskevi N; Seshadri, Rekha; Tripp, James H; Mandalakis, Manolis; Paez-Espino, David A; Pati, Amrita; Chain, Patrick; Nomikou, Paraskevi; Carey, Steven; Kilias, Stephanos; Christakis, Christos; Kotoulas, Georgios; Magoulas, Antonios; Ivanova, Natalia N; Kyrpides, Nikos C Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology. Journal Article Environmental Microbiology, 18 (4), pp. 1122–1136, 2016, ISSN: 1462-2920. @article{oulas_metagenomic_2016, title = {Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology.}, author = {Anastasis Oulas and Paraskevi N Polymenakou and Rekha Seshadri and James H Tripp and Manolis Mandalakis and David A Paez-Espino and Amrita Pati and Patrick Chain and Paraskevi Nomikou and Steven Carey and Stephanos Kilias and Christos Christakis and Georgios Kotoulas and Antonios Magoulas and Natalia N Ivanova and Nikos C Kyrpides}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26487573}, doi = {10.1111/1462-2920.13095}, issn = {1462-2920}, year = {2016}, date = {2016-01-01}, journal = {Environmental Microbiology}, volume = {18}, number = {4}, pages = {1122--1136}, abstract = {Hydrothermal vents represent a deep, hot, aphotic biosphere where chemosynthetic primary producers, fuelled by chemicals from Earth's subsurface, form the basis of life. In this study, we examined microbial mats from two distinct volcanic sites within the Hellenic Volcanic Arc (HVA). The HVA is geologically and ecologically unique, with reported emissions of CO2 -saturated fluids at temperatures up to 220°C and a notable absence of macrofauna. Metagenomic data reveals highly complex prokaryotic communities composed of chemolithoautotrophs, some methanotrophs, and to our surprise, heterotrophs capable of anaerobic degradation of aromatic hydrocarbons. Our data suggest that aromatic hydrocarbons may indeed be a significant source of carbon in these sites, and instigate additional research into the nature and origin of these compounds in the HVA. Novel physiology was assigned to several uncultured prokaryotic lineages; most notably, a SAR406 representative is attributed with a role in anaerobic hydrocarbon degradation. This dataset, the largest to date from submarine volcanic ecosystems, constitutes a significant resource of novel genes and pathways with potential biotechnological applications.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Hydrothermal vents represent a deep, hot, aphotic biosphere where chemosynthetic primary producers, fuelled by chemicals from Earth's subsurface, form the basis of life. In this study, we examined microbial mats from two distinct volcanic sites within the Hellenic Volcanic Arc (HVA). The HVA is geologically and ecologically unique, with reported emissions of CO2 -saturated fluids at temperatures up to 220°C and a notable absence of macrofauna. Metagenomic data reveals highly complex prokaryotic communities composed of chemolithoautotrophs, some methanotrophs, and to our surprise, heterotrophs capable of anaerobic degradation of aromatic hydrocarbons. Our data suggest that aromatic hydrocarbons may indeed be a significant source of carbon in these sites, and instigate additional research into the nature and origin of these compounds in the HVA. Novel physiology was assigned to several uncultured prokaryotic lineages; most notably, a SAR406 representative is attributed with a role in anaerobic hydrocarbon degradation. This dataset, the largest to date from submarine volcanic ecosystems, constitutes a significant resource of novel genes and pathways with potential biotechnological applications. |
Vasileiadou, K; Pavloudi, C; Sarropoulou, E; Fragopoulou, N; Kotoulas, G; Arvanitidis, C Unique COI haplotypes in hediste diversicolor populations in lagoons adjoining the Ionian Sea Journal Article Aquatic Biology, 25 , pp. 7–15, 2016, ISSN: 18647782, (Publisher: Inter-Research). @article{vasileiadou_unique_2016, title = {Unique COI haplotypes in hediste diversicolor populations in lagoons adjoining the Ionian Sea}, author = {K Vasileiadou and C Pavloudi and E Sarropoulou and N Fragopoulou and G Kotoulas and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84971596901&doi=10.3354%2fab00654&partnerID=40&md5=4039a8b37d89de3fef4adb17862554df}, doi = {10.3354/ab00654}, issn = {18647782}, year = {2016}, date = {2016-01-01}, journal = {Aquatic Biology}, volume = {25}, pages = {7--15}, abstract = {The present study examines the genetic diversity (using cytochrome c oxidase subunit I [COI] haplotypes) of polychaete Hediste diversicolor populations in the Amvrakikos Gulf (western Greece) in order to test Cognetti’s hypothesis on the formation of distinct isolated populations of species living in stressed transitional water habitats. To this purpose, the intraspecific diversity of H. diversicolor and the similarities among its populations in the brackish water habitats of the Eastern Mediterranean were investigated. Samples were collected from the lagoonal complex of Am - vrakikos Gulf in 2010 and 2011. Analysis showed that populations in the Amvrakikos Gulf share unique haplotypes which are distinct from the haplotypes hitherto reported, suggesting that these populations are highly isolated. This evidence partially supports Cognetti’s hypothesis. The results indicate that the genetic differentiation in the studied populations was probably caused by the complete isolation of the gulf and periodic hypoxic conditions during its formation history. The occurrence of unique haplotypes in the gulf underlines the importance of considering genetic diversity in the design of long-term biodiversity management and conservation plans. © The authors 2016.}, note = {Publisher: Inter-Research}, keywords = {}, pubstate = {published}, tppubtype = {article} } The present study examines the genetic diversity (using cytochrome c oxidase subunit I [COI] haplotypes) of polychaete Hediste diversicolor populations in the Amvrakikos Gulf (western Greece) in order to test Cognetti’s hypothesis on the formation of distinct isolated populations of species living in stressed transitional water habitats. To this purpose, the intraspecific diversity of H. diversicolor and the similarities among its populations in the brackish water habitats of the Eastern Mediterranean were investigated. Samples were collected from the lagoonal complex of Am - vrakikos Gulf in 2010 and 2011. Analysis showed that populations in the Amvrakikos Gulf share unique haplotypes which are distinct from the haplotypes hitherto reported, suggesting that these populations are highly isolated. This evidence partially supports Cognetti’s hypothesis. The results indicate that the genetic differentiation in the studied populations was probably caused by the complete isolation of the gulf and periodic hypoxic conditions during its formation history. The occurrence of unique haplotypes in the gulf underlines the importance of considering genetic diversity in the design of long-term biodiversity management and conservation plans. © The authors 2016. |
Davies, N; Field, D; Gavaghan, D; Holbrook, S J; Planes, S; Troyer, M; Bonsall, M; Claudet, J; Roderick, G; Schmitt, R J; Zettler, L A; Berteaux, V; Bossin, H C; Cabasse, C; Collin, A; Deck, J; Dell, T; Dunne, J; Gates, R; Harfoot, M; Hench, J L; Hopuare, M; Kirch, P; Kotoulas, G; Kosenkov, A; Kusenko, A; Leichter, J J; Lenihan, H; Magoulas, A; Martinez, N; Meyer, C; Stoll, B; Swalla, B; Tartakovsky, D M; Murphy, H T; Turyshev, S; Valdvinos, F; Williams, R; Wood, S Simulating social-ecological systems: The Island Digital Ecosystem Avatars (IDEA) consortium Journal Article GigaScience, 5 (1), 2016, ISSN: 2047217X, (Publisher: BioMed Central Ltd.). @article{davies_simulating_2016, title = {Simulating social-ecological systems: The Island Digital Ecosystem Avatars (IDEA) consortium}, author = {N Davies and D Field and D Gavaghan and S J Holbrook and S Planes and M Troyer and M Bonsall and J Claudet and G Roderick and R J Schmitt and L A Zettler and V Berteaux and H C Bossin and C Cabasse and A Collin and J Deck and T Dell and J Dunne and R Gates and M Harfoot and J L Hench and M Hopuare and P Kirch and G Kotoulas and A Kosenkov and A Kusenko and J J Leichter and H Lenihan and A Magoulas and N Martinez and C Meyer and B Stoll and B Swalla and D M Tartakovsky and H T Murphy and S Turyshev and F Valdvinos and R Williams and S Wood}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84991529168&doi=10.1186%2fs13742-016-0118-5&partnerID=40&md5=8cee8d8941e5eaf5d39db97438c349a6}, doi = {10.1186/s13742-016-0118-5}, issn = {2047217X}, year = {2016}, date = {2016-01-01}, journal = {GigaScience}, volume = {5}, number = {1}, abstract = {Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine-terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions. © 2016 Davies et al.}, note = {Publisher: BioMed Central Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine-terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions. © 2016 Davies et al. |
Rizzo, A L; Caracausi, A; Chavagnac, V; Nomikou, P; Polymenakou, P N; Mandalakis, M; Kotoulas, G; Magoulas, A; Castillo, A; Lampridou, D Kolumbo submarine volcano (Greece): An active window into the Aegean subduction system Journal Article Scientific Reports, 6 , 2016, ISSN: 20452322, (Publisher: Nature Publishing Group). @article{rizzo_kolumbo_2016, title = {Kolumbo submarine volcano (Greece): An active window into the Aegean subduction system}, author = {A L Rizzo and A Caracausi and V Chavagnac and P Nomikou and P N Polymenakou and M Mandalakis and G Kotoulas and A Magoulas and A Castillo and D Lampridou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84975454736&doi=10.1038%2fsrep28013&partnerID=40&md5=e24dc2fa03414abaf410e586529f758d}, doi = {10.1038/srep28013}, issn = {20452322}, year = {2016}, date = {2016-01-01}, journal = {Scientific Reports}, volume = {6}, abstract = {Submarine volcanism represents ∼80% of the volcanic activity on Earth and is an important source of mantle-derived gases. These gases are of basic importance for the comprehension of mantle characteristics in areas where subaerial volcanism is missing or strongly modified by the presence of crustal/atmospheric components. Though, the study of submarine volcanism remains a challenge due to their hazardousness and sea-depth. Here, we report 3He/4He measurements in CO2-dominated gases discharged at 500 m below sea level from the high-temperature (∼220 °C) hydrothermal system of the Kolumbo submarine volcano (Greece), located 7 km northeast off Santorini Island in the central part of the Hellenic Volcanic Arc (HVA). We highlight that the mantle below Kolumbo and Santorini has a 3He/4He signature of at least 7.0 Ra (being Ra the 3He/4He ratio of atmospheric He equal to 1.39×10-6), 3 Ra units higher than actually known for gases-rocks from Santorini. This ratio is also the highest measured across the HVA and is indicative of the direct degassing of a Mid-Ocean-Ridge-Basalts (MORB)-like mantle through lithospheric faults. We finally highlight that the degassing of high-temperature fluids with a MORB-like 3He/4He ratio corroborates a vigorous outgassing of mantle-derived volatiles with potential hazard at the Kolumbo submarine volcano.}, note = {Publisher: Nature Publishing Group}, keywords = {}, pubstate = {published}, tppubtype = {article} } Submarine volcanism represents ∼80% of the volcanic activity on Earth and is an important source of mantle-derived gases. These gases are of basic importance for the comprehension of mantle characteristics in areas where subaerial volcanism is missing or strongly modified by the presence of crustal/atmospheric components. Though, the study of submarine volcanism remains a challenge due to their hazardousness and sea-depth. Here, we report 3He/4He measurements in CO2-dominated gases discharged at 500 m below sea level from the high-temperature (∼220 °C) hydrothermal system of the Kolumbo submarine volcano (Greece), located 7 km northeast off Santorini Island in the central part of the Hellenic Volcanic Arc (HVA). We highlight that the mantle below Kolumbo and Santorini has a 3He/4He signature of at least 7.0 Ra (being Ra the 3He/4He ratio of atmospheric He equal to 1.39×10-6), 3 Ra units higher than actually known for gases-rocks from Santorini. This ratio is also the highest measured across the HVA and is indicative of the direct degassing of a Mid-Ocean-Ridge-Basalts (MORB)-like mantle through lithospheric faults. We finally highlight that the degassing of high-temperature fluids with a MORB-like 3He/4He ratio corroborates a vigorous outgassing of mantle-derived volatiles with potential hazard at the Kolumbo submarine volcano. |
Bravakos, P; Kotoulas, G; Skaraki, K; Pantazidou, A; Economou-Amilli, A A polyphasic taxonomic approach in isolated strains of Cyanobacteria from thermal springs of Greece Journal Article Molecular Phylogenetics and Evolution, 98 , pp. 147–160, 2016, ISSN: 10557903, (Publisher: Academic Press Inc.). @article{bravakos_polyphasic_2016, title = {A polyphasic taxonomic approach in isolated strains of Cyanobacteria from thermal springs of Greece}, author = {P Bravakos and G Kotoulas and K Skaraki and A Pantazidou and A Economou-Amilli}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84959209388&doi=10.1016%2fj.ympev.2016.02.009&partnerID=40&md5=e4f85b36c7ffd4404af7ca17e083364e}, doi = {10.1016/j.ympev.2016.02.009}, issn = {10557903}, year = {2016}, date = {2016-01-01}, journal = {Molecular Phylogenetics and Evolution}, volume = {98}, pages = {147--160}, abstract = {Strains of Cyanobacteria isolated from mats of 9 thermal springs of Greece have been studied for their taxonomic evaluation. A polyphasic taxonomic approach was employed which included: morphological observations by light microscopy and scanning electron microscopy, maximum parsimony, maximum likelihood and Bayesian analysis of 16S rDNA sequences, secondary structural comparisons of 16S-23S rRNA Internal Transcribed Spacer sequences, and finally environmental data. The 17 cyanobacterial isolates formed a diverse group that contained filamentous, coccoid and heterocytous strains. These included representatives of the polyphyletic genera of Synechococcus and Phormidium, and the orders Oscillatoriales, Spirulinales, Chroococcales and Nostocales. After analysis, at least 6 new taxa at the genus level provide new evidence in the taxonomy of Cyanobacteria and highlight the abundant diversity of thermal spring environments with many potential endemic species or ecotypes. © 2016 Elsevier Inc.}, note = {Publisher: Academic Press Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Strains of Cyanobacteria isolated from mats of 9 thermal springs of Greece have been studied for their taxonomic evaluation. A polyphasic taxonomic approach was employed which included: morphological observations by light microscopy and scanning electron microscopy, maximum parsimony, maximum likelihood and Bayesian analysis of 16S rDNA sequences, secondary structural comparisons of 16S-23S rRNA Internal Transcribed Spacer sequences, and finally environmental data. The 17 cyanobacterial isolates formed a diverse group that contained filamentous, coccoid and heterocytous strains. These included representatives of the polyphyletic genera of Synechococcus and Phormidium, and the orders Oscillatoriales, Spirulinales, Chroococcales and Nostocales. After analysis, at least 6 new taxa at the genus level provide new evidence in the taxonomy of Cyanobacteria and highlight the abundant diversity of thermal spring environments with many potential endemic species or ecotypes. © 2016 Elsevier Inc. |
Sarropoulou, E; Tsalafouta, A; Sundaram, A Y M; Gilfillan, G D; Kotoulas, G; Papandroulakis, N; Pavlidis, M Transcriptomic changes in relation to early-life events in the gilthead sea bream (Sparus aurata) Journal Article BMC Genomics, 17 (1), 2016, ISSN: 14712164, (Publisher: BioMed Central Ltd.). @article{sarropoulou_transcriptomic_2016, title = {Transcriptomic changes in relation to early-life events in the gilthead sea bream (Sparus aurata)}, author = {E Sarropoulou and A Tsalafouta and A Y M Sundaram and G D Gilfillan and G Kotoulas and N Papandroulakis and M Pavlidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84984849269&doi=10.1186%2fs12864-016-2874-0&partnerID=40&md5=0cba8ed79f3200cb9be9e48551ecc2e7}, doi = {10.1186/s12864-016-2874-0}, issn = {14712164}, year = {2016}, date = {2016-01-01}, journal = {BMC Genomics}, volume = {17}, number = {1}, abstract = {Background: Teleosts are exposed to a broad range of external stimuli, which may be either of acute or chronic nature. The larval phase of certain fish species offer a unique opportunity to study the interactions between genes and environmental factors during early life. The present study investigates the effects of early-life events, applied at different time points of early ontogeny (first feeding, flexion and development of all fins; Phase 1) as well as on the subsequent juvenile stage after the application of an additional acute stressor (Phase 2) in the gilthead sea bream (Sparus aurata), a commercially important European aquaculture species. Animal performance, the cortisol response and gene expression patterns during early development as well as on the subsequent phases (juveniles) after the application of additional acute stressors were investigated. Results: Significant differences on fish performance were found only for juveniles exposed to early-life events at the phase of the formation of all fins. On the transcriptome level distinct expression patterns were obtained for larvae as well as for juveniles with the most divergent expression pattern found to be again at the phase of the development of all fins, which showed to have also an impact later on in the acute stress response of juveniles. Conclusions: The present study showed that applying an early-life protocol, characterized by the unpredictable, variable and moderate intensity of the applied stimuli provides a relative realistic model to evaluate the impact of daily aquaculture practices on fish performance. In addition, the power of investigating global gene expression patterns is shown, providing significant insights regarding the response of early-life events during development and as juveniles after the application of extra acute stressors. © 2016 The Author(s).}, note = {Publisher: BioMed Central Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background: Teleosts are exposed to a broad range of external stimuli, which may be either of acute or chronic nature. The larval phase of certain fish species offer a unique opportunity to study the interactions between genes and environmental factors during early life. The present study investigates the effects of early-life events, applied at different time points of early ontogeny (first feeding, flexion and development of all fins; Phase 1) as well as on the subsequent juvenile stage after the application of an additional acute stressor (Phase 2) in the gilthead sea bream (Sparus aurata), a commercially important European aquaculture species. Animal performance, the cortisol response and gene expression patterns during early development as well as on the subsequent phases (juveniles) after the application of additional acute stressors were investigated. Results: Significant differences on fish performance were found only for juveniles exposed to early-life events at the phase of the formation of all fins. On the transcriptome level distinct expression patterns were obtained for larvae as well as for juveniles with the most divergent expression pattern found to be again at the phase of the development of all fins, which showed to have also an impact later on in the acute stress response of juveniles. Conclusions: The present study showed that applying an early-life protocol, characterized by the unpredictable, variable and moderate intensity of the applied stimuli provides a relative realistic model to evaluate the impact of daily aquaculture practices on fish performance. In addition, the power of investigating global gene expression patterns is shown, providing significant insights regarding the response of early-life events during development and as juveniles after the application of extra acute stressors. © 2016 The Author(s). |
Kousteni, V; Kasapidis, P; Kotoulas, G; Megalofonou, P Evidence of high genetic connectivity for the longnose spurdog Squalus blainville in the Mediterranean Sea Journal Article Mediterranean Marine Science, 17 (2), pp. 371–383, 2016, ISSN: 1108393X, (Publisher: Hellenic Centre for Marine Research). @article{kousteni_evidence_2016, title = {Evidence of high genetic connectivity for the longnose spurdog Squalus blainville in the Mediterranean Sea}, author = {V Kousteni and P Kasapidis and G Kotoulas and P Megalofonou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85019545144&doi=10.12681%2fmms.1222&partnerID=40&md5=2e93879e948e1d3748c29224910104e5}, doi = {10.12681/mms.1222}, issn = {1108393X}, year = {2016}, date = {2016-01-01}, journal = {Mediterranean Marine Science}, volume = {17}, number = {2}, pages = {371--383}, abstract = {Squalus blainville is one of the least studied Mediterranean shark species. Despite being intensively fished in several locations, biological knowledge is limited and no genetic structure information is available. This is the first study to examine the genetic structure of S. blainville in the Mediterranean Sea. Considering the high dispersal potential inferred for other squalid sharks, the hypothesis of panmixia was tested based on a 585 bp fragment of the mitochondrial DNA cytochrome c oxidase subunit I gene from 107 individuals and six nuclear microsatellite loci from 577 individuals. Samples were collected across the Ionian, Aegean and Libyan Seas and off the Balearic Islands. Twenty three additional sequences of Mediterranean and South African origin were retrieved from GenBank and included in the mitochondrial DNA analysis. The overall haplotype diversity was high, in contrast to the low nucleotide diversity. Low and non-significant pairwise FST and FST values along with a Bayesian cluster analysis suggested high connectivity with subsequent genetic homogeneity among the populations studied, and thus a high dispersal potential for S. blainville similar to other squalids. The historical demography of the species was also assessed, revealing a pattern of population expansion since the middle Pleistocene. These findings could be considered in species-specific conservation plans, although sampling over a larger spatial scale and more genetic markers are required to fully elucidate the genetic structure and dispersal potential of S. blainville.}, note = {Publisher: Hellenic Centre for Marine Research}, keywords = {}, pubstate = {published}, tppubtype = {article} } Squalus blainville is one of the least studied Mediterranean shark species. Despite being intensively fished in several locations, biological knowledge is limited and no genetic structure information is available. This is the first study to examine the genetic structure of S. blainville in the Mediterranean Sea. Considering the high dispersal potential inferred for other squalid sharks, the hypothesis of panmixia was tested based on a 585 bp fragment of the mitochondrial DNA cytochrome c oxidase subunit I gene from 107 individuals and six nuclear microsatellite loci from 577 individuals. Samples were collected across the Ionian, Aegean and Libyan Seas and off the Balearic Islands. Twenty three additional sequences of Mediterranean and South African origin were retrieved from GenBank and included in the mitochondrial DNA analysis. The overall haplotype diversity was high, in contrast to the low nucleotide diversity. Low and non-significant pairwise FST and FST values along with a Bayesian cluster analysis suggested high connectivity with subsequent genetic homogeneity among the populations studied, and thus a high dispersal potential for S. blainville similar to other squalids. The historical demography of the species was also assessed, revealing a pattern of population expansion since the middle Pleistocene. These findings could be considered in species-specific conservation plans, although sampling over a larger spatial scale and more genetic markers are required to fully elucidate the genetic structure and dispersal potential of S. blainville. |
Rizzo, A L; Caracausi, A; Chavagnac, V; Nomikou, P; Polymenakou, P N; Mandalakis, M; Kotoulas, Georgios; Magoulas, A; Castillo, A Kolumbo active seamount (Greece): a window into the Aegean mantle Inproceedings Nancy, France, 2016, (Publication Title: DINGUE ⋕4, Developments in Noble Gas Understanding and Expertise). @inproceedings{rizzo_kolumbo_2016-1, title = {Kolumbo active seamount (Greece): a window into the Aegean mantle}, author = {A L Rizzo and A Caracausi and V Chavagnac and P Nomikou and P N Polymenakou and M Mandalakis and Georgios Kotoulas and A Magoulas and A Castillo}, year = {2016}, date = {2016-01-01}, address = {Nancy, France}, note = {Publication Title: DINGUE ⋕4, Developments in Noble Gas Understanding and Expertise}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
2015 |
Oulas, A; Pavloudi, C; Polymenakou, P; Pavlopoulos, G A; Papanikolaou, N; Kotoulas, G; Arvanitidis, C; Iliopoulos, I Metagenomics: Tools and insights for analyzing next-generation sequencing data derived from biodiversity studies Journal Article Bioinformatics and Biology Insights, 9 , pp. 75–88, 2015, ISSN: 11779322, (Publisher: Libertas Academica Ltd.). @article{oulas_metagenomics_2015, title = {Metagenomics: Tools and insights for analyzing next-generation sequencing data derived from biodiversity studies}, author = {A Oulas and C Pavloudi and P Polymenakou and G A Pavlopoulos and N Papanikolaou and G Kotoulas and C Arvanitidis and I Iliopoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84981483022&doi=10.4137%2fBBI.S12462&partnerID=40&md5=c1dbc4e466d691d4a86eecd6ba7d7a08}, doi = {10.4137/BBI.S12462}, issn = {11779322}, year = {2015}, date = {2015-01-01}, journal = {Bioinformatics and Biology Insights}, volume = {9}, pages = {75--88}, abstract = {Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of "metagenomics", often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards. © the authors.}, note = {Publisher: Libertas Academica Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of "metagenomics", often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards. © the authors. |
Kousteni, V; Kasapidis, P; Kotoulas, G; Megalofonou, P Heredity, 114 (3), pp. 333–343, 2015, ISSN: 0018067X, (Publisher: Nature Publishing Group). @article{kousteni_strong_2015, title = {Strong population genetic structure and contrasting demographic histories for the small-spotted catshark (Scyliorhinus canicula) in the Mediterranean Sea}, author = {V Kousteni and P Kasapidis and G Kotoulas and P Megalofonou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84922647393&doi=10.1038%2fhdy.2014.107&partnerID=40&md5=8214d4d9474b3495446e06c1ce805396}, doi = {10.1038/hdy.2014.107}, issn = {0018067X}, year = {2015}, date = {2015-01-01}, journal = {Heredity}, volume = {114}, number = {3}, pages = {333--343}, abstract = {Coastal and demersal chondrichthyans, such as the small-spotted catshark, are expected to exhibit genetic differentiation in areas of complex geomorphology like the Mediterranean Basin because of their limited dispersal ability. To test this hypothesis, we used a fragment of the mitochondrial cytochrome c oxidase subunit I gene and 12 nuclear microsatellite loci in order to investigate the genetic structure and historical demography of this species, and to identify potential barriers to gene flow. Samples were collected from the Balearic Islands, the Algerian Basin, the Ionian Sea, the Corinthian Gulf and various locations across the Aegean Sea. Additional sequences from the Atlantic and the Levantine Basin retrieved from GenBank were included in the mitochondrial DNA analysis. Both mitochondrial and nuclear microsatellite DNA data revealed a strong genetic subdivision, mainly between the western and eastern Mediterranean, whereas the Levantine Basin shared haplotypes with both areas. The geographic isolation of the Mediterranean basins seems to enforce the population genetic differentiation of the species, with the deep sea acting as a strong barrier to its dispersal. Contrasting historical demographic patterns were also observed in different parts of the species' distribution, most notably a population growth trend in the western Mediterranean/Atlantic area and a slight decreasing one in the Aegean Sea. The different effects of the Pleistocene glacial periods on the habitat availability may explain the contrasting demographic patterns observed. The current findings suggest that the small-spotted catshark exhibits several genetic stocks in the Mediterranean, although further study is needed. © 2015 Macmillan Publishers Limited.}, note = {Publisher: Nature Publishing Group}, keywords = {}, pubstate = {published}, tppubtype = {article} } Coastal and demersal chondrichthyans, such as the small-spotted catshark, are expected to exhibit genetic differentiation in areas of complex geomorphology like the Mediterranean Basin because of their limited dispersal ability. To test this hypothesis, we used a fragment of the mitochondrial cytochrome c oxidase subunit I gene and 12 nuclear microsatellite loci in order to investigate the genetic structure and historical demography of this species, and to identify potential barriers to gene flow. Samples were collected from the Balearic Islands, the Algerian Basin, the Ionian Sea, the Corinthian Gulf and various locations across the Aegean Sea. Additional sequences from the Atlantic and the Levantine Basin retrieved from GenBank were included in the mitochondrial DNA analysis. Both mitochondrial and nuclear microsatellite DNA data revealed a strong genetic subdivision, mainly between the western and eastern Mediterranean, whereas the Levantine Basin shared haplotypes with both areas. The geographic isolation of the Mediterranean basins seems to enforce the population genetic differentiation of the species, with the deep sea acting as a strong barrier to its dispersal. Contrasting historical demographic patterns were also observed in different parts of the species' distribution, most notably a population growth trend in the western Mediterranean/Atlantic area and a slight decreasing one in the Aegean Sea. The different effects of the Pleistocene glacial periods on the habitat availability may explain the contrasting demographic patterns observed. The current findings suggest that the small-spotted catshark exhibits several genetic stocks in the Mediterranean, although further study is needed. © 2015 Macmillan Publishers Limited. |
Kopf, A; Bicak, M; Kottmann, R; Schnetzer, J; Kostadinov, I; Lehmann, K; Fernandez-Guerra, A; Jeanthon, C; Rahav, E; Ullrich, M; Wichels, A; Gerdts, G; Polymenakou, P; Kotoulas, G; Siam, R; Abdallah, R Z; Sonnenschein, E C; Cariou, T; O'Gara, F; Jackson, S; Orlic, S; Steinke, M; Busch, J; Duarte, B; Caçador, I; Canning-Clode, J; Bobrova, O; Marteinsson, V; Reynisson, E; Loureiro, C M; Luna, G M; Quero, G M; Löscher, C R; Kremp, A; DeLorenzo, M E; Øvreås, L; Tolman, J; LaRoche, J; Penna, A; Frischer, M; Davis, T; Katherine, B; Meyer, C P; Ramos, S; Magalhães, C; Jude-Lemeilleur, F; Aguirre-Macedo, M L; Wang, S; Poulton, N; Jones, S; Collin, R; Fuhrman, J A; Conan, P; Alonso, C; Stambler, N; Goodwin, K; Yakimov, M M; Baltar, F; Bodrossy, L; Kamp, Van De J; Frampton, D E F; Ostrowski, M; Ruth, Van P; Malthouse, P; Claus, S; Deneudt, K; Mortelmans, J; Pitois, S; Wallom, D; Salter, I; Costa, R; Schroeder, D C; Kandil, M M; Amaral, V; Biancalana, F; Santana, R; Pedrotti, M L; Yoshida, T; Ogata, H; Ingleton, T; Munnik, K; Rodriguez-Ezpeleta, N; Berteaux-Lecellier, V; Wecker, P; Cancio, I; Vaulot, D; Bienhold, C; Ghazal, H; Chaouni, B; Essayeh, S; Ettamimi, S; Zaid, E H; Boukhatem, N; Bouali, A; Chahboune, R; Barrijal, S; Timinouni, M; Otmani, El F; Bennani, M; Mea, M; Todorova, N; Karamfilov, V; Hoopen, Ten P; Cochrane, G; L'Haridon, S; Bizsel, Can K; Vezzi, A; Lauro, F M; Martin, P; Jensen, R M; Hinks, J; Gebbels, S; Rosselli, R; Pascale, De F; Schiavon, R; Santos, Dos A; Villar, E; Pesant, S; Cataletto, B; Malfatti, F; Edirisinghe, R; Silveira, Herrera J A; Barbier, M; Turk, V; Tinta, T; Fuller, W J; Salihoglu, I; Serakinci, N; Ergoren, M C; Bresnan, E; Iriberri, J; Nyhus, P A F; Bente, E; Karlsen, H E; Golyshin, P N; Gasol, J M; Moncheva, S; Dzhembekova, N; Johnson, Z; Sinigalliano, C D; Gidley, M L; Zingone, A; Danovaro, R; Tsiamis, G; Clark, M S; Costa, A C; Bour, El A; Martins, A M; Collins, Eric R; Ducluzeau, A -L; Martinez, J; Costello, M J; Amaral-Zettler, L A; Gilbert, J A; Davies, N; Field, D; Glöckner, F O The ocean sampling day consortium Journal Article GigaScience, 4 (1), 2015, ISSN: 2047217X, (Publisher: BioMed Central Ltd.). @article{kopf_ocean_2015, title = {The ocean sampling day consortium}, author = {A Kopf and M Bicak and R Kottmann and J Schnetzer and I Kostadinov and K Lehmann and A Fernandez-Guerra and C Jeanthon and E Rahav and M Ullrich and A Wichels and G Gerdts and P Polymenakou and G Kotoulas and R Siam and R Z Abdallah and E C Sonnenschein and T Cariou and F O'Gara and S Jackson and S Orlic and M Steinke and J Busch and B Duarte and I Caçador and J Canning-Clode and O Bobrova and V Marteinsson and E Reynisson and C M Loureiro and G M Luna and G M Quero and C R Löscher and A Kremp and M E DeLorenzo and L Øvreås and J Tolman and J LaRoche and A Penna and M Frischer and T Davis and B Katherine and C P Meyer and S Ramos and C Magalhães and F Jude-Lemeilleur and M L Aguirre-Macedo and S Wang and N Poulton and S Jones and R Collin and J A Fuhrman and P Conan and C Alonso and N Stambler and K Goodwin and M M Yakimov and F Baltar and L Bodrossy and J Van De Kamp and D E F Frampton and M Ostrowski and P Van Ruth and P Malthouse and S Claus and K Deneudt and J Mortelmans and S Pitois and D Wallom and I Salter and R Costa and D C Schroeder and M M Kandil and V Amaral and F Biancalana and R Santana and M L Pedrotti and T Yoshida and H Ogata and T Ingleton and K Munnik and N Rodriguez-Ezpeleta and V Berteaux-Lecellier and P Wecker and I Cancio and D Vaulot and C Bienhold and H Ghazal and B Chaouni and S Essayeh and S Ettamimi and E H Zaid and N Boukhatem and A Bouali and R Chahboune and S Barrijal and M Timinouni and F El Otmani and M Bennani and M Mea and N Todorova and V Karamfilov and P Ten Hoopen and G Cochrane and S L'Haridon and K Can Bizsel and A Vezzi and F M Lauro and P Martin and R M Jensen and J Hinks and S Gebbels and R Rosselli and F De Pascale and R Schiavon and A Dos Santos and E Villar and S Pesant and B Cataletto and F Malfatti and R Edirisinghe and J A Herrera Silveira and M Barbier and V Turk and T Tinta and W J Fuller and I Salihoglu and N Serakinci and M C Ergoren and E Bresnan and J Iriberri and P A F Nyhus and E Bente and H E Karlsen and P N Golyshin and J M Gasol and S Moncheva and N Dzhembekova and Z Johnson and C D Sinigalliano and M L Gidley and A Zingone and R Danovaro and G Tsiamis and M S Clark and A C Costa and A El Bour and A M Martins and R Eric Collins and A -L Ducluzeau and J Martinez and M J Costello and L A Amaral-Zettler and J A Gilbert and N Davies and D Field and F O Glöckner}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84939478521&doi=10.1186%2fs13742-015-0066-5&partnerID=40&md5=d32573d75989ec6d70dd25bebc32dff4}, doi = {10.1186/s13742-015-0066-5}, issn = {2047217X}, year = {2015}, date = {2015-01-01}, journal = {GigaScience}, volume = {4}, number = {1}, abstract = {Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits. © 2015 Kopf et al.}, note = {Publisher: BioMed Central Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits. © 2015 Kopf et al. |
Loukovitis, D; Ioannidi, B; Chatziplis, D; Kotoulas, G; Magoulas, A; Tsigenopoulos, C S Mediterranean Marine Science, 16 (1), pp. 197–200, 2015, ISSN: 1108393X, (Publisher: Hellenic Centre for Marine Research). @article{loukovitis_loss_2015, title = {Loss of genetic variation in Greek hatchery populations of the European sea bass (Dicentrarchus labrax L.) as revealed by microsatellite DNA analysis}, author = {D Loukovitis and B Ioannidi and D Chatziplis and G Kotoulas and A Magoulas and C S Tsigenopoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84924862323&doi=10.12681%2fmms.1033&partnerID=40&md5=d6f2f3b1764f0f707f4f4015dcabe4bb}, doi = {10.12681/mms.1033}, issn = {1108393X}, year = {2015}, date = {2015-01-01}, journal = {Mediterranean Marine Science}, volume = {16}, number = {1}, pages = {197--200}, abstract = {Genetic variation in four reared stocks of European sea bass Dicentrarchus labrax L., originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of three natural populations from Greece and France. The total number of alleles per marker ranged from 8 to 22 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic richness and expected heterozygosity. The genetic differentiation of cultivated samples between them as well as from the wild origin fish was significant, as indicated by Fst analysis. All population pairwise comparisons were statistically significant, except for the pair of the two natural Greek populations. Results of microsatellite DNA analysis herein showed a 37 % reduction of the mean allele number in the hatchery samples compared to the wild ones, suggesting random genetic drift and inbreeding events operating in the hatcheries. Knowledge of the genetic variation in D. labrax cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes.}, note = {Publisher: Hellenic Centre for Marine Research}, keywords = {}, pubstate = {published}, tppubtype = {article} } Genetic variation in four reared stocks of European sea bass Dicentrarchus labrax L., originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of three natural populations from Greece and France. The total number of alleles per marker ranged from 8 to 22 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic richness and expected heterozygosity. The genetic differentiation of cultivated samples between them as well as from the wild origin fish was significant, as indicated by Fst analysis. All population pairwise comparisons were statistically significant, except for the pair of the two natural Greek populations. Results of microsatellite DNA analysis herein showed a 37 % reduction of the mean allele number in the hatchery samples compared to the wild ones, suggesting random genetic drift and inbreeding events operating in the hatcheries. Knowledge of the genetic variation in D. labrax cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes. |
Daskalakis, M I; Rigas, F; Bakolas, A; Magoulas, A; Kotoulas, G; Katsikis, I; Karageorgis, A P; Mavridou, A Vaterite bio-precipitation induced by Bacillus pumilus isolated from a solutional cave in Paiania, Athens, Greece Journal Article International Biodeterioration and Biodegradation, 99 , pp. 73–84, 2015, ISSN: 09648305, (Publisher: Elsevier Ltd). @article{daskalakis_vaterite_2015, title = {Vaterite bio-precipitation induced by Bacillus pumilus isolated from a solutional cave in Paiania, Athens, Greece}, author = {M I Daskalakis and F Rigas and A Bakolas and A Magoulas and G Kotoulas and I Katsikis and A P Karageorgis and A Mavridou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84922670670&doi=10.1016%2fj.ibiod.2014.12.005&partnerID=40&md5=562ec5c40d1639e7fe95fee9946262eb}, doi = {10.1016/j.ibiod.2014.12.005}, issn = {09648305}, year = {2015}, date = {2015-01-01}, journal = {International Biodeterioration and Biodegradation}, volume = {99}, pages = {73--84}, abstract = {In this work, Bacillus pumilus ACA-DC 4061 was selected for its increased capability for biomineralization on marble, under different nutrient media concentrations and temperature conditions. The optimum conditions for the CaCO3 bacterially-induced precipitation were determined with the aid of testing based on the Design of Experiments (DoE). Biomineral (vaterite) precipitation was favored in both the temperatures (25 and 30°C) investigated. Stone loss rate was reduced when the samples were subjected to sonication. Thin sections of the substrate confirmed that vaterite was able to adhere onto the surface. Finally, under non-sterile conditions mimicking an in situ application, B. pumilus ACA-DC 4061 formed a fine layer of calcium carbonate. Therefore, this microorganism showed that vaterite formation may consistently occur under specific conditions and could prove useful as a candidate for on-site applications for stone conservation. © 2014 Elsevier Ltd.}, note = {Publisher: Elsevier Ltd}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this work, Bacillus pumilus ACA-DC 4061 was selected for its increased capability for biomineralization on marble, under different nutrient media concentrations and temperature conditions. The optimum conditions for the CaCO3 bacterially-induced precipitation were determined with the aid of testing based on the Design of Experiments (DoE). Biomineral (vaterite) precipitation was favored in both the temperatures (25 and 30°C) investigated. Stone loss rate was reduced when the samples were subjected to sonication. Thin sections of the substrate confirmed that vaterite was able to adhere onto the surface. Finally, under non-sterile conditions mimicking an in situ application, B. pumilus ACA-DC 4061 formed a fine layer of calcium carbonate. Therefore, this microorganism showed that vaterite formation may consistently occur under specific conditions and could prove useful as a candidate for on-site applications for stone conservation. © 2014 Elsevier Ltd. |
2014 |
Tsigenopoulos, C S; Louro, B; Chatziplis, D; Lagnel, J; Vogiatzi, E; Loukovitis, D; Franch, R; Sarropoulou, E; Power, D M; Patarnello, T; Mylonas, C C; Magoulas, A; Bargelloni, L; Canario, A; Kotoulas, G Second generation genetic linkage map for the gilthead sea bream Sparus aurata L. Journal Article Marine Genomics, 18 (PA), pp. 77–82, 2014, ISSN: 18747787, (Publisher: Elsevier B.V.). @article{tsigenopoulos_second_2014, title = {Second generation genetic linkage map for the gilthead sea bream Sparus aurata L.}, author = {C S Tsigenopoulos and B Louro and D Chatziplis and J Lagnel and E Vogiatzi and D Loukovitis and R Franch and E Sarropoulou and D M Power and T Patarnello and C C Mylonas and A Magoulas and L Bargelloni and A Canario and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84922896860&doi=10.1016%2fj.margen.2014.09.008&partnerID=40&md5=c3bdc2b59c298f1c4d2cf093183db7ab}, doi = {10.1016/j.margen.2014.09.008}, issn = {18747787}, year = {2014}, date = {2014-01-01}, journal = {Marine Genomics}, volume = {18}, number = {PA}, pages = {77--82}, abstract = {An updated second linkage map was constructed for the gilthead sea bream, Sparus aurata L., a fish species of great economic importance for the Mediterranean aquaculture industry. In contrast to the first linkage map which mainly consisted of genomic microsatellites (SSRs), the new linkage map is highly enriched with SSRs found in Expressed Sequence Tags (EST-SSRs), which greatly facilitates comparative mapping with other teleosts. The new map consists of 321 genetic markers in 27 linkage groups (LGs): 232 genomic microsatellites, 85 EST-SSRs and 4 SNPs; of those, 13 markers were linked to LGs but were not ordered. Eleven markers (5 SSRs, 5 EST-SSRs and 1 SNP) are not assigned to any LG. The total length of the sex-averaged map is 1769.7. cM, 42% longer than the previously published one, and the number of markers in each LG ranges from 2 to 30. The inter-marker distance varies from 0 to 75.6. cM, with an average of 5.75. cM. The male and female maps have a length of 1349.2 and 2172.1. cM, respectively, and the average distance between markers is 4.38 and 7.05. cM, respectively. Comparative mapping with the three-spined stickleback (Gasterosteus acuulatus) chromosomes and scaffolds showed conserved synteny with 132 S. aurata markers (42.9% of those mapped) having a hit on the stickleback genome. © 2014 Elsevier B.V.}, note = {Publisher: Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } An updated second linkage map was constructed for the gilthead sea bream, Sparus aurata L., a fish species of great economic importance for the Mediterranean aquaculture industry. In contrast to the first linkage map which mainly consisted of genomic microsatellites (SSRs), the new linkage map is highly enriched with SSRs found in Expressed Sequence Tags (EST-SSRs), which greatly facilitates comparative mapping with other teleosts. The new map consists of 321 genetic markers in 27 linkage groups (LGs): 232 genomic microsatellites, 85 EST-SSRs and 4 SNPs; of those, 13 markers were linked to LGs but were not ordered. Eleven markers (5 SSRs, 5 EST-SSRs and 1 SNP) are not assigned to any LG. The total length of the sex-averaged map is 1769.7. cM, 42% longer than the previously published one, and the number of markers in each LG ranges from 2 to 30. The inter-marker distance varies from 0 to 75.6. cM, with an average of 5.75. cM. The male and female maps have a length of 1349.2 and 2172.1. cM, respectively, and the average distance between markers is 4.38 and 7.05. cM, respectively. Comparative mapping with the three-spined stickleback (Gasterosteus acuulatus) chromosomes and scaffolds showed conserved synteny with 132 S. aurata markers (42.9% of those mapped) having a hit on the stickleback genome. © 2014 Elsevier B.V. |
Chatzigeorgiou, G; Sarropoulou, E; Vasileiadou, K; Brown, C; Faulwetter, S; Kotoulas, G; Arvanitidis, C D Community structure and population genetics of Eastern Mediterranean polychaetes Journal Article Frontiers in Marine Science, 1 (OCT), 2014, ISSN: 22967745, (Publisher: Frontiers Media S. A). @article{chatzigeorgiou_community_2014, title = {Community structure and population genetics of Eastern Mediterranean polychaetes}, author = {G Chatzigeorgiou and E Sarropoulou and K Vasileiadou and C Brown and S Faulwetter and G Kotoulas and C D Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85008950428&doi=10.3389%2ffmars.2014.00047&partnerID=40&md5=594f48af64289b71d3a629d8968248df}, doi = {10.3389/fmars.2014.00047}, issn = {22967745}, year = {2014}, date = {2014-01-01}, journal = {Frontiers in Marine Science}, volume = {1}, number = {OCT}, abstract = {Species and genetic diversity are often found to co-vary since they are influenced by external factors in similar ways. In this paper, we analyse the genetic differences of the abundant polychaete Hermodice carunculata (Pallas, 1766) during two successive years at two locations in northern Crete (Aegean Sea) and compare them to other populations in the Mediterranean Sea and the Atlantic Ocean. The genetic analysis is combined with an analysis of ecological divergence of the total polychaete community structure (beta diversity) at these locations. The phylogenetic analysis of all included H. carunculata populations revealed two main clades, one exclusively found in the Mediterranean and a second occurring in both the Mediterranean and the Atlantic. Genetic diversity indices reveal unexpectedly high differences between the two Cretan populations, despite the absence of apparent oceanographic barriers. A similarly high divergence, represented by a high beta diversity index, was observed between the polychaete communities at the two locations. This comparatively high divergence of the genetic structure of a dominant species and the total polychaete community might be explained by the strong influence of local environmental factors as well as inter-specific interactions between the dominance of a single species and the members of the community. © 2014 Chatzigeorgiou, Sarropoulou, Vasileiadou, Brown, Faulwetter, Kotoulas and Arvanitidis.}, note = {Publisher: Frontiers Media S. A}, keywords = {}, pubstate = {published}, tppubtype = {article} } Species and genetic diversity are often found to co-vary since they are influenced by external factors in similar ways. In this paper, we analyse the genetic differences of the abundant polychaete Hermodice carunculata (Pallas, 1766) during two successive years at two locations in northern Crete (Aegean Sea) and compare them to other populations in the Mediterranean Sea and the Atlantic Ocean. The genetic analysis is combined with an analysis of ecological divergence of the total polychaete community structure (beta diversity) at these locations. The phylogenetic analysis of all included H. carunculata populations revealed two main clades, one exclusively found in the Mediterranean and a second occurring in both the Mediterranean and the Atlantic. Genetic diversity indices reveal unexpectedly high differences between the two Cretan populations, despite the absence of apparent oceanographic barriers. A similarly high divergence, represented by a high beta diversity index, was observed between the polychaete communities at the two locations. This comparatively high divergence of the genetic structure of a dominant species and the total polychaete community might be explained by the strong influence of local environmental factors as well as inter-specific interactions between the dominance of a single species and the members of the community. © 2014 Chatzigeorgiou, Sarropoulou, Vasileiadou, Brown, Faulwetter, Kotoulas and Arvanitidis. |
Daskalakis, M I; Magoulas, A; Kotoulas, G; Katsikis, I; Bakolas, A; Karageorgis, A P; Mavridou, A; Doulia, D; Rigas, F Cupriavidus metallidurans biomineralization ability and its application as a bioconsolidation enhancer for ornamental marble stone Journal Article Applied Microbiology and Biotechnology, 98 (15), pp. 6871–6883, 2014, ISSN: 01757598, (Publisher: Springer Verlag). @article{daskalakis_cupriavidus_2014, title = {Cupriavidus metallidurans biomineralization ability and its application as a bioconsolidation enhancer for ornamental marble stone}, author = {M I Daskalakis and A Magoulas and G Kotoulas and I Katsikis and A Bakolas and A P Karageorgis and A Mavridou and D Doulia and F Rigas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84905058974&doi=10.1007%2fs00253-014-5753-0&partnerID=40&md5=e810152ea01bb2be6c740ba9c5d1b590}, doi = {10.1007/s00253-014-5753-0}, issn = {01757598}, year = {2014}, date = {2014-01-01}, journal = {Applied Microbiology and Biotechnology}, volume = {98}, number = {15}, pages = {6871--6883}, abstract = {Bacterially induced calcium carbonate precipitation of a Cupriavidus metallidurans isolate was investigated to develop an environmentally friendly method for restoration and preservation of ornamental stones. Biomineralization performance was carried out in a growth medium via a Design of Experiments (DoE) approach using, as design factors, the temperature, growth medium concentration, and inoculum concentration. The optimum conditions were determined with the aid of consecutive experiments based on response surface methodology (RSM) and were successfully validated thereafter. Statistical analysis can be utilized as a tool for screening bacterial bioprecipitation as it considerably reduced the experimental time and effort needed for bacterial evaluation. Analytical methods provided an insight to the biomineral characteristics, and sonication tests proved that our isolate could create a solid new layer of vaterite on marble substrate withstanding sonication forces. C. metallidurans ACA-DC 4073 provided a compact vaterite layer on the marble substrate with morphological characteristics that assisted in its differentiation. The latter proved valuable during spraying minimum amount of inoculated media on marble substrate under conditions close to an in situ application. A sufficient and clearly distinguishable layer was identified. © 2014 Springer-Verlag.}, note = {Publisher: Springer Verlag}, keywords = {}, pubstate = {published}, tppubtype = {article} } Bacterially induced calcium carbonate precipitation of a Cupriavidus metallidurans isolate was investigated to develop an environmentally friendly method for restoration and preservation of ornamental stones. Biomineralization performance was carried out in a growth medium via a Design of Experiments (DoE) approach using, as design factors, the temperature, growth medium concentration, and inoculum concentration. The optimum conditions were determined with the aid of consecutive experiments based on response surface methodology (RSM) and were successfully validated thereafter. Statistical analysis can be utilized as a tool for screening bacterial bioprecipitation as it considerably reduced the experimental time and effort needed for bacterial evaluation. Analytical methods provided an insight to the biomineral characteristics, and sonication tests proved that our isolate could create a solid new layer of vaterite on marble substrate withstanding sonication forces. C. metallidurans ACA-DC 4073 provided a compact vaterite layer on the marble substrate with morphological characteristics that assisted in its differentiation. The latter proved valuable during spraying minimum amount of inoculated media on marble substrate under conditions close to an in situ application. A sufficient and clearly distinguishable layer was identified. © 2014 Springer-Verlag. |
Davies, N; Field, D; Amaral-Zettler, L; Clark, M S; Deck, J; Drummond, A; Faith, D P; Geller, J; Gilbert, J; Glöckner, F O; Hirsch, P R; Leong, J -A; Meyer, C; Obst, M; Planes, S; Scholin, C; Vogler, A P; Gates, R D; Toonen, R; Berteaux-Lecellier, V; Barbier, M; Barker, K; Bertilsson, S; Bicak, M; Bietz, M J; Bobe, J; Bodrossy, L; Borja, A; Coddington, J; Fuhrman, J; Gerdts, G; Gillespie, R; Goodwin, K; Hanson, P C; Hero, J -M; Hoekman, D; Jansson, J; Jeanthon, C; Kao, R; Klindworth, A; Knight, R; Kottmann, R; Koo, M S; Kotoulas, G; Lowe, A J; Marteinsson, V T; Meyer, F; Morrison, N; Myrold, D D; Pafilis, E; Parker, S; Parnell, J J; Polymenakou, P N; Ratnasingham, S; Roderick, G K; Rodriguez-Ezpeleta, N; Schonrogge, K; Simon, N; Valette-Silver, N J; Springer, Y P; Stone, G N; Stones-Havas, S; Sansone, S -A; Thibault, K M; Wecker, P; Wichels, A; Wooley, J C; Yahara, T; Zingone, A The founding charter of the Genomic Observatories Network Journal Article GigaScience, 3 (1), 2014, ISSN: 2047217X, (Publisher: BioMed Central Ltd.). @article{davies_founding_2014, title = {The founding charter of the Genomic Observatories Network}, author = {N Davies and D Field and L Amaral-Zettler and M S Clark and J Deck and A Drummond and D P Faith and J Geller and J Gilbert and F O Glöckner and P R Hirsch and J -A Leong and C Meyer and M Obst and S Planes and C Scholin and A P Vogler and R D Gates and R Toonen and V Berteaux-Lecellier and M Barbier and K Barker and S Bertilsson and M Bicak and M J Bietz and J Bobe and L Bodrossy and A Borja and J Coddington and J Fuhrman and G Gerdts and R Gillespie and K Goodwin and P C Hanson and J -M Hero and D Hoekman and J Jansson and C Jeanthon and R Kao and A Klindworth and R Knight and R Kottmann and M S Koo and G Kotoulas and A J Lowe and V T Marteinsson and F Meyer and N Morrison and D D Myrold and E Pafilis and S Parker and J J Parnell and P N Polymenakou and S Ratnasingham and G K Roderick and N Rodriguez-Ezpeleta and K Schonrogge and N Simon and N J Valette-Silver and Y P Springer and G N Stone and S Stones-Havas and S -A Sansone and K M Thibault and P Wecker and A Wichels and J C Wooley and T Yahara and A Zingone}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84920397295&doi=10.1186%2f2047-217X-3-2&partnerID=40&md5=a043d700cdaaf754ee7c91c668fc964c}, doi = {10.1186/2047-217X-3-2}, issn = {2047217X}, year = {2014}, date = {2014-01-01}, journal = {GigaScience}, volume = {3}, number = {1}, abstract = {The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated. © 2014 Davies et al.; licensee BioMed Central Ltd.}, note = {Publisher: BioMed Central Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated. © 2014 Davies et al.; licensee BioMed Central Ltd. |
2013 |
Antoniou, A; Magoulas, A; Platis, P; Kotoulas, G Assessing the genetic landscape of a contact zone: The case of European hare in northeastern Greece Journal Article Genetica, 141 (1-3), 2013, ISSN: 00166707. @article{antoniou_assessing_2013, title = {Assessing the genetic landscape of a contact zone: The case of European hare in northeastern Greece}, author = {A Antoniou and A Magoulas and P Platis and G Kotoulas}, doi = {10.1007/s10709-013-9703-z}, issn = {00166707}, year = {2013}, date = {2013-01-01}, journal = {Genetica}, volume = {141}, number = {1-3}, abstract = {The European hare populations of the Balkan Peninsula comprise two divergent phylogenetic lineages with discrete geographical distribution slightly overlapping in the area of northeastern Greece and Bulgaria. Here we elucidate their contact zone, by defining the spatial distributional pattern of the two highly divergent groups, detecting individuals of hybrid origin, and identifying genetic barriers present in the area of their co-existence. Specimens from northeastern Greece were assayed for lineage assignment and population genetic inference based on a 511 bp fragment of mitochondrial DNA control region and allelic data from 10 microsatellite loci. Bayesian analyses on original and simulated genotypes were performed allowing for the contact zone delineation. Our results indicate high genetic diversity in both nuclear and mitochondrial DNA, strong population structure and non random spatial distribution of the differentiated gene pools. The information provided by the two types of molecular markers yielded consistent results. This study comprises a fine scale analysis of the contact zone between the two evolutionary lineages of European brown hares in northeastern Greece. Specific questions on the spatial patterns where addressed for the first time. Furthermore, hypotheses regarding the presence of hybrids were also tested. As a result, interpretive power to the diversity patterns observed today in the Balkans was added and previously overlooked aspects of the species biology were highlighted. ? 2013 Springer Science+Business Media Dordrecht.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The European hare populations of the Balkan Peninsula comprise two divergent phylogenetic lineages with discrete geographical distribution slightly overlapping in the area of northeastern Greece and Bulgaria. Here we elucidate their contact zone, by defining the spatial distributional pattern of the two highly divergent groups, detecting individuals of hybrid origin, and identifying genetic barriers present in the area of their co-existence. Specimens from northeastern Greece were assayed for lineage assignment and population genetic inference based on a 511 bp fragment of mitochondrial DNA control region and allelic data from 10 microsatellite loci. Bayesian analyses on original and simulated genotypes were performed allowing for the contact zone delineation. Our results indicate high genetic diversity in both nuclear and mitochondrial DNA, strong population structure and non random spatial distribution of the differentiated gene pools. The information provided by the two types of molecular markers yielded consistent results. This study comprises a fine scale analysis of the contact zone between the two evolutionary lineages of European brown hares in northeastern Greece. Specific questions on the spatial patterns where addressed for the first time. Furthermore, hypotheses regarding the presence of hybrids were also tested. As a result, interpretive power to the diversity patterns observed today in the Balkans was added and previously overlooked aspects of the species biology were highlighted. ? 2013 Springer Science+Business Media Dordrecht. |
Sotiropoulos, K; Eleftherakos, K; Tsaparis, D; Kasapidis, P; Giokas, S; Legakis, A; Kotoulas, G Fine scale spatial genetic structure of two syntopic newts across a network of ponds: Implications for conservation Journal Article Conservation Genetics, 14 (2), pp. 385–400, 2013, ISSN: 15660621. @article{sotiropoulos_fine_2013, title = {Fine scale spatial genetic structure of two syntopic newts across a network of ponds: Implications for conservation}, author = {K Sotiropoulos and K Eleftherakos and D Tsaparis and P Kasapidis and S Giokas and A Legakis and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84875694931&doi=10.1007%2fs10592-013-0452-4&partnerID=40&md5=bdc097a5f03307fe2303be30e8f62c02}, doi = {10.1007/s10592-013-0452-4}, issn = {15660621}, year = {2013}, date = {2013-01-01}, journal = {Conservation Genetics}, volume = {14}, number = {2}, pages = {385--400}, abstract = {In this study we used genetic approaches to assess the influence of landscape features on the dispersal patterns and genetic structure of two newt species (Triturus macedonicus and Lissotriton vulgaris) living syntopically in a network of ponds. Multilocus genotypes were used to detect and measure genetic variation patterns, population genetic structure and levels of gene flow. We interpret results on the basis of the different dispersal properties of the two species and explored the influence of certain landscape features, such as road and channel networks, on population connectivity. We found marked differences in the spatial genetic patterns of the respective species, which can be explained by their different dispersal properties. The road network seems to act as a barrier to dispersal in the overland dispersing L. vulgaris, while the channel network maintains connectivity in the aquatic dispersing T. macedonicus. The simultaneous and comparative consideration of species in a given area offers a much better understanding of the processes that govern population dynamics and persistence, providing valuable knowledge useful in conservation and management design. © 2013 Springer Science+Business Media Dordrecht.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this study we used genetic approaches to assess the influence of landscape features on the dispersal patterns and genetic structure of two newt species (Triturus macedonicus and Lissotriton vulgaris) living syntopically in a network of ponds. Multilocus genotypes were used to detect and measure genetic variation patterns, population genetic structure and levels of gene flow. We interpret results on the basis of the different dispersal properties of the two species and explored the influence of certain landscape features, such as road and channel networks, on population connectivity. We found marked differences in the spatial genetic patterns of the respective species, which can be explained by their different dispersal properties. The road network seems to act as a barrier to dispersal in the overland dispersing L. vulgaris, while the channel network maintains connectivity in the aquatic dispersing T. macedonicus. The simultaneous and comparative consideration of species in a given area offers a much better understanding of the processes that govern population dynamics and persistence, providing valuable knowledge useful in conservation and management design. © 2013 Springer Science+Business Media Dordrecht. |
Daskalakis, M I; Magoulas, A; Kotoulas, G; Catsikis, I; Bakolas, A; Karageorgis, A P; Mavridou, A; Doulia, D; Rigas, F Pseudomonas, Pantoea and Cupriavidus isolates induce calcium carbonate precipitation for biorestoration of ornamental stone Journal Article Journal of Applied Microbiology, 115 (2), pp. 409–423, 2013, ISSN: 13645072. @article{daskalakis_pseudomonas_2013, title = {Pseudomonas, Pantoea and Cupriavidus isolates induce calcium carbonate precipitation for biorestoration of ornamental stone}, author = {M I Daskalakis and A Magoulas and G Kotoulas and I Catsikis and A Bakolas and A P Karageorgis and A Mavridou and D Doulia and F Rigas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84880592623&doi=10.1111%2fjam.12234&partnerID=40&md5=ff0439bcd9c18b73d46fd4b0d361e34d}, doi = {10.1111/jam.12234}, issn = {13645072}, year = {2013}, date = {2013-01-01}, journal = {Journal of Applied Microbiology}, volume = {115}, number = {2}, pages = {409--423}, abstract = {Aims: Bacterially induced calcium carbonate precipitation from various isolates was investigated aiming at developing an environmentally friendly technique for ornamental stone protection and restoration. Methods and Results: Micro-organisms isolated from stone samples and identified using 16S rDNA and biochemical tests promoted calcium carbonate precipitation in solid and novel liquid growth media. Biomineral morphology was studied on marble samples with scanning electron microscopy. Most isolates demonstrated specimen weight increase, covering partially or even completely the marble surfaces mainly with vaterite. The conditions under which vaterite precipitated and its stability throughout the experimental runs are presented. Conclusions: A growth medium that facilitated bacterial growth of different species and promoted biomineralization was formulated. Most isolates induced biomineralization of CaCO3. Micro-organisms may actually be a milestone in the investigation of vaterite formation facilitating our understanding of geomicrobiological interactions. Pseudomonas, Pantoea and Cupriavidus strains could be candidates for bioconsolidation of ornamental stone protection. Significance and Impact of the Study: Characterization of biomineralization capacity of different bacterial species improves understanding of the bacterially induced mineralization processes and enriches the list of candidates for biorestoration applications. Knowledge of biomineral morphology assists in differentiating mineral from biologically induced precipitates. © 2013 The Society for Applied Microbiology.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Aims: Bacterially induced calcium carbonate precipitation from various isolates was investigated aiming at developing an environmentally friendly technique for ornamental stone protection and restoration. Methods and Results: Micro-organisms isolated from stone samples and identified using 16S rDNA and biochemical tests promoted calcium carbonate precipitation in solid and novel liquid growth media. Biomineral morphology was studied on marble samples with scanning electron microscopy. Most isolates demonstrated specimen weight increase, covering partially or even completely the marble surfaces mainly with vaterite. The conditions under which vaterite precipitated and its stability throughout the experimental runs are presented. Conclusions: A growth medium that facilitated bacterial growth of different species and promoted biomineralization was formulated. Most isolates induced biomineralization of CaCO3. Micro-organisms may actually be a milestone in the investigation of vaterite formation facilitating our understanding of geomicrobiological interactions. Pseudomonas, Pantoea and Cupriavidus strains could be candidates for bioconsolidation of ornamental stone protection. Significance and Impact of the Study: Characterization of biomineralization capacity of different bacterial species improves understanding of the bacterially induced mineralization processes and enriches the list of candidates for biorestoration applications. Knowledge of biomineral morphology assists in differentiating mineral from biologically induced precipitates. © 2013 The Society for Applied Microbiology. |
Loukovitis, D; Batargias, C; Sarropoulou, E; Apostolidis, A P; Kotoulas, G; Magoulas, A; Tsigenopoulos, C S; Chatziplis, D Quantitative trait loci affecting morphology traits in gilthead seabream (Sparus aurata L.) Journal Article Animal Genetics, 44 (4), pp. 480–483, 2013, ISSN: 02689146. @article{loukovitis_quantitative_2013, title = {Quantitative trait loci affecting morphology traits in gilthead seabream (Sparus aurata L.)}, author = {D Loukovitis and C Batargias and E Sarropoulou and A P Apostolidis and G Kotoulas and A Magoulas and C S Tsigenopoulos and D Chatziplis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84879694158&doi=10.1111%2fage.12027&partnerID=40&md5=8646dd0a21752e42aadd08f5cc9b92b9}, doi = {10.1111/age.12027}, issn = {02689146}, year = {2013}, date = {2013-01-01}, journal = {Animal Genetics}, volume = {44}, number = {4}, pages = {480--483}, abstract = {We report a quantitative trait loci (QTL) mapping study on 18 morphometric characters in gilthead seabream based on a total of 74 informative microsatellite markers genotyped in 409 offspring coming from 10 paternal half-sib families. Statistical analysis was carried out using a linear regression approach, and various suggestive and significant morphology QTL were detected in three (9, 21 and 25) of nine linkage groups examined. Fitting body weight as a covariate reduced the significance of some QTL but revealed three new QTL in other linkage groups (LG6 and LG10). Current results combined with those obtained from previous studies underline highly significant loci affecting overall growth and morphology in S. aurata. © 2013 The Authors, Animal Genetics © 2013 Stichting International Foundation for Animal Genetics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report a quantitative trait loci (QTL) mapping study on 18 morphometric characters in gilthead seabream based on a total of 74 informative microsatellite markers genotyped in 409 offspring coming from 10 paternal half-sib families. Statistical analysis was carried out using a linear regression approach, and various suggestive and significant morphology QTL were detected in three (9, 21 and 25) of nine linkage groups examined. Fitting body weight as a covariate reduced the significance of some QTL but revealed three new QTL in other linkage groups (LG6 and LG10). Current results combined with those obtained from previous studies underline highly significant loci affecting overall growth and morphology in S. aurata. © 2013 The Authors, Animal Genetics © 2013 Stichting International Foundation for Animal Genetics. |
Oulas, Anastasis; Polymenakou, Paraskevi N; Mandalakis, Manolis; Nomikou, Paraskevi; Carey, Steven; Christakis, Christos; Kotoulas, Georgios; Magoulas, Antonios; Tripp, James H; Espino, David Paez A; Ivanova, Natalia N; Kyrpides, Nikos C Metagenomics of microbial communities inhabiting the Kolumbo volcano shallow-sea hydrothermal vent field and Santorini (caldera) Inproceedings 2013, (Publication Title: The 8th conference of the Hellenic Society for Computational Biology and Bioinformatics - HSCBB13). @inproceedings{oulas_metagenomics_2013, title = {Metagenomics of microbial communities inhabiting the Kolumbo volcano shallow-sea hydrothermal vent field and Santorini (caldera)}, author = {Anastasis Oulas and Paraskevi N Polymenakou and Manolis Mandalakis and Paraskevi Nomikou and Steven Carey and Christos Christakis and Georgios Kotoulas and Antonios Magoulas and James H Tripp and David Paez A Espino and Natalia N Ivanova and Nikos C Kyrpides}, year = {2013}, date = {2013-01-01}, note = {Publication Title: The 8th conference of the Hellenic Society for Computational Biology and Bioinformatics - HSCBB13}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Polymenakou, P N; Nomikou, P; Mandalakis, M; Kilias, S P; Christakis, C; Kyrpides, N; Ivanova, N; Oulas, A; Dailianis, Thanos; Carey, S; Kotoulas, G; Magoulas, A; Papanikolaou, D Microbiological exploration of a unique CO2-rich shallow submarine hydrothermal vent field (Kolumbo, Santorini island, Aegean Sea) Inproceedings Heraklion Crete, Greece, 2013, (Publication Title: Mediterranean Marine Biodiversity Conference Type: Oral Presentation). @inproceedings{polymenakou_microbiological_2013, title = {Microbiological exploration of a unique CO2-rich shallow submarine hydrothermal vent field (Kolumbo, Santorini island, Aegean Sea)}, author = {P N Polymenakou and P Nomikou and M Mandalakis and S P Kilias and C Christakis and N Kyrpides and N Ivanova and A Oulas and Thanos Dailianis and S Carey and G Kotoulas and A Magoulas and D Papanikolaou}, year = {2013}, date = {2013-01-01}, address = {Heraklion Crete, Greece}, note = {Publication Title: Mediterranean Marine Biodiversity Conference Type: Oral Presentation}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Vasileiadou, A; Pavloudi, C; Chatzinikolaou, E; Gonzalez-Wanguemert, M; Tsikopoulou, I; Kotoulas, G; Arvanitidis, C Genetic diversity patterns of macrobenthic populations from lagoonal ecosystems Inproceedings Lisbon (Portugal), 2013, (Publication Title: 14th Congress of European Society for Evolutionary Biology, 19-24 August 2013 Type: Poster). @inproceedings{vasileiadou_genetic_2013, title = {Genetic diversity patterns of macrobenthic populations from lagoonal ecosystems}, author = {A Vasileiadou and C Pavloudi and E Chatzinikolaou and M Gonzalez-Wanguemert and I Tsikopoulou and G Kotoulas and C Arvanitidis}, year = {2013}, date = {2013-01-01}, address = {Lisbon (Portugal)}, note = {Publication Title: 14th Congress of European Society for Evolutionary Biology, 19-24 August 2013 Type: Poster}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Lamprinou, V; Skaraki, K; Kotoulas, G; Anagnostidis, K; Economou-Amilli, A; Pantazidou, A A new species of Phormidium (Cyanobacteria, Oscillatoriales) from three Greek Caves: Morphological and molecular analysis Journal Article Fundamental and Applied Limnology, 182 (2), pp. 109–116, 2013, ISSN: 18639135. @article{lamprinou_new_2013, title = {A new species of Phormidium (Cyanobacteria, Oscillatoriales) from three Greek Caves: Morphological and molecular analysis}, author = {V Lamprinou and K Skaraki and G Kotoulas and K Anagnostidis and A Economou-Amilli and A Pantazidou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84885039547&doi=10.1127%2f1863-9135%2f2013%2f0323&partnerID=40&md5=9080ff65cd6b2a9276d0755a471a5e0c}, doi = {10.1127/1863-9135/2013/0323}, issn = {18639135}, year = {2013}, date = {2013-01-01}, journal = {Fundamental and Applied Limnology}, volume = {182}, number = {2}, pages = {109--116}, abstract = {Specimens of cyanobacteria were collected from three geographically distant caves in Greece, and an interesting species of the Oscillatoriales was isolated and analyzed. Morphological characters were analyzed from fresh and cultured material using LM, SEM and TEM; moreover, molecular analysis based on the 16 S rRNA sequence was applied. This cyanobacterium bears a characteristic blackish, stratified, mucilaginous sheath and it is characterized by entangled flaments, facultative presence of false branching, presence of necridia and peripheral arrangement of thylakoids. The autapomorpic blackish mucilaginous sheath and the pseudobranching flaments are unique morphological characters within the genus Phormidium, according to classical taxonomy. The 16 S rRNA sequence showed relatedness to Phormidium priestleyi ANT L52.6 with 97-98 % similarity, but without morphological support. Both phenotypic and genetic traits supported the designation of a new species, under the name Phormidium melanochroun Lamprinou & Pantazidou sp. nov. © 2013 E. Schweizerbart'sche Verlagsbuchhandlung.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Specimens of cyanobacteria were collected from three geographically distant caves in Greece, and an interesting species of the Oscillatoriales was isolated and analyzed. Morphological characters were analyzed from fresh and cultured material using LM, SEM and TEM; moreover, molecular analysis based on the 16 S rRNA sequence was applied. This cyanobacterium bears a characteristic blackish, stratified, mucilaginous sheath and it is characterized by entangled flaments, facultative presence of false branching, presence of necridia and peripheral arrangement of thylakoids. The autapomorpic blackish mucilaginous sheath and the pseudobranching flaments are unique morphological characters within the genus Phormidium, according to classical taxonomy. The 16 S rRNA sequence showed relatedness to Phormidium priestleyi ANT L52.6 with 97-98 % similarity, but without morphological support. Both phenotypic and genetic traits supported the designation of a new species, under the name Phormidium melanochroun Lamprinou & Pantazidou sp. nov. © 2013 E. Schweizerbart'sche Verlagsbuchhandlung. |
2012 |
Loukovitis, D; Sarropoulou, E; Vogiatzi, E; Tsigenopoulos, C S; Kotoulas, G; Magoulas, A; Chatziplis, D Genetic variation in farmed populations of the gilthead sea bream Sparus aurata in Greece using microsatellite DNA markers Journal Article Aquaculture Research, 43 (2), pp. 239–246, 2012, ISSN: 1355557X. @article{loukovitis_genetic_2012, title = {Genetic variation in farmed populations of the gilthead sea bream Sparus aurata in Greece using microsatellite DNA markers}, author = {D Loukovitis and E Sarropoulou and E Vogiatzi and C S Tsigenopoulos and G Kotoulas and A Magoulas and D Chatziplis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-83255167256&doi=10.1111%2fj.1365-2109.2011.02821.x&partnerID=40&md5=36672ab78be0cf614702105a4a50327f}, doi = {10.1111/j.1365-2109.2011.02821.x}, issn = {1355557X}, year = {2012}, date = {2012-01-01}, journal = {Aquaculture Research}, volume = {43}, number = {2}, pages = {239--246}, abstract = {Genetic variation in seven reared stocks of gilthead sea bream Sparus aurata, originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of two natural populations from the Ionian and the Adriatic Seas. The total number of alleles per marker ranged from 11 to 19 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic diversity and expected heterozygosity. The global genetic differentiation for the cultivated samples was significant as indicated by F st analysis, which might indicate random genetic drift and inbreeding events operating in the hatcheries. On the contrary, no significant difference was found between the two wild populations. Population pairwise tests between farmed and wild stocks were also significant, with the exception of one hatchery sample, the Central Greece 1, which was not significantly different from the two wild samples perhaps due to its recent use in aquaculture from wild-caught animals. The UPGMA tree topology grouped the wild samples together with the Central Greece 1 stock, and showed a clear division between wild and farmed sample sets for the six remaining hatchery samples. Knowledge of the genetic variation in S. aurata cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for the proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes. © 2011 Blackwell Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Genetic variation in seven reared stocks of gilthead sea bream Sparus aurata, originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of two natural populations from the Ionian and the Adriatic Seas. The total number of alleles per marker ranged from 11 to 19 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic diversity and expected heterozygosity. The global genetic differentiation for the cultivated samples was significant as indicated by F st analysis, which might indicate random genetic drift and inbreeding events operating in the hatcheries. On the contrary, no significant difference was found between the two wild populations. Population pairwise tests between farmed and wild stocks were also significant, with the exception of one hatchery sample, the Central Greece 1, which was not significantly different from the two wild samples perhaps due to its recent use in aquaculture from wild-caught animals. The UPGMA tree topology grouped the wild samples together with the Central Greece 1 stock, and showed a clear division between wild and farmed sample sets for the six remaining hatchery samples. Knowledge of the genetic variation in S. aurata cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for the proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes. © 2011 Blackwell Publishing Ltd. |
Loukovitis, D; Sarropoulou, E; Batargias, C; Apostolidis, A P; Kotoulas, G; Tsigenopoulos, C S; Chatziplis, D Quantitative trait loci for body growth and sex determination in the hermaphrodite teleost fish Sparus aurata L. Journal Article Animal Genetics, 43 (6), pp. 753–759, 2012, ISSN: 02689146. @article{loukovitis_quantitative_2012, title = {Quantitative trait loci for body growth and sex determination in the hermaphrodite teleost fish Sparus aurata L.}, author = {D Loukovitis and E Sarropoulou and C Batargias and A P Apostolidis and G Kotoulas and C S Tsigenopoulos and D Chatziplis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84867582764&doi=10.1111%2fj.1365-2052.2012.02346.x&partnerID=40&md5=b7ebfa1bdacb7395e50fdd78be54840c}, doi = {10.1111/j.1365-2052.2012.02346.x}, issn = {02689146}, year = {2012}, date = {2012-01-01}, journal = {Animal Genetics}, volume = {43}, number = {6}, pages = {753--759}, abstract = {Gilthead sea bream (Sparus aurata L.) is an important marine fish in Mediterranean aquaculture. Sex determination by age and/or body weight is a critical life-history trait, the genetic basis for which is largely unknown in this sequential hermaphrodite species. Herein, we performed a partial genome scan to map quantitative trait loci (QTL) affecting body weight and sex using 74 informative microsatellite markers from 10 paternal half-sib families to construct nine linkage groups (LG). In total, four growth-related QTL (two chromosome-wide and two genome-wide) and six QTL related to sex determination (three pairs in three different LGs) were detected (two chromosome-wide and one genome-wide). The proportion of phenotypic variation explained by the body-weight QTL ranged from 9.3% to 17.2%, showing their potential for use in marker-assisted selection. The results obtained offer solid ground to investigate the structure and function of the genomic regions involved in the mechanisms of sex reversal. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Gilthead sea bream (Sparus aurata L.) is an important marine fish in Mediterranean aquaculture. Sex determination by age and/or body weight is a critical life-history trait, the genetic basis for which is largely unknown in this sequential hermaphrodite species. Herein, we performed a partial genome scan to map quantitative trait loci (QTL) affecting body weight and sex using 74 informative microsatellite markers from 10 paternal half-sib families to construct nine linkage groups (LG). In total, four growth-related QTL (two chromosome-wide and two genome-wide) and six QTL related to sex determination (three pairs in three different LGs) were detected (two chromosome-wide and one genome-wide). The proportion of phenotypic variation explained by the body-weight QTL ranged from 9.3% to 17.2%, showing their potential for use in marker-assisted selection. The results obtained offer solid ground to investigate the structure and function of the genomic regions involved in the mechanisms of sex reversal. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics. |
Chrysos, G; Sotiriades, E; Rousopoulos, C; Dollas, A; Papadopoulos, A; Kirmitzoglou, I; Promponas, V; Theocharides, T; Petihakis, G; Lagnel, J; Vavylis, P; Kotoulas, G Opportunities from the use of FPGAs as platforms for bioinformatics algorithms Inproceedings IEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012, pp. 559–565, 2012, ISBN: 978-1-4673-4358-9. @inproceedings{chrysos_opportunities_2012, title = {Opportunities from the use of FPGAs as platforms for bioinformatics algorithms}, author = {G Chrysos and E Sotiriades and C Rousopoulos and A Dollas and A Papadopoulos and I Kirmitzoglou and V Promponas and T Theocharides and G Petihakis and J Lagnel and P Vavylis and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84872834499&doi=10.1109%2fBIBE.2012.6399733&partnerID=40&md5=93234c49ded04716bf009ae62c7be366}, doi = {10.1109/BIBE.2012.6399733}, isbn = {978-1-4673-4358-9}, year = {2012}, date = {2012-01-01}, booktitle = {IEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012}, pages = {559--565}, abstract = {This paper presents an in-depth look of how FPGA computing can offer substantial speedups in the execution of bioinformatics algorithms, with specific results achieved to date for a broad range of algorithms. Examples and case studies are presented for sequence comparison (BLAST, CAST), multiple sequence alignment (MAFFT, T-Coffee), RNA and protein secondary structure prediction (Zuker, Predator), gene prediction (Glimmer/GlimmerHMM) and phylogenetic tree computation (RAxML), running on mainstream FPGA technologies as well as high-end FPGA-based systems (Convey HC1, BeeCube). This work also presents technological and other obstacles that need to be overcome in order for FPGA computing to become a mainstream technology in Bioinformatics. © 2012 IEEE.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } This paper presents an in-depth look of how FPGA computing can offer substantial speedups in the execution of bioinformatics algorithms, with specific results achieved to date for a broad range of algorithms. Examples and case studies are presented for sequence comparison (BLAST, CAST), multiple sequence alignment (MAFFT, T-Coffee), RNA and protein secondary structure prediction (Zuker, Predator), gene prediction (Glimmer/GlimmerHMM) and phylogenetic tree computation (RAxML), running on mainstream FPGA technologies as well as high-end FPGA-based systems (Convey HC1, BeeCube). This work also presents technological and other obstacles that need to be overcome in order for FPGA computing to become a mainstream technology in Bioinformatics. © 2012 IEEE. |
Lamprinou, V; Skaraki, K; Kotoulas, G; Economou-Amilli, A; Pantazidou, A International Journal of Systematic and Evolutionary Microbiology, 62 (12), pp. 2870–2877, 2012, ISSN: 14665026. @article{lamprinou_toxopsis_2012, title = {Toxopsis calypsus gen. nov., sp. nov. (Cyanobacteria, Nostocales) from cave 'Francthi', Peloponnese, Greece: A morphological and molecular evaluation}, author = {V Lamprinou and K Skaraki and G Kotoulas and A Economou-Amilli and A Pantazidou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84862304939&doi=10.1099%2fijs.0.038679-0&partnerID=40&md5=9d149d4a638ec4c6388d7dabf6c7a89f}, doi = {10.1099/ijs.0.038679-0}, issn = {14665026}, year = {2012}, date = {2012-01-01}, journal = {International Journal of Systematic and Evolutionary Microbiology}, volume = {62}, number = {12}, pages = {2870--2877}, abstract = {Representatives of a new cyanobacterial genus, Toxopsis Lamprinou & Pantazidou gen. nov., were found in fresh material from Cave 'Francthi' (Peloponnese, Greece) and isolated in cultures. Ecological data relating to the environmental parameters of the sampling sites are provided, such as the photosynthetically active radiation (PAR), temperature and relative humidity. Morphological characteristics and the life cycle of the type species Toxopsis calypsus Lamprinou & Pantazidou sp. nov. were studied using light microscopy and scanning and transmission microscopy. Molecular analysis based on the 16S rRNA gene sequence was also conducted. Toxopsis calypsus sp. nov. is a false-branched nostocalean cyanobacterium with both isopolar and heteropolar filaments bearing mono-pored and bi-pored heterocysts, and also hormogonia and akinetes. Isopolar filaments adhere by the centre to the substrate and are found mainly in fresh material and in young cultures; heteropolar filaments bearing a basic mono-pore heterocyst are dominant in aged (more than one-year-old) cultures. According to the revised taxonomic classification system of Komárek & Anagnostidis (1989) [Komárek, J. & Anagnostidis, K. (1989). Algol Stud, 56, 247-345] based mainly on morphological data, the new genus described here shares morphological characters with both nostocalean families Scytonemataceae and Microchaetaceae, showing similarities in particular to Scytonematopsis contorta [Vaccarino, M. A. & Johansen, J. R. (2011). Fottea 11, 149-161], Microchaetaceae. Molecular data from the 16S rRNA sequence determined in this paper showed that Toxopsis calypsus sp. nov. is more related to the family Microchaetaceae, and the five phylotypes analysed by PCR showed that the closest nostocalean relatives are Tolypothrix distorta SAG 93.79 (GenBank accession no. GQ287651) and Coleodesmium sp. ANT.L52B.5 (AY493596) with 95-96 % and 96 % similarity, respectively. In contrast, the five phylotypes showed a distant similarity to Scytonematopsis contorta (textless91 %). The phenotypic and genetic traits strongly supported the classification of the five phylotypes as a new taxon for which the name Toxopsis calypsus Lamprinou & Pantazidou gen. nov., sp. nov. is proposed. © 2012 IUMS.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Representatives of a new cyanobacterial genus, Toxopsis Lamprinou & Pantazidou gen. nov., were found in fresh material from Cave 'Francthi' (Peloponnese, Greece) and isolated in cultures. Ecological data relating to the environmental parameters of the sampling sites are provided, such as the photosynthetically active radiation (PAR), temperature and relative humidity. Morphological characteristics and the life cycle of the type species Toxopsis calypsus Lamprinou & Pantazidou sp. nov. were studied using light microscopy and scanning and transmission microscopy. Molecular analysis based on the 16S rRNA gene sequence was also conducted. Toxopsis calypsus sp. nov. is a false-branched nostocalean cyanobacterium with both isopolar and heteropolar filaments bearing mono-pored and bi-pored heterocysts, and also hormogonia and akinetes. Isopolar filaments adhere by the centre to the substrate and are found mainly in fresh material and in young cultures; heteropolar filaments bearing a basic mono-pore heterocyst are dominant in aged (more than one-year-old) cultures. According to the revised taxonomic classification system of Komárek & Anagnostidis (1989) [Komárek, J. & Anagnostidis, K. (1989). Algol Stud, 56, 247-345] based mainly on morphological data, the new genus described here shares morphological characters with both nostocalean families Scytonemataceae and Microchaetaceae, showing similarities in particular to Scytonematopsis contorta [Vaccarino, M. A. & Johansen, J. R. (2011). Fottea 11, 149-161], Microchaetaceae. Molecular data from the 16S rRNA sequence determined in this paper showed that Toxopsis calypsus sp. nov. is more related to the family Microchaetaceae, and the five phylotypes analysed by PCR showed that the closest nostocalean relatives are Tolypothrix distorta SAG 93.79 (GenBank accession no. GQ287651) and Coleodesmium sp. ANT.L52B.5 (AY493596) with 95-96 % and 96 % similarity, respectively. In contrast, the five phylotypes showed a distant similarity to Scytonematopsis contorta (textless91 %). The phenotypic and genetic traits strongly supported the classification of the five phylotypes as a new taxon for which the name Toxopsis calypsus Lamprinou & Pantazidou gen. nov., sp. nov. is proposed. © 2012 IUMS. |
Coscia, Ilaria; Vogiatzi, Emmanouella; Kotoulas, Giorgios; Tsigenopoulos, C S; Mariani, Stefano Neutral and adaptive genetic variation in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic Journal Article Heredity, 108 , pp. 537–546, 2012. @article{coscia_neutral_2012, title = {Neutral and adaptive genetic variation in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic}, author = {Ilaria Coscia and Emmanouella Vogiatzi and Giorgios Kotoulas and C S Tsigenopoulos and Stefano Mariani}, year = {2012}, date = {2012-01-01}, journal = {Heredity}, volume = {108}, pages = {537--546}, abstract = {Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of Ireland, and genetically assayed using a suite of species-specific markers, including 15 putatively neutral microsatellites and 23 Expressed Sequence Tag-linked (ESTs) markers, as well as a portion of the mitochondrial DNA (mtDNA) Control Region. Two of the putatively neutral markers, Bld-10 and Ad-10, bore signatures of strong directional selection, particularly in the newly established Irish population, though the potential ‘surfing effect’ of rare alleles at the edge of the expansion front was also considered. Analyses after the removal of these loci suggest low but significant population structure likely affected by some degree of gene flow counteracting random genetic drift. No signal of historic divergence was detected at mtDNA. BLAST searches conducted with all 38 markers used failed to identify specific genomic regions associated to adaptive functions. However, the availability of genomic resources for this commercially valuable species is rapidly increasing, bringing us closer to the understanding of the interplay between selective and neutral evolutionary forces, shaping population divergence of an expanding species in a heterogeneous milieu.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of Ireland, and genetically assayed using a suite of species-specific markers, including 15 putatively neutral microsatellites and 23 Expressed Sequence Tag-linked (ESTs) markers, as well as a portion of the mitochondrial DNA (mtDNA) Control Region. Two of the putatively neutral markers, Bld-10 and Ad-10, bore signatures of strong directional selection, particularly in the newly established Irish population, though the potential ‘surfing effect’ of rare alleles at the edge of the expansion front was also considered. Analyses after the removal of these loci suggest low but significant population structure likely affected by some degree of gene flow counteracting random genetic drift. No signal of historic divergence was detected at mtDNA. BLAST searches conducted with all 38 markers used failed to identify specific genomic regions associated to adaptive functions. However, the availability of genomic resources for this commercially valuable species is rapidly increasing, bringing us closer to the understanding of the interplay between selective and neutral evolutionary forces, shaping population divergence of an expanding species in a heterogeneous milieu. |
Vasileiadou, A; Sarropoulou, E; Tsigenopoulos, C S; Reizopoulou, S; Nikolaidou, A; Orfanidis, S; Simboura, N; Kotoulas, G; Arvanitidis, C Genetic vs community diversity patterns of macrobenthic species: preliminary results from the lagoonal ecosystem Journal Article Transitional Waters Bulletin, 6 , pp. 20–33, 2012. @article{vasileiadou_genetic_2012, title = {Genetic vs community diversity patterns of macrobenthic species: preliminary results from the lagoonal ecosystem}, author = {A Vasileiadou and E Sarropoulou and C S Tsigenopoulos and S Reizopoulou and A Nikolaidou and S Orfanidis and N Simboura and G Kotoulas and C Arvanitidis}, url = {http://siba-ese.unisalento.it/index.php/twb/article/view/12797/11396}, doi = {10.1285/i1825229Xv6n2p20}, year = {2012}, date = {2012-01-01}, journal = {Transitional Waters Bulletin}, volume = {6}, pages = {20--33}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2011 |
Loukovitis, D; Sarropoulou, E; Tsigenopoulos, C S; Batargias, C; Magoulas, A; Apostolidis, A P; Chatziplis, D; Kotoulas, G Quantitative Trait Loci involved in sex determination and body growth in the gilthead sea bream (Sparus aurata L.) through targeted genome scan Journal Article PLoS ONE, 6 (1), 2011, ISSN: 19326203. @article{loukovitis_quantitative_2011, title = {Quantitative Trait Loci involved in sex determination and body growth in the gilthead sea bream (Sparus aurata L.) through targeted genome scan}, author = {D Loukovitis and E Sarropoulou and C S Tsigenopoulos and C Batargias and A Magoulas and A P Apostolidis and D Chatziplis and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79551624871&doi=10.1371%2fjournal.pone.0016599&partnerID=40&md5=97db8af3b120b4907100b6c1e8c87376}, doi = {10.1371/journal.pone.0016599}, issn = {19326203}, year = {2011}, date = {2011-01-01}, journal = {PLoS ONE}, volume = {6}, number = {1}, abstract = {Among vertebrates, teleost fish exhibit a considerably wide range of sex determination patterns that may be influenced by extrinsic parameters. However even for model fish species like the zebrafish Danio rerio the precise mechanisms involved in primary sex determination have not been studied extensively. The zebrafish, a gonochoristic species, is lacking discernible sex chromosomes and the sex of juvenile fish is difficult to determine. Sequential protandrous hermaphrodite species provide distinct determination of the gender and allow studying the sex determination process by looking at the mechanism of sex reversal. This is the first attempt to understand the genetic basis of phenotypic variation for sex determination and body weight in a sequential protandrous hermaphrodite species, the gilthead sea bream (Sparus aurata). This work demonstrates a fast and efficient strategy for Quantitative Trait Loci (QTL) detection in the gilthead sea bream, a non-model but target hermaphrodite fish species. Therefore a comparative mapping approach was performed to query syntenies against two other Perciformes, the European sea bass (Dicentrarchus labrax), a gonochoristic species and the Asian sea bass (Lates calcarifer) a protandrous hermaphrodite. In this manner two significant QTLs, one QTL affecting both body weight and sex and one QTL affecting sex, were detected on the same linkage group. The co-segregation of the two QTLs provides a genomic base to the observed genetic correlation between these two traits in sea bream as well as in other teleosts. The identification of QTLs linked to sex reversal and growth, will contribute significantly to a better understanding of the complex nature of sex determination in S. aurata where most individuals reverse to the female sex at the age of two years through development and maturation of the ovarian portion of the gonad and regression of the testicular area. [Genomic sequences reported in this manuscript have been submitted to GenBank under accession numbers HQ021443- HQ021749.]. © 2011 Loukovitis et al.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Among vertebrates, teleost fish exhibit a considerably wide range of sex determination patterns that may be influenced by extrinsic parameters. However even for model fish species like the zebrafish Danio rerio the precise mechanisms involved in primary sex determination have not been studied extensively. The zebrafish, a gonochoristic species, is lacking discernible sex chromosomes and the sex of juvenile fish is difficult to determine. Sequential protandrous hermaphrodite species provide distinct determination of the gender and allow studying the sex determination process by looking at the mechanism of sex reversal. This is the first attempt to understand the genetic basis of phenotypic variation for sex determination and body weight in a sequential protandrous hermaphrodite species, the gilthead sea bream (Sparus aurata). This work demonstrates a fast and efficient strategy for Quantitative Trait Loci (QTL) detection in the gilthead sea bream, a non-model but target hermaphrodite fish species. Therefore a comparative mapping approach was performed to query syntenies against two other Perciformes, the European sea bass (Dicentrarchus labrax), a gonochoristic species and the Asian sea bass (Lates calcarifer) a protandrous hermaphrodite. In this manner two significant QTLs, one QTL affecting both body weight and sex and one QTL affecting sex, were detected on the same linkage group. The co-segregation of the two QTLs provides a genomic base to the observed genetic correlation between these two traits in sea bream as well as in other teleosts. The identification of QTLs linked to sex reversal and growth, will contribute significantly to a better understanding of the complex nature of sex determination in S. aurata where most individuals reverse to the female sex at the age of two years through development and maturation of the ovarian portion of the gonad and regression of the testicular area. [Genomic sequences reported in this manuscript have been submitted to GenBank under accession numbers HQ021443- HQ021749.]. © 2011 Loukovitis et al. |
Boulton, K; Massault, C; Houston, R D; de Koning, D J; Haley, C S; Bovenhuis, H; Batargias, C; Canario, A V M; Kotoulas, G; Tsigenopoulos, C S QTL affecting morphometric traits and stress response in the gilthead seabream (Sparus aurata) Journal Article Aquaculture, 319 (1-2), pp. 58–66, 2011, ISSN: 00448486. @article{boulton_qtl_2011, title = {QTL affecting morphometric traits and stress response in the gilthead seabream (Sparus aurata)}, author = {K Boulton and C Massault and R D Houston and D J de Koning and C S Haley and H Bovenhuis and C Batargias and A V M Canario and G Kotoulas and C S Tsigenopoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80051590556&doi=10.1016%2fj.aquaculture.2011.06.044&partnerID=40&md5=51eee2954b6d4d2f2757c520ddc3bd70}, doi = {10.1016/j.aquaculture.2011.06.044}, issn = {00448486}, year = {2011}, date = {2011-01-01}, journal = {Aquaculture}, volume = {319}, number = {1-2}, pages = {58--66}, abstract = {The gilthead seabream (Sparus aurata) is an important aquaculture species that has only been subject to an incipient selective breeding programme. This study, which examined the genetic architecture of seabream morphology and stress response to confinement, takes a step toward the use of marker assisted selection in this species. Major loci affecting these traits were mapped, using data from 460 offspring derived from seven paternal and 73 maternal half-sib families. Fish were killed following a four-hour confinement experiment to induce stress, after which 15 morphometric measurements were collected and blood was sampled for DNA extraction and plasma cortisol level determination. Heritabilities for the morphometric traits were moderate to high (0.24-0.58), with genetic and phenotypic correlations between the traits generally very high. However, the heritability of plasma cortisol level was not significantly different from zero.A population-specific genetic linkage map was built for 56 microsatellite markers, comprising 16 linkage groups (LG) and ten unlinked markers. Half-sib and variance components QTL analyses detected a single genome-wide significant QTL (SaimbcF7b), a single unlinked marker explaining 13-23% of the phenotypic variance in the majority of the morphometric traits. Several other putative QTL were identified for morphometric traits (on LG 4a, 7, 9, 18, A, C, F and I), along with two other QTL (LG10 and B) that were suggestive for stress response. Fitting body weight as a covariate for the morphometric traits resulted in three genome-wide significant QTL affecting aspects of body shape independent of overall body size. For stress response we only identified suggestive evidence for QTL. These findings contribute to understanding the genetic regulation of important economic traits in seabream. © 2011.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The gilthead seabream (Sparus aurata) is an important aquaculture species that has only been subject to an incipient selective breeding programme. This study, which examined the genetic architecture of seabream morphology and stress response to confinement, takes a step toward the use of marker assisted selection in this species. Major loci affecting these traits were mapped, using data from 460 offspring derived from seven paternal and 73 maternal half-sib families. Fish were killed following a four-hour confinement experiment to induce stress, after which 15 morphometric measurements were collected and blood was sampled for DNA extraction and plasma cortisol level determination. Heritabilities for the morphometric traits were moderate to high (0.24-0.58), with genetic and phenotypic correlations between the traits generally very high. However, the heritability of plasma cortisol level was not significantly different from zero.A population-specific genetic linkage map was built for 56 microsatellite markers, comprising 16 linkage groups (LG) and ten unlinked markers. Half-sib and variance components QTL analyses detected a single genome-wide significant QTL (SaimbcF7b), a single unlinked marker explaining 13-23% of the phenotypic variance in the majority of the morphometric traits. Several other putative QTL were identified for morphometric traits (on LG 4a, 7, 9, 18, A, C, F and I), along with two other QTL (LG10 and B) that were suggestive for stress response. Fitting body weight as a covariate for the morphometric traits resulted in three genome-wide significant QTL affecting aspects of body shape independent of overall body size. For stress response we only identified suggestive evidence for QTL. These findings contribute to understanding the genetic regulation of important economic traits in seabream. © 2011. |
Vogiatzi, E; Lagnel, J; Pakaki, V; Louro, B; Canario, A V M; Reinhardt, R; Kotoulas, G; Magoulas, A; Tsigenopoulos, C S Marine Genomics, 4 (2), pp. 83–91, 2011, ISSN: 18747787. @article{vogiatzi_silico_2011, title = {In silico mining and characterization of simple sequence repeats from gilthead sea bream (Sparus aurata) expressed sequence tags (EST-SSRs); PCR amplification, polymorphism evaluation and multiplexing and cross-species assays}, author = {E Vogiatzi and J Lagnel and V Pakaki and B Louro and A V.M. Canario and R Reinhardt and G Kotoulas and A Magoulas and C S Tsigenopoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79956354483&doi=10.1016%2fj.margen.2011.01.003&partnerID=40&md5=3775ee5dbda814501d9fd8660740563b}, doi = {10.1016/j.margen.2011.01.003}, issn = {18747787}, year = {2011}, date = {2011-01-01}, journal = {Marine Genomics}, volume = {4}, number = {2}, pages = {83--91}, abstract = {We screened for simple sequence repeats (SSRs) found in ESTs derived from an EST-database development project ('Marine Genomics Europe' Network of Excellence). Different motifs of di-, tri-, tetra-, penta- and hexanucleotide SSRs were evaluated for variation in length and position in the expressed sequences, relative abundance and distribution in gilthead sea bream (Sparus aurata). We found 899 ESTs that harbor 997 SSRs (4.94%). On average, one SSR was found per 2.95. kb of EST sequence and the dinucleotide SSRs are the most abundant accounting for 47.6% of the total number.EST-SSRs were used as template for primer design. 664 primer pairs could be successfully identified and a subset of 206 pairs of primers was synthesized, PCR-tested and visualized on ethidium bromide stained agarose gels. The main objective was to further assess the potential of EST-SSRs as informative markers and investigate their cross-species amplification in sixteen teleost fish species: seven sparid species and nine other species from different families. Approximately 78% of the primer pairs gave PCR products of expected size in gilthead sea bream, and as expected, the rate of successful amplification of sea bream EST-SSRs was higher in sparids, lower in other perciforms and even lower in species of the Clupeiform and Gadiform orders. We finally determined the polymorphism and the heterozygosity of 63 markers in a wild gilthead sea bream population; fifty-eight loci were found to be polymorphic with the expected heterozygosity and the number of alleles ranging from 0.089 to 0.946 and from 2 to 27, respectively. These tools and markers are expected to enhance the available genetic linkage map in gilthead sea bream, to assist comparative mapping and genome analyses for this species and further with other model fish species and finally to help advance genetic analysis for cultivated and wild populations and accelerate breeding programs. © 2011 Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We screened for simple sequence repeats (SSRs) found in ESTs derived from an EST-database development project ('Marine Genomics Europe' Network of Excellence). Different motifs of di-, tri-, tetra-, penta- and hexanucleotide SSRs were evaluated for variation in length and position in the expressed sequences, relative abundance and distribution in gilthead sea bream (Sparus aurata). We found 899 ESTs that harbor 997 SSRs (4.94%). On average, one SSR was found per 2.95. kb of EST sequence and the dinucleotide SSRs are the most abundant accounting for 47.6% of the total number.EST-SSRs were used as template for primer design. 664 primer pairs could be successfully identified and a subset of 206 pairs of primers was synthesized, PCR-tested and visualized on ethidium bromide stained agarose gels. The main objective was to further assess the potential of EST-SSRs as informative markers and investigate their cross-species amplification in sixteen teleost fish species: seven sparid species and nine other species from different families. Approximately 78% of the primer pairs gave PCR products of expected size in gilthead sea bream, and as expected, the rate of successful amplification of sea bream EST-SSRs was higher in sparids, lower in other perciforms and even lower in species of the Clupeiform and Gadiform orders. We finally determined the polymorphism and the heterozygosity of 63 markers in a wild gilthead sea bream population; fifty-eight loci were found to be polymorphic with the expected heterozygosity and the number of alleles ranging from 0.089 to 0.946 and from 2 to 27, respectively. These tools and markers are expected to enhance the available genetic linkage map in gilthead sea bream, to assist comparative mapping and genome analyses for this species and further with other model fish species and finally to help advance genetic analysis for cultivated and wild populations and accelerate breeding programs. © 2011 Elsevier B.V. |
Sarropoulou, E; Nousdili, D; Kotoulas, G; Magoulas, A Functional Divergences of GAPDH Isoforms During Early Development in Two Perciform Fish Species Journal Article Marine Biotechnology, 13 (6), pp. 1115–1124, 2011, ISSN: 14362228. @article{sarropoulou_functional_2011, title = {Functional Divergences of GAPDH Isoforms During Early Development in Two Perciform Fish Species}, author = {E Sarropoulou and D Nousdili and G Kotoulas and A Magoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80255123494&doi=10.1007%2fs10126-011-9375-6&partnerID=40&md5=3c8235e29f2fd9b4620e515d6bf00c6c}, doi = {10.1007/s10126-011-9375-6}, issn = {14362228}, year = {2011}, date = {2011-01-01}, journal = {Marine Biotechnology}, volume = {13}, number = {6}, pages = {1115--1124}, abstract = {Glyceraldehyde-3-phospate dehydrogenase (GAPDH) is involved in basic cell catabolic processes and, as it is thought to be continuously expressed, belongs to the group of housekeeping genes. Thus, it is frequently used as an internal control in quantitative gene expression studies. However, the evidence of different expression patterns in a broad range of organisms and tissues, as well as the occurrence of different isoforms, shows that GAPDH has to be reevaluated as an internal control in qPCR studies, and its annotation has to be enriched. GAPDH has been shown to be involved in the pathway of energy and carbon molecule supply as well as in transcription and apoptosis. In the present study, we isolated the two isoforms, GAPDH-1 and GAPDH-2, of the gilthead sea bream (Sparus aurata) and the European sea bass (Dicentrarchus labrax). We inferred the phylogenetic relationships to ten other fish species and gave the gene structure of both genes. We further investigated gene expression analysis in both species for different developmental stages showing divergent gene expression of the two isoforms and the possible function of GAPDH-1 as a maternal gene. © 2011 Springer Science+Business Media, LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Glyceraldehyde-3-phospate dehydrogenase (GAPDH) is involved in basic cell catabolic processes and, as it is thought to be continuously expressed, belongs to the group of housekeeping genes. Thus, it is frequently used as an internal control in quantitative gene expression studies. However, the evidence of different expression patterns in a broad range of organisms and tissues, as well as the occurrence of different isoforms, shows that GAPDH has to be reevaluated as an internal control in qPCR studies, and its annotation has to be enriched. GAPDH has been shown to be involved in the pathway of energy and carbon molecule supply as well as in transcription and apoptosis. In the present study, we isolated the two isoforms, GAPDH-1 and GAPDH-2, of the gilthead sea bream (Sparus aurata) and the European sea bass (Dicentrarchus labrax). We inferred the phylogenetic relationships to ten other fish species and gave the gene structure of both genes. We further investigated gene expression analysis in both species for different developmental stages showing divergent gene expression of the two isoforms and the possible function of GAPDH-1 as a maternal gene. © 2011 Springer Science+Business Media, LLC. |
Kuhl, H; Sarropoulou, E; Tine, M; Kotoulas, G; Magoulas, A; Reinhardt, R A comparative BAC map for the gilthead sea bream (Sparus aurata L.) Journal Article Journal of Biomedicine and Biotechnology, 2011 , 2011, ISSN: 11107243. @article{kuhl_comparative_2011, title = {A comparative BAC map for the gilthead sea bream (Sparus aurata L.)}, author = {H Kuhl and E Sarropoulou and M Tine and G Kotoulas and A Magoulas and R Reinhardt}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78349264993&doi=10.1155%2f2011%2f329025&partnerID=40&md5=ca64bd3429a9d3215bd26e61a9c5afdb}, doi = {10.1155/2011/329025}, issn = {11107243}, year = {2011}, date = {2011-01-01}, journal = {Journal of Biomedicine and Biotechnology}, volume = {2011}, abstract = {This study presents the first comparative BAC map of the gilthead sea bream (Sparus aurata), a highly valuated marine aquaculture fish species in the Mediterranean. High-throughput end sequencing of a BAC library yielded 92,468 reads (60.6Mbp). Comparative mapping was achieved by anchoring BAC end sequences to the three-spined stickleback (Gasterosteus aculeatus) genome. BACs that were consistently ordered along the stickleback chromosomes accounted for 14,265 clones. A fraction of 5,249 BACs constituted a minimal tiling path that covers 73.5 of the stickleback chromosomes and 70.2 of the genes that have been annotated. The N50 size of 1,485 BACtigs consisting of redundant BACs is 337,253bp. The largest BACtig covers 2.15Mbp in the stickleback genome. According to the insert size distribution of mapped BACs the sea bream genome is 1.71-fold larger than the stickleback genome. These results represent a valuable tool to researchers in the field and may support future projects to elucidate the whole sea bream genome. Copyright © 2011 Heiner Kuhl et al.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study presents the first comparative BAC map of the gilthead sea bream (Sparus aurata), a highly valuated marine aquaculture fish species in the Mediterranean. High-throughput end sequencing of a BAC library yielded 92,468 reads (60.6Mbp). Comparative mapping was achieved by anchoring BAC end sequences to the three-spined stickleback (Gasterosteus aculeatus) genome. BACs that were consistently ordered along the stickleback chromosomes accounted for 14,265 clones. A fraction of 5,249 BACs constituted a minimal tiling path that covers 73.5 of the stickleback chromosomes and 70.2 of the genes that have been annotated. The N50 size of 1,485 BACtigs consisting of redundant BACs is 337,253bp. The largest BACtig covers 2.15Mbp in the stickleback genome. According to the insert size distribution of mapped BACs the sea bream genome is 1.71-fold larger than the stickleback genome. These results represent a valuable tool to researchers in the field and may support future projects to elucidate the whole sea bream genome. Copyright © 2011 Heiner Kuhl et al. |
2010 |
Skaraki, K; Kotoulas, Giorgios; Pantazidou, Adriani Description of bacterial association with two sponge species inhabit hard substrates of Northern Crete Inproceedings Athens, Greece, 2010, (Publication Title: 2nd EFMS Conference, Athens, Greece,15-16 October). @inproceedings{skaraki_description_2010, title = {Description of bacterial association with two sponge species inhabit hard substrates of Northern Crete}, author = {K Skaraki and Giorgios Kotoulas and Adriani Pantazidou}, year = {2010}, date = {2010-10-01}, address = {Athens, Greece}, note = {Publication Title: 2nd EFMS Conference, Athens, Greece,15-16 October}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Sarropoulou, E; Fernandes, J M O; Mitter, K; Magoulas, A; Mulero, V; Sepulcre, M P; Figueras, A; Novoa, B; Kotoulas, G Evolution of a multifunctional gene: The warm temperature acclimation protein Wap65 in the European seabass Dicentrarchus labrax Journal Article Molecular Phylogenetics and Evolution, 55 (2), pp. 640–649, 2010, ISSN: 10557903. @article{sarropoulou_evolution_2010, title = {Evolution of a multifunctional gene: The warm temperature acclimation protein Wap65 in the European seabass Dicentrarchus labrax}, author = {E Sarropoulou and J M O Fernandes and K Mitter and A Magoulas and V Mulero and M P Sepulcre and A Figueras and B Novoa and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77950028567&doi=10.1016%2fj.ympev.2009.10.001&partnerID=40&md5=3f221df31801c535de9cf8d09a14bb2e}, doi = {10.1016/j.ympev.2009.10.001}, issn = {10557903}, year = {2010}, date = {2010-01-01}, journal = {Molecular Phylogenetics and Evolution}, volume = {55}, number = {2}, pages = {640--649}, abstract = {The warm temperature acclimation protein Wap65 has been shown to be involved in temperature acclimation, in immune response as well as in development. In teleosts, two types of Wap65 proteins, Wap65-1 and Wap65-2 are found, both acting as a multifunctional agent in several biological processes. In the present study we identified both transcripts Wap65-1 and Wap65-2 for the European seabass (Dicentrarchus labrax), examined their evolutionary rate and performed selection tests. The two paralogues were shown to be under moderate positive selection indicating their evolutionary adaptation. This functional diversification was further explored through expression studies. Both transcripts were differentially expressed during development as well as in various tissues and pathogen challenges, showing that Wap65-1 and Wap65-2 have evolved diverse functions. These results direct to the hypothesis that Wap65 proteins may, similarly to heat-shock proteins, have a general role in cell physiology. © 2009 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The warm temperature acclimation protein Wap65 has been shown to be involved in temperature acclimation, in immune response as well as in development. In teleosts, two types of Wap65 proteins, Wap65-1 and Wap65-2 are found, both acting as a multifunctional agent in several biological processes. In the present study we identified both transcripts Wap65-1 and Wap65-2 for the European seabass (Dicentrarchus labrax), examined their evolutionary rate and performed selection tests. The two paralogues were shown to be under moderate positive selection indicating their evolutionary adaptation. This functional diversification was further explored through expression studies. Both transcripts were differentially expressed during development as well as in various tissues and pathogen challenges, showing that Wap65-1 and Wap65-2 have evolved diverse functions. These results direct to the hypothesis that Wap65 proteins may, similarly to heat-shock proteins, have a general role in cell physiology. © 2009 Elsevier Inc. All rights reserved. |
2009 |
Kasapidis, P; Pakaki, V; Kotoulas, G; Magoulas, A Isolation and characterization of 18 new polymorphic microsatellite loci for the swordfish, Xiphias gladius Journal Article Molecular Ecology Resources, 9 (5), pp. 1383–1386, 2009, ISSN: 1755098X. @article{kasapidis_isolation_2009, title = {Isolation and characterization of 18 new polymorphic microsatellite loci for the swordfish, Xiphias gladius}, author = {P Kasapidis and V Pakaki and G Kotoulas and A Magoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-68949088416&doi=10.1111%2fj.1755-0998.2009.02665.x&partnerID=40&md5=1d9054fa754b8be29bee29ef86e5c592}, doi = {10.1111/j.1755-0998.2009.02665.x}, issn = {1755098X}, year = {2009}, date = {2009-01-01}, journal = {Molecular Ecology Resources}, volume = {9}, number = {5}, pages = {1383--1386}, abstract = {Eighteen microsatellite loci (13 di- and 5 tri-repeats) were isolated from swordfish and characterized in two populations from the Atlantic Ocean and Mediterranean Sea. The number of alleles per locus ranged from two to 29 and the observed heterozygosity from 0.302 to 0.953. All but one locus conformed to Hardy-Weinberg expectations and there was no evidence for linkage disequilibrium between loci. © 2009 Blackwell Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Eighteen microsatellite loci (13 di- and 5 tri-repeats) were isolated from swordfish and characterized in two populations from the Atlantic Ocean and Mediterranean Sea. The number of alleles per locus ranged from two to 29 and the observed heterozygosity from 0.302 to 0.953. All but one locus conformed to Hardy-Weinberg expectations and there was no evidence for linkage disequilibrium between loci. © 2009 Blackwell Publishing Ltd. |
Sarropoulou, E; Sepulcre, P; Poisa-Beiro, L; Mulero, V; Meseguer, J; Figueras, A; Novoa, B; Terzoglou, V; Reinhardt, R; Magoulas, A; Kotoulas, G Profiling of infection specific mRNA transcripts of the European seabass Dicentrarchus labrax Journal Article BMC Genomics, 10 , 2009, ISSN: 14712164. @article{sarropoulou_profiling_2009, title = {Profiling of infection specific mRNA transcripts of the European seabass Dicentrarchus labrax}, author = {E Sarropoulou and P Sepulcre and L Poisa-Beiro and V Mulero and J Meseguer and A Figueras and B Novoa and V Terzoglou and R Reinhardt and A Magoulas and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-65449174874&doi=10.1186%2f1471-2164-10-157&partnerID=40&md5=fc9c5760823ecfa4f4b04e26d52e3c4c}, doi = {10.1186/1471-2164-10-157}, issn = {14712164}, year = {2009}, date = {2009-01-01}, journal = {BMC Genomics}, volume = {10}, abstract = {Background: The European seabass (Dicentrarchus labrax), one of the most extensively cultured species in European aquaculture productions, is, along with the gilthead sea bream (Sparus aurata), a prospective model species for the Perciformes which includes several other commercially important species. Massive mortalities may be caused by bacterial or viral infections in intensive aquaculture production. Revealing transcripts involved in immune response and studying their relative expression enhances the understanding of the immune response mechanism and consequently also the creation of vaccines. The analysis of expressed sequence tags (EST) is an efficient and easy approach for gene discovery, comparative genomics and for examining gene expression in specific tissues in a qualitative and quantitative way. Results: Here we describe the construction, analysis and comparison of a total of ten cDNA libraries, six from different tissues infected with V. anguillarum (liver, spleen, head kidney, gill, peritoneal exudates and intestine) and four cDNA libraries from different tissues infected with Nodavirus (liver, spleen, head kidney and brain). In total 9605 sequences representing 3075 (32%) unique sequences (set of sequences obtained after clustering) were obtained and analysed. Among the sequences several immune-related proteins were identified for the first time in the order of Perciformes as well as in Teleostei. Conclusion: The present study provides new information to the Gene Index of seabass. It gives a unigene set that will make a significant contribution to functional genomic studies and to studies of differential gene expression in relation to the immune system. In addition some of the potentially interesting genes identified by in silico analysis and confirmed by real-time PCR are putative biomarkers for bacterial and viral infections in fish. © 2009 Sarropoulou et al; licensee BioMed Central Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background: The European seabass (Dicentrarchus labrax), one of the most extensively cultured species in European aquaculture productions, is, along with the gilthead sea bream (Sparus aurata), a prospective model species for the Perciformes which includes several other commercially important species. Massive mortalities may be caused by bacterial or viral infections in intensive aquaculture production. Revealing transcripts involved in immune response and studying their relative expression enhances the understanding of the immune response mechanism and consequently also the creation of vaccines. The analysis of expressed sequence tags (EST) is an efficient and easy approach for gene discovery, comparative genomics and for examining gene expression in specific tissues in a qualitative and quantitative way. Results: Here we describe the construction, analysis and comparison of a total of ten cDNA libraries, six from different tissues infected with V. anguillarum (liver, spleen, head kidney, gill, peritoneal exudates and intestine) and four cDNA libraries from different tissues infected with Nodavirus (liver, spleen, head kidney and brain). In total 9605 sequences representing 3075 (32%) unique sequences (set of sequences obtained after clustering) were obtained and analysed. Among the sequences several immune-related proteins were identified for the first time in the order of Perciformes as well as in Teleostei. Conclusion: The present study provides new information to the Gene Index of seabass. It gives a unigene set that will make a significant contribution to functional genomic studies and to studies of differential gene expression in relation to the immune system. In addition some of the potentially interesting genes identified by in silico analysis and confirmed by real-time PCR are putative biomarkers for bacterial and viral infections in fish. © 2009 Sarropoulou et al; licensee BioMed Central Ltd. |
Mitter, K; Kotoulas, G; Magoulas, A; Mulero, V; Sepulcre, P; Figueras, A; Novoa, B; Sarropoulou, E Evaluation of candidate reference genes for QPCR during ontogenesis and of immune-relevant tissues of European seabass (Dicentrarchus labrax) Journal Article Comparative Biochemistry and Physiology - B Biochemistry and Molecular Biology, 153 (4), pp. 340–347, 2009, ISSN: 10964959. @article{mitter_evaluation_2009, title = {Evaluation of candidate reference genes for QPCR during ontogenesis and of immune-relevant tissues of European seabass (Dicentrarchus labrax)}, author = {K Mitter and G Kotoulas and A Magoulas and V Mulero and P Sepulcre and A Figueras and B Novoa and E Sarropoulou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-66949114543&doi=10.1016%2fj.cbpb.2009.04.009&partnerID=40&md5=bed24032b15be5942ff65a1f48e41d30}, doi = {10.1016/j.cbpb.2009.04.009}, issn = {10964959}, year = {2009}, date = {2009-01-01}, journal = {Comparative Biochemistry and Physiology - B Biochemistry and Molecular Biology}, volume = {153}, number = {4}, pages = {340--347}, abstract = {The expression level of mRNA can vary significantly in different experimental conditions, such as stress, infection, developmental stage or tissue. Suitable reference genes are expected to exhibit constant expression levels. However no single gene is constitutively expressed in all cell types and under all experimental conditions. It has become clear that expression stability of the intended reference gene has to be examined before each experiment. For expression studies using quantitative real-time PCR (qPCR) at least two reference genes have to be applied. So far expression studies in the European seabass (Dicentrarchus labrax) as well as in the Gilthead seabream (Sparus aurata) have been performed with only one reference gene (S18, Ef-1 alpha or Gapdh). Though significant variations showed up in other teleost species such as the Atlantic halibut and the zebrafish affirming the need for proper normalization strategies, the present study aims at identifying suitable reference genes among nine candidates [glyceraldehyde-phosphate-dehydrogenase (Gapdh), β-actin (two regions of β-actin), 40S ribosomal protein S30 (Fau), ribosomal protein L13 a (L13a), β2-tubulin (Tubb2) and tyrosine 3 monooxygenase/tryptophan 5-monooxygenase activation protein (Tyr)] for expression analysis of 8 developmental stages and a tissue panel (spleen, liver, kidney and brain) with samples infected with Nodavirus and Vibrio anguillarum in D. labrax. Besides the analysis of raw Ct-values, the gene expression stability was determined using two different software applications BestKeeper and NormFinder. According to both algorithms the best two reference genes for an appropriate normalization approach during D. labrax development are Ef-1 alpha and L13a whereas in the tissue panel Fau and L13a are recommended for qPCR normalization. © 2009 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The expression level of mRNA can vary significantly in different experimental conditions, such as stress, infection, developmental stage or tissue. Suitable reference genes are expected to exhibit constant expression levels. However no single gene is constitutively expressed in all cell types and under all experimental conditions. It has become clear that expression stability of the intended reference gene has to be examined before each experiment. For expression studies using quantitative real-time PCR (qPCR) at least two reference genes have to be applied. So far expression studies in the European seabass (Dicentrarchus labrax) as well as in the Gilthead seabream (Sparus aurata) have been performed with only one reference gene (S18, Ef-1 alpha or Gapdh). Though significant variations showed up in other teleost species such as the Atlantic halibut and the zebrafish affirming the need for proper normalization strategies, the present study aims at identifying suitable reference genes among nine candidates [glyceraldehyde-phosphate-dehydrogenase (Gapdh), β-actin (two regions of β-actin), 40S ribosomal protein S30 (Fau), ribosomal protein L13 a (L13a), β2-tubulin (Tubb2) and tyrosine 3 monooxygenase/tryptophan 5-monooxygenase activation protein (Tyr)] for expression analysis of 8 developmental stages and a tissue panel (spleen, liver, kidney and brain) with samples infected with Nodavirus and Vibrio anguillarum in D. labrax. Besides the analysis of raw Ct-values, the gene expression stability was determined using two different software applications BestKeeper and NormFinder. According to both algorithms the best two reference genes for an appropriate normalization approach during D. labrax development are Ef-1 alpha and L13a whereas in the tissue panel Fau and L13a are recommended for qPCR normalization. © 2009 Elsevier Inc. All rights reserved. |
2008 |
Skaraki, K; Kotoulas, Giorgios; Nicolaidou, Artemis; A, Magoulas; Pantazidou, Adriani Bacterial symbiosis in marine polychaete Hermodice carunculata Pallas 1766 Inproceedings Athens, Greece, 2008, (Publication Title: 1st National MikroBioKosmos Society Conference, Athens, Greece, 12-14 December). @inproceedings{skaraki_bacterial_2008, title = {Bacterial symbiosis in marine polychaete Hermodice carunculata Pallas 1766}, author = {K Skaraki and Giorgios Kotoulas and Artemis Nicolaidou and Magoulas A and Adriani Pantazidou}, year = {2008}, date = {2008-12-01}, address = {Athens, Greece}, note = {Publication Title: 1st National MikroBioKosmos Society Conference, Athens, Greece, 12-14 December}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Sotiropoulos, K; Tsaparis, D; Eleftherakos, K; Kotoulas, G; Legakis, A; Kasapidis, P Molecular Ecology Resources, 8 (6), pp. 1402–1404, 2008, ISSN: 1755098X. @article{sotiropoulos_new_2008, title = {New polymorphic microsatellite loci for the Macedonian crested newt, Triturus macedonicus, and cross-priming testing in four other crested newt species}, author = {K Sotiropoulos and D Tsaparis and K Eleftherakos and G Kotoulas and A Legakis and P Kasapidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-55149089288&doi=10.1111%2fj.1755-0998.2008.02318.x&partnerID=40&md5=fb01beea4ddfaf49596cc574066f8b1d}, doi = {10.1111/j.1755-0998.2008.02318.x}, issn = {1755098X}, year = {2008}, date = {2008-01-01}, journal = {Molecular Ecology Resources}, volume = {8}, number = {6}, pages = {1402--1404}, abstract = {Eleven microsatellites have been characterized for Triturus macedonicus. Nine loci showed different variation patterns in a sample of 40 individuals from a single breeding pond in Zagori province (Greece), with an average number of 4.2 alleles per locus and an expected heterozygosity ranging from 0.1199 to 0.8079. Distinct cross-priming amplification rates were recovered on four additional crested newt species. Two monomorphic T. macedonicus loci were polymorphic in other Triturus species. The microsatellites developed herein could be a useful intraspecific genetic tool to undertake fine-scale population genetic analyses as well as in the study of contact zones between crested newt species. © 2008 The Authors.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Eleven microsatellites have been characterized for Triturus macedonicus. Nine loci showed different variation patterns in a sample of 40 individuals from a single breeding pond in Zagori province (Greece), with an average number of 4.2 alleles per locus and an expected heterozygosity ranging from 0.1199 to 0.8079. Distinct cross-priming amplification rates were recovered on four additional crested newt species. Two monomorphic T. macedonicus loci were polymorphic in other Triturus species. The microsatellites developed herein could be a useful intraspecific genetic tool to undertake fine-scale population genetic analyses as well as in the study of contact zones between crested newt species. © 2008 The Authors. |
Antoniou, Aglaia; Kotoulas, Georgios; Magoulas, Antonios; Alves, Paulo Célio Evidence of autumn reproduction in female European hares (Lepus europaeus) from southern Europe Journal Article European Journal of Wildlife Research, 2008, ISSN: 16124642, (ISBN: 1612-4642). @article{antoniou_evidence_2008, title = {Evidence of autumn reproduction in female European hares (Lepus europaeus) from southern Europe}, author = {Aglaia Antoniou and Georgios Kotoulas and Antonios Magoulas and Paulo Célio Alves}, doi = {10.1007/s10344-008-0182-y}, issn = {16124642}, year = {2008}, date = {2008-01-01}, journal = {European Journal of Wildlife Research}, abstract = {Information on reproductive biology of the European hare (Lepus europaeus) in different environmental and landscape conditions comprises part of fundamental knowledge regarding species' adaptive responses as well as many aspects of its biology. Most of the studies conducted on European hare reproduction are confined to midlatitude and northern populations, whereas no data exist on the indigenous southern populations. Here, we present information on reproductive characteristics of European hares inhabiting Mediterranean ecosystems on the island of Crete, Greece for two successive hunting seasons. Although the annual reproductive cycle of the species is well known, with an autumn sexual inactivity, the duration of this period is subjected to fluctuations in different years and for different areas. According to our data, hare populations of Crete present an autumn-early winter reproductive activity with high proportions of pregnant females observed in all the months of the study. Furthermore, the estimated mean litter size (1.54 SE +/- 0.07) while signed to the lowest values ever observed for European hares is similar to values obtained in continuous breeding species of the same genus, Lepus granatensis, Lepus corsicanus, Lepus (capensis) mediterraneus, and Lepus capensis also inhabiting warm climates. In conclusion, our results suggest that Cretan European hare populations exhibit a reproductively active period during autumn-early winter where proportions of pregnant females and litter size give a strong indication of a continuous reproduction throughout the year.}, note = {ISBN: 1612-4642}, keywords = {}, pubstate = {published}, tppubtype = {article} } Information on reproductive biology of the European hare (Lepus europaeus) in different environmental and landscape conditions comprises part of fundamental knowledge regarding species' adaptive responses as well as many aspects of its biology. Most of the studies conducted on European hare reproduction are confined to midlatitude and northern populations, whereas no data exist on the indigenous southern populations. Here, we present information on reproductive characteristics of European hares inhabiting Mediterranean ecosystems on the island of Crete, Greece for two successive hunting seasons. Although the annual reproductive cycle of the species is well known, with an autumn sexual inactivity, the duration of this period is subjected to fluctuations in different years and for different areas. According to our data, hare populations of Crete present an autumn-early winter reproductive activity with high proportions of pregnant females observed in all the months of the study. Furthermore, the estimated mean litter size (1.54 SE +/- 0.07) while signed to the lowest values ever observed for European hares is similar to values obtained in continuous breeding species of the same genus, Lepus granatensis, Lepus corsicanus, Lepus (capensis) mediterraneus, and Lepus capensis also inhabiting warm climates. In conclusion, our results suggest that Cretan European hare populations exhibit a reproductively active period during autumn-early winter where proportions of pregnant females and litter size give a strong indication of a continuous reproduction throughout the year. |
Sarropoulou, E; Nousdili, D; Magoulas, A; Kotoulas, G Linking the genomes of nonmodel teleosts through comparative genomics Journal Article Marine Biotechnology, 10 (3), pp. 227–233, 2008, ISSN: 14362228. @article{sarropoulou_linking_2008, title = {Linking the genomes of nonmodel teleosts through comparative genomics}, author = {E Sarropoulou and D Nousdili and A Magoulas and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-42149158792&doi=10.1007%2fs10126-007-9066-5&partnerID=40&md5=2b3b32a93f61d0a2349b4a40f65afc40}, doi = {10.1007/s10126-007-9066-5}, issn = {14362228}, year = {2008}, date = {2008-01-01}, journal = {Marine Biotechnology}, volume = {10}, number = {3}, pages = {227--233}, abstract = {Recently the genomes of two more teleost species have been released: the medaka (Oryzias latipes), and the three-spined stickleback (Gasterosteus aculateus). The rapid developments in genomics of fish species paved the way to new and valuable research in comparative genetics and genomics. With the accumulation of information in model species, the genetic and genomic characterization of nonmodel, but economically important species, is now feasible. Furthermore, comparison of low coverage gene maps of aquacultured fish species against fully sequenced fish species will enhance the efficiency of candidate genes identification projected for quantitative trait loci (QTL) scans for traits of commercial interest. This study shows the syntenic relationship between the genomes of six different teleost species, including three fully sequenced model species: Tetraodon nigroviridis, Oryzias latipes, Gasterosteus aculateus, and three marine species of commercial and evolutionary interest: Sparus aurata, Dicentrarchus labrax, Oreochromis spp. All three commercial fish species belong to the order Perciformes, which is the richest in number of species (approximately 10,000) but poor in terms of available genomic information and tools. Syntenic relationships were established by using 800 EST and microsatellites sequences successfully mapped on the RH map of seabream. Comparison to the stickleback genome produced most positive BLAT hits (58%) followed by medaka (32%) and Tetraodon (30%). Thus, stickleback was used as the major stepping stone to compare seabass and tilapia to seabream. In addition to the significance for the aquaculture industry, this approach can encompass important ecological and evolutionary implications. © 2007 Springer Science+Business Media, LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recently the genomes of two more teleost species have been released: the medaka (Oryzias latipes), and the three-spined stickleback (Gasterosteus aculateus). The rapid developments in genomics of fish species paved the way to new and valuable research in comparative genetics and genomics. With the accumulation of information in model species, the genetic and genomic characterization of nonmodel, but economically important species, is now feasible. Furthermore, comparison of low coverage gene maps of aquacultured fish species against fully sequenced fish species will enhance the efficiency of candidate genes identification projected for quantitative trait loci (QTL) scans for traits of commercial interest. This study shows the syntenic relationship between the genomes of six different teleost species, including three fully sequenced model species: Tetraodon nigroviridis, Oryzias latipes, Gasterosteus aculateus, and three marine species of commercial and evolutionary interest: Sparus aurata, Dicentrarchus labrax, Oreochromis spp. All three commercial fish species belong to the order Perciformes, which is the richest in number of species (approximately 10,000) but poor in terms of available genomic information and tools. Syntenic relationships were established by using 800 EST and microsatellites sequences successfully mapped on the RH map of seabream. Comparison to the stickleback genome produced most positive BLAT hits (58%) followed by medaka (32%) and Tetraodon (30%). Thus, stickleback was used as the major stepping stone to compare seabass and tilapia to seabream. In addition to the significance for the aquaculture industry, this approach can encompass important ecological and evolutionary implications. © 2007 Springer Science+Business Media, LLC. |
Daskalakis, M; Rigas, F; A, Magoulas; Kotoulas, Giorgios; Katsikis, I; Bakolas, A; Karageorgis, A; Antoniou, A; Skaraki, K Development of a biotechnological method for the restoration of stone monuments Inproceedings pp. 61–62, Athens, Greece, 2008, (Publication Title: 1st National MikroBioKosmos Society Conference, Athens, Greece, 12-14 December Type: Poster). @inproceedings{daskalakis_development_2008, title = {Development of a biotechnological method for the restoration of stone monuments}, author = {M Daskalakis and F Rigas and Magoulas A and Giorgios Kotoulas and I Katsikis and A Bakolas and A Karageorgis and A Antoniou and K Skaraki}, year = {2008}, date = {2008-01-01}, pages = {61--62}, address = {Athens, Greece}, note = {Publication Title: 1st National MikroBioKosmos Society Conference, Athens, Greece, 12-14 December Type: Poster}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Chistiakov, D A; Tsigenopoulos, C S; Lagnel, J; Guo, Y -M; Hellemans, B; Haley, C S; Volckaert, F A M; Kotoulas, G A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bass Dicentrarchus labrax L. Journal Article Animal Genetics, 39 (6), pp. 623–634, 2008, ISSN: 02689146. @article{chistiakov_combined_2008, title = {A combined AFLP and microsatellite linkage map and pilot comparative genomic analysis of European sea bass Dicentrarchus labrax L.}, author = {D A Chistiakov and C S Tsigenopoulos and J Lagnel and Y -M Guo and B Hellemans and C S Haley and F A M Volckaert and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-55949121630&doi=10.1111%2fj.1365-2052.2008.01786.x&partnerID=40&md5=02380f0e77a85dcbee993dc81962661e}, doi = {10.1111/j.1365-2052.2008.01786.x}, issn = {02689146}, year = {2008}, date = {2008-01-01}, journal = {Animal Genetics}, volume = {39}, number = {6}, pages = {623--634}, abstract = {European sea bass (Dicentrarchus labrax L., Moronidae, Teleostei) sustains a regional fishery and is commonly farmed in the Mediterranean basin, but has not undergone much long-term genetic improvement. An updated genetic linkage map of the European sea bass was constructed using 190 microsatellites, 176 amplified fragment length polymorphisms and two single nucleotide polymorphisms. From the 45 new microsatellite markers (including 31 type I markers) reported in this study, 28 were mapped. A total of 368 markers were assembled into 35 linkage groups. Among these markers, 28 represented type I (coding) markers, including those located within the peptide Y, SOX10, PXN1, ERA and TCRB genes (linkage groups 1, 7, 16, 17 and 27 respectively). The sex-averaged map spanned 1373.1 centimorgans (cM) of the genome. The female map measured 1380.0 cM, whereas the male map measured 1046.9 cM, leading to a female-to-male (F:M) recombination rate ratio of 1.32:1. The intermarker spacing of the second-generation linkage map of the European sea bass was 3.67 cM, which is smaller than that of the first-generation linkage map (5.03 cM). Comparative mapping of microsatellite flanking regions was performed with five model teleosts and this revealed a high percentage (33.6%) of evolutionarily conserved regions with the three-spined stickleback. © 2008 The Authors.}, keywords = {}, pubstate = {published}, tppubtype = {article} } European sea bass (Dicentrarchus labrax L., Moronidae, Teleostei) sustains a regional fishery and is commonly farmed in the Mediterranean basin, but has not undergone much long-term genetic improvement. An updated genetic linkage map of the European sea bass was constructed using 190 microsatellites, 176 amplified fragment length polymorphisms and two single nucleotide polymorphisms. From the 45 new microsatellite markers (including 31 type I markers) reported in this study, 28 were mapped. A total of 368 markers were assembled into 35 linkage groups. Among these markers, 28 represented type I (coding) markers, including those located within the peptide Y, SOX10, PXN1, ERA and TCRB genes (linkage groups 1, 7, 16, 17 and 27 respectively). The sex-averaged map spanned 1373.1 centimorgans (cM) of the genome. The female map measured 1380.0 cM, whereas the male map measured 1046.9 cM, leading to a female-to-male (F:M) recombination rate ratio of 1.32:1. The intermarker spacing of the second-generation linkage map of the European sea bass was 3.67 cM, which is smaller than that of the first-generation linkage map (5.03 cM). Comparative mapping of microsatellite flanking regions was performed with five model teleosts and this revealed a high percentage (33.6%) of evolutionarily conserved regions with the three-spined stickleback. © 2008 The Authors. |
2007 |
Kotoulas, G; Mejuto, J; Antoniou, A; Kasapidis, P; Tserpes, G; Piccineti, C; Peristeraki, P; Garcia-Cortes, B; Oikonomaki, K; la Serna, De M J; Magoulas, A Global genetic structure of the swordfish Xiphias gladius, as revealed by microsatellite markers Journal Article Collect. Vol. Sci. Pap. ICCAT, 61 , pp. 79–88, 2007. @article{kotoulas_global_2007, title = {Global genetic structure of the swordfish Xiphias gladius, as revealed by microsatellite markers}, author = {G Kotoulas and J Mejuto and A Antoniou and P Kasapidis and G Tserpes and C Piccineti and P Peristeraki and B Garcia-Cortes and K Oikonomaki and M J De la Serna and A Magoulas}, year = {2007}, date = {2007-01-01}, journal = {Collect. Vol. Sci. Pap. ICCAT}, volume = {61}, pages = {79--88}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kasapidis, P; Valeiras, X; Antoniou, A; Kotoulas, Giorgios; Garcia-Cortes, B; Mejuto, J Genetic and growth profiles of three specimens of swordfish (Xiphias gladius) tagged and recaptured in the North Atlantic Journal Article Col. Vol. Sci. Pap., ICCAT SCRS-06-119, 60 (6), pp. 1964–1973, 2007. @article{kasapidis_genetic_2007, title = {Genetic and growth profiles of three specimens of swordfish (Xiphias gladius) tagged and recaptured in the North Atlantic}, author = {P Kasapidis and X Valeiras and A Antoniou and Giorgios Kotoulas and B Garcia-Cortes and J Mejuto}, year = {2007}, date = {2007-01-01}, journal = {Col. Vol. Sci. Pap., ICCAT SCRS-06-119}, volume = {60}, number = {6}, pages = {1964--1973}, abstract = {This paper presents an analysis of the genetic and growth patterns of three swordfish specimens (two males and one female) tagged with traditional tags and later recaptured over a period of time ranging from 2.7 to 5.4 years. Two of these specimens were tagged and recaptured in the NW Atlantic, while the third individual was tagged and recaptured in the NE Atlantic. These three specimens were genotyped for four micro-satellite loci and were analysed together with additional genotyped specimens from Atlantic and Mediterranean areas using a Bayesian cluster analyses. The results suggest that the three recaptured swordfish have a genetic profile that is characteristic of the Atlantic. The growth patterns were seen to differ in two of the specimens analysed (male and female): the male was assumed as a single ring pattern, while the female was assumed as a mostly double ring pattern. The age estimation of these two specimens according to these premises could be accommodated to previous growth studies. The third specimen which is known to be a male at least 6 years of age, tagged and recaptured in the NW Atlantic, was not possible to accommodate to previous growth studies. The examination of genetic data in combination with tagging-recapture information may facilitate the study of aspects related to individual and stock specific growth and elucidate the patterns of ring formation on the hard parts (spines). It would be advisable to enhance the tagging-recapture protocols of swordfish and to include the routine sampling of tissues and hard parts in all the recaptures made by the different fleets.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This paper presents an analysis of the genetic and growth patterns of three swordfish specimens (two males and one female) tagged with traditional tags and later recaptured over a period of time ranging from 2.7 to 5.4 years. Two of these specimens were tagged and recaptured in the NW Atlantic, while the third individual was tagged and recaptured in the NE Atlantic. These three specimens were genotyped for four micro-satellite loci and were analysed together with additional genotyped specimens from Atlantic and Mediterranean areas using a Bayesian cluster analyses. The results suggest that the three recaptured swordfish have a genetic profile that is characteristic of the Atlantic. The growth patterns were seen to differ in two of the specimens analysed (male and female): the male was assumed as a single ring pattern, while the female was assumed as a mostly double ring pattern. The age estimation of these two specimens according to these premises could be accommodated to previous growth studies. The third specimen which is known to be a male at least 6 years of age, tagged and recaptured in the NW Atlantic, was not possible to accommodate to previous growth studies. The examination of genetic data in combination with tagging-recapture information may facilitate the study of aspects related to individual and stock specific growth and elucidate the patterns of ring formation on the hard parts (spines). It would be advisable to enhance the tagging-recapture protocols of swordfish and to include the routine sampling of tissues and hard parts in all the recaptures made by the different fleets. |
Kasapidis, P; Mejuto, J; Tserpes, G; Antoniou, A; Garcia-Cortes, B; Peristeraki, P; Oikonomaki, K; Kotoulas, Giorgios; A., Magoulas Genetic structure of the swordfish (Xiphias gladius) stocks in the Atlantic using microsatellite DNA analysis Journal Article Col. Vol. Sci. Pap., ICCAT SCRS-06-035, 61 , pp. 89–98, 2007. @article{kasapidis_genetic_2007-1, title = {Genetic structure of the swordfish (Xiphias gladius) stocks in the Atlantic using microsatellite DNA analysis}, author = {P Kasapidis and J Mejuto and G Tserpes and A Antoniou and B Garcia-Cortes and P Peristeraki and K Oikonomaki and Giorgios Kotoulas and Magoulas A.}, year = {2007}, date = {2007-01-01}, journal = {Col. Vol. Sci. Pap., ICCAT SCRS-06-035}, volume = {61}, pages = {89--98}, abstract = {The genetic structure of the swordfish (Xiphias gladius) in the Atlantic Ocean was examined by genotyping 1179 individuals for 4 microsatellite loci. These individuals were collected during the years 1999-2002 from the following regions: south Atlantic (up to 5oN), mid-Atlantic (9oN to 20oN), northeast Atlantic (North of 30oN and East of 31oW), northwest Atlantic (North of 30oN and West of 31oW). Gene diversity was very high (textbackslashtextgreater0.96) for all four loci. Heterogeneity tests and pairwise Fsts showed that the South Atlantic group was significantly different from all the other groups (ptextbackslashtextless0.000).These results are in agreement with previous mitochondrial DNA data and do not support a need for changing the 5oN latitude as a boundary for fisheries. Some individuals were also genotyped for the Calmodulin intron 4 gene (CaM) to compare with an earlier dataset for this marker. Allele frequencies found for CaM were in agreement with previous observation and showed a different population structure pattern compared to that revealed by microsatellites. However, the pattern reflected in CaM should be treated with caution, since CaM is only a single diallelic locus, possibly under strong selection. The genotyping of the samples for more microsatellite loci, which is in progress, is expected to further elucidate the genetic structure of the swordfish in the Atlantic, by further increasing resolution.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The genetic structure of the swordfish (Xiphias gladius) in the Atlantic Ocean was examined by genotyping 1179 individuals for 4 microsatellite loci. These individuals were collected during the years 1999-2002 from the following regions: south Atlantic (up to 5oN), mid-Atlantic (9oN to 20oN), northeast Atlantic (North of 30oN and East of 31oW), northwest Atlantic (North of 30oN and West of 31oW). Gene diversity was very high (textbackslashtextgreater0.96) for all four loci. Heterogeneity tests and pairwise Fsts showed that the South Atlantic group was significantly different from all the other groups (ptextbackslashtextless0.000).These results are in agreement with previous mitochondrial DNA data and do not support a need for changing the 5oN latitude as a boundary for fisheries. Some individuals were also genotyped for the Calmodulin intron 4 gene (CaM) to compare with an earlier dataset for this marker. Allele frequencies found for CaM were in agreement with previous observation and showed a different population structure pattern compared to that revealed by microsatellites. However, the pattern reflected in CaM should be treated with caution, since CaM is only a single diallelic locus, possibly under strong selection. The genotyping of the samples for more microsatellite loci, which is in progress, is expected to further elucidate the genetic structure of the swordfish in the Atlantic, by further increasing resolution. |
Sepulcre, M P; Sarropoulou, E; Kotoulas, G; Meseguer, J; Mulero, V Molecular Immunology, 44 (15), pp. 3751–3757, 2007, ISSN: 01615890. @article{sepulcre_vibrio_2007, title = {Vibrio anguillarum evades the immune response of the bony fish sea bass (Dicentrarchus labrax L.) through the inhibition of leukocyte respiratory burst and down-regulation of apoptotic caspases}, author = {M P Sepulcre and E Sarropoulou and G Kotoulas and J Meseguer and V Mulero}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34249287368&doi=10.1016%2fj.molimm.2007.03.021&partnerID=40&md5=1c808da77367528dacb98bc0213effaf}, doi = {10.1016/j.molimm.2007.03.021}, issn = {01615890}, year = {2007}, date = {2007-01-01}, journal = {Molecular Immunology}, volume = {44}, number = {15}, pages = {3751--3757}, abstract = {The mechanisms of the cellular immune response involved in the protection of fish against infection by the pathogenic bacterium Vibrio anguillarum are largely unknown. In the present study, sea bass specimens were injected with live or formalin-killed V. anguillarum and the respiratory burst of leukocytes was measured. The infection of fish resulted in a strong inhibition of the respiratory burst, in contrast with the slight increase in respiratory burst of leukocytes from fish injected with dead bacteria. In addition, we observed a concomitant down-regulation of p22phox and p40phox, two components of the NADPH oxidase, in the leukocytes from infected fish. To investigate whether these differences may be the result of a dysregulation of cytokines expression in infected fish, we cloned several sea bass cytokines, including interleukin-6 (IL-6), IL-8 and three CC chemokines, and performed a detailed expression study with these and other cytokines. Surprisingly, cytokine expression was fairly similar in leukocytes from both live and formalin-killed V. anguillarum-challenged fish, the response being even higher and longer lasting in infected fish. Furthermore, the expression of two key apoptotic caspases, caspase-3 and -9, was down-regulated in leukocytes from infected fish, but remained unaltered in fish injected with formalin-killed bacteria. These results suggest that the virulence mechanisms of V. anguillarum in sea bass involve the inhibition of leukocyte respiratory burst and apoptosis, and thereby providing a safe haven for growth. © 2007 Elsevier Ltd. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The mechanisms of the cellular immune response involved in the protection of fish against infection by the pathogenic bacterium Vibrio anguillarum are largely unknown. In the present study, sea bass specimens were injected with live or formalin-killed V. anguillarum and the respiratory burst of leukocytes was measured. The infection of fish resulted in a strong inhibition of the respiratory burst, in contrast with the slight increase in respiratory burst of leukocytes from fish injected with dead bacteria. In addition, we observed a concomitant down-regulation of p22phox and p40phox, two components of the NADPH oxidase, in the leukocytes from infected fish. To investigate whether these differences may be the result of a dysregulation of cytokines expression in infected fish, we cloned several sea bass cytokines, including interleukin-6 (IL-6), IL-8 and three CC chemokines, and performed a detailed expression study with these and other cytokines. Surprisingly, cytokine expression was fairly similar in leukocytes from both live and formalin-killed V. anguillarum-challenged fish, the response being even higher and longer lasting in infected fish. Furthermore, the expression of two key apoptotic caspases, caspase-3 and -9, was down-regulated in leukocytes from infected fish, but remained unaltered in fish injected with formalin-killed bacteria. These results suggest that the virulence mechanisms of V. anguillarum in sea bass involve the inhibition of leukocyte respiratory burst and apoptosis, and thereby providing a safe haven for growth. © 2007 Elsevier Ltd. All rights reserved. |
Chatziplis, D; Batargias, C; Tsigenopoulos, C S; Magoulas, A; Kollias, S; Kotoulas, G; Volckaert, F A M; Haley, C S Mapping quantitative trait loci in European sea bass (Dicentrarchus labrax): The BASSMAP pilot study Journal Article Aquaculture, 272 (SUPPL. 1), pp. S172–S182, 2007, ISSN: 00448486. @article{chatziplis_mapping_2007, title = {Mapping quantitative trait loci in European sea bass (Dicentrarchus labrax): The BASSMAP pilot study}, author = {D Chatziplis and C Batargias and C S Tsigenopoulos and A Magoulas and S Kollias and G Kotoulas and F A M Volckaert and C S Haley}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-36448952022&doi=10.1016%2fj.aquaculture.2007.08.022&partnerID=40&md5=f7a9a7535621e9b63de89635c3dcf961}, doi = {10.1016/j.aquaculture.2007.08.022}, issn = {00448486}, year = {2007}, date = {2007-01-01}, journal = {Aquaculture}, volume = {272}, number = {SUPPL. 1}, pages = {S172--S182}, abstract = {There are great opportunities for genetic improvement in recently domesticated aquaculture species. However, the lack of appropriate tools limits the application of advanced techniques including the mapping of quantitative trait loci (QTL) and marker-assisted selection (MAS). The recent development of a genetic linkage map for the European sea bass allows the application of such methods for the first time in this species. We report a pilot trial of QTL mapping in a commercial sea bass population as a precursor to the application of MAS. Fertilized eggs collected on a single spawning day produced a population composed of a few large families. Fish were grown under commercial conditions, slaughtered at approximately 470 g and measurements were taken for several traits. Parentage analysis showed that the population consisted of 26 full sib families, with a common dam and several sires. Seven microsatellite markers spanning the largest linkage group (LG1) were then genotyped in 27 parents and their 422 progeny, in order to perform a QTL scan using half-sib interval mapping approaches. Significant QTL affecting six morphometric traits including length and depth, are reported. The success of the procedure demonstrates that QTL analysis can be applied in this species and will contribute to the study and future improvement of traits associated with production, profitability and sustainability. © 2007 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } There are great opportunities for genetic improvement in recently domesticated aquaculture species. However, the lack of appropriate tools limits the application of advanced techniques including the mapping of quantitative trait loci (QTL) and marker-assisted selection (MAS). The recent development of a genetic linkage map for the European sea bass allows the application of such methods for the first time in this species. We report a pilot trial of QTL mapping in a commercial sea bass population as a precursor to the application of MAS. Fertilized eggs collected on a single spawning day produced a population composed of a few large families. Fish were grown under commercial conditions, slaughtered at approximately 470 g and measurements were taken for several traits. Parentage analysis showed that the population consisted of 26 full sib families, with a common dam and several sires. Seven microsatellite markers spanning the largest linkage group (LG1) were then genotyped in 27 parents and their 422 progeny, in order to perform a QTL scan using half-sib interval mapping approaches. Significant QTL affecting six morphometric traits including length and depth, are reported. The success of the procedure demonstrates that QTL analysis can be applied in this species and will contribute to the study and future improvement of traits associated with production, profitability and sustainability. © 2007 Elsevier B.V. All rights reserved. |
Vasileiadou, A; Sarropoulou, E; Tsigenopoulos, K; Reizopoulou, S; Nikolaidou, A; Orfanidis, S; Simboura, M; Kotoulas, G; Arvanitidis, C Polychaete community genetics from the northwestern Greek lagoons sampling: Preliminary results Journal Article MarBEF Newsletter, 6 , pp. 26–27, 2007. @article{vasileiadou_polychaete_2007, title = {Polychaete community genetics from the northwestern Greek lagoons sampling: Preliminary results}, author = {A Vasileiadou and E Sarropoulou and K Tsigenopoulos and S Reizopoulou and A Nikolaidou and S Orfanidis and M Simboura and G Kotoulas and C Arvanitidis}, url = {http://www.marbef.org/outreach/newsletter.php}, year = {2007}, date = {2007-01-01}, journal = {MarBEF Newsletter}, volume = {6}, pages = {26--27}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sarropoulou, E; Franch, R; Louro, B; Power, D M; Bargelloni, L; Magoulas, A; Senger, F; Tsalavouta, M; Patarnello, T; Galibert, F; Kotoulas, G; Geisler, R A gene-based radiation hybrid map of the gilthead sea bream Sparus aurata refines and exploits conserved synteny with Tetraodon nigroviridis Journal Article BMC Genomics, 8 , 2007, ISSN: 14712164. @article{sarropoulou_gene-based_2007, title = {A gene-based radiation hybrid map of the gilthead sea bream Sparus aurata refines and exploits conserved synteny with Tetraodon nigroviridis}, author = {E Sarropoulou and R Franch and B Louro and D M Power and L Bargelloni and A Magoulas and F Senger and M Tsalavouta and T Patarnello and F Galibert and G Kotoulas and R Geisler}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33847690282&doi=10.1186%2f1471-2164-8-44&partnerID=40&md5=0cfe261c54d70945aba802471e9849e7}, doi = {10.1186/1471-2164-8-44}, issn = {14712164}, year = {2007}, date = {2007-01-01}, journal = {BMC Genomics}, volume = {8}, abstract = {Background: Comparative teleost studies are of great interest since they are important in aquaculture and in evolutionary issues. Comparing genomes of fully sequenced model fish species with those of farmed fish species through comparative mapping offers shortcuts for quantitative trait loci (QTL) detections and for studying genome evolution through the identification of regions of conserved synteny in teleosts. Here a comparative mapping study is presented by radiation hybrid (RH) mapping genes of the gilthead sea bream Sparus aurata, a non-model teleost fish of commercial and evolutionary interest, as it represents the worldwide distributed species-rich family of Sparidae. Results: An additional 74 microsatellite markers and 428 gene-based markers appropriate for comparative mapping studies were mapped on the existing RH map of Sparus aurata. The anchoring of the RH map to the genetic linkage map resulted in 24 groups matching the karyotype of Sparus aurata. Homologous sequences to Tetraodon were identified for 301 of the gene-based markers positioned on the RH map of Sparus aurata. Comparison between Sparus aurata RH groups and Tetraodon chromosomes (karyotype of Tetraodon consists of 21 chromosomes) in this study reveals an unambiguous one-to-one relationship suggesting that three Tetraodon chromosomes correspond to six Sparus aurata radiation hybrid groups. The exploitation of this conserved synteny relationship is furthermore demonstrated by in silico mapping of gilthead sea bream expressed sequence tags (EST) that give a significant similarity hit to Tetraodon. Conclusion: The addition of primarily gene-based markers increased substantially the density of the existing RH map and facilitated comparative analysis. The anchoring of this gene-based radiation hybrid map to the genome maps of model species broadened the pool of candidate genes that mainly control growth, disease resistance, sex determination and reversal, reproduction as well as environmental tolerance in this species, all traits of great importance for QTL mapping and marker assisted selection. Furthermore this comparative mapping approach will facilitate to give insights into chromosome evolution and into the genetic make up of the gilthead sea bream. © 2007 Sarropoulou et al; licensee BioMed Central Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background: Comparative teleost studies are of great interest since they are important in aquaculture and in evolutionary issues. Comparing genomes of fully sequenced model fish species with those of farmed fish species through comparative mapping offers shortcuts for quantitative trait loci (QTL) detections and for studying genome evolution through the identification of regions of conserved synteny in teleosts. Here a comparative mapping study is presented by radiation hybrid (RH) mapping genes of the gilthead sea bream Sparus aurata, a non-model teleost fish of commercial and evolutionary interest, as it represents the worldwide distributed species-rich family of Sparidae. Results: An additional 74 microsatellite markers and 428 gene-based markers appropriate for comparative mapping studies were mapped on the existing RH map of Sparus aurata. The anchoring of the RH map to the genetic linkage map resulted in 24 groups matching the karyotype of Sparus aurata. Homologous sequences to Tetraodon were identified for 301 of the gene-based markers positioned on the RH map of Sparus aurata. Comparison between Sparus aurata RH groups and Tetraodon chromosomes (karyotype of Tetraodon consists of 21 chromosomes) in this study reveals an unambiguous one-to-one relationship suggesting that three Tetraodon chromosomes correspond to six Sparus aurata radiation hybrid groups. The exploitation of this conserved synteny relationship is furthermore demonstrated by in silico mapping of gilthead sea bream expressed sequence tags (EST) that give a significant similarity hit to Tetraodon. Conclusion: The addition of primarily gene-based markers increased substantially the density of the existing RH map and facilitated comparative analysis. The anchoring of this gene-based radiation hybrid map to the genome maps of model species broadened the pool of candidate genes that mainly control growth, disease resistance, sex determination and reversal, reproduction as well as environmental tolerance in this species, all traits of great importance for QTL mapping and marker assisted selection. Furthermore this comparative mapping approach will facilitate to give insights into chromosome evolution and into the genetic make up of the gilthead sea bream. © 2007 Sarropoulou et al; licensee BioMed Central Ltd. |
Volckaert, F A M J; Batargias, C; Bonhomme, F; Canario, A; Chistiakov, D; Choudhuri, J V; Galibert, F; Georgoudis, A; Haley, C S; Hellemans, B; Kuhl, H; Kotoulas, G; Law, A; Libertini, A; Magoulas, A; McAndrew, B J; Reinhardt, R; Senger, F; Souche, E; Tsigenopoulos, C; Whitaker, H A Genomic resources for the aquaculture of European sea bass Journal Article Aquaculture, 272 , pp. S316–S317, 2007, ISSN: 00448486. @article{volckaert_genomic_2007, title = {Genomic resources for the aquaculture of European sea bass}, author = {F A M J Volckaert and C Batargias and F Bonhomme and A Canario and D Chistiakov and J V Choudhuri and F Galibert and A Georgoudis and C S Haley and B Hellemans and H Kuhl and G Kotoulas and A Law and A Libertini and A Magoulas and B J McAndrew and R Reinhardt and F Senger and E Souche and C Tsigenopoulos and H A Whitaker}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848607007831}, doi = {10.1016/j.aquaculture.2007.07.199}, issn = {00448486}, year = {2007}, date = {2007-01-01}, urldate = {2020-08-09}, journal = {Aquaculture}, volume = {272}, pages = {S316--S317}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2006 |
Franch, R; Louro, B; Tsalavouta, M; Chatziplis, D; Tsigenopoulos, C S; Sarropoulou, E; Antonello, J; Magoulas, A; Mylonas, C C; Babbucci, M; Patarnello, T; Power, D M; Kotoulas, G; Bargelloni, L A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L. Journal Article Genetics, 174 (2), pp. 851–861, 2006, ISSN: 00166731. @article{franch_genetic_2006, title = {A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L.}, author = {R Franch and B Louro and M Tsalavouta and D Chatziplis and C S Tsigenopoulos and E Sarropoulou and J Antonello and A Magoulas and C C Mylonas and M Babbucci and T Patarnello and D M Power and G Kotoulas and L Bargelloni}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33750471928&doi=10.1534%2fgenetics.106.059014&partnerID=40&md5=5223c21cec86860a04d8be5eff57e24c}, doi = {10.1534/genetics.106.059014}, issn = {00166731}, year = {2006}, date = {2006-01-01}, journal = {Genetics}, volume = {174}, number = {2}, pages = {851--861}, abstract = {The gilthead sea bream (Sparus aurata L.) is a marine fish of great importance for fisheries and aquaculture. It has also a peculiar sex-determination system, being a protandrous hermaphrodite. Here we report the construction of a first-generation genetic linkage map for S. aurata, based on 204 microsatellite markers. Twenty-six linkage groups (LG) were found. The total map length was 1241.9 cM. The ratio between sex-specific map lengths was 1:1.2 (male:female). Comparison with a preliminary radiation hybrid (RH) map reveals a good concordance, as all markers located in a single LG are located in a single RH group, except for Ad-25 and CId-31. Comparison with the Tetraodon nigroviridis genome revealed a considerable number of evolutionary conserved regions (ECRs) between the two species. The mean size of ECRs was 182 bp (sequence identity 60-90%). Forty-one ECRs have a known chromosomal location in the pufferfish genome. Despite the limited number of anchoring points, significant syntenic relationships were found. The linkage map presented here provides a robust comparative framework for QTL analysis in S. aurata and is a step toward the identification of genetic loci involved both in the determination of economically important traits and in the individual timing of sex reversal. Copyright © 2006 by the Genetics Society of America.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The gilthead sea bream (Sparus aurata L.) is a marine fish of great importance for fisheries and aquaculture. It has also a peculiar sex-determination system, being a protandrous hermaphrodite. Here we report the construction of a first-generation genetic linkage map for S. aurata, based on 204 microsatellite markers. Twenty-six linkage groups (LG) were found. The total map length was 1241.9 cM. The ratio between sex-specific map lengths was 1:1.2 (male:female). Comparison with a preliminary radiation hybrid (RH) map reveals a good concordance, as all markers located in a single LG are located in a single RH group, except for Ad-25 and CId-31. Comparison with the Tetraodon nigroviridis genome revealed a considerable number of evolutionary conserved regions (ECRs) between the two species. The mean size of ECRs was 182 bp (sequence identity 60-90%). Forty-one ECRs have a known chromosomal location in the pufferfish genome. Despite the limited number of anchoring points, significant syntenic relationships were found. The linkage map presented here provides a robust comparative framework for QTL analysis in S. aurata and is a step toward the identification of genetic loci involved both in the determination of economically important traits and in the individual timing of sex reversal. Copyright © 2006 by the Genetics Society of America. |
Kotoulas, G Aspects of comparative genomics in the gilthead sea bream, Sparus auratus Journal Article Israeli Journal of Aquaculture - Bamidgeh, 58 (4), pp. 347–349, 2006, ISSN: 0792156X. @article{kotoulas_aspects_2006, title = {Aspects of comparative genomics in the gilthead sea bream, Sparus auratus}, author = {G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33847651233&partnerID=40&md5=2923cb7afd6ef7dd6a555c1e356a5305}, issn = {0792156X}, year = {2006}, date = {2006-01-01}, journal = {Israeli Journal of Aquaculture - Bamidgeh}, volume = {58}, number = {4}, pages = {347--349}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2005 |
Kasapidis, P; Suchentrunk, F; Magoulas, A; Kotoulas, G Molecular Phylogenetics and Evolution, 34 (1), pp. 55–66, 2005, ISSN: 10557903. @article{kasapidis_shaping_2005, title = {The shaping of mitochondrial DNA phylogeographic patterns of the brown hare (Lepus europaeus) under the combined influence of Late Pleistocene climatic fluctuations and anthropogenic translocations}, author = {P Kasapidis and F Suchentrunk and A Magoulas and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-9744258860&doi=10.1016%2fj.ympev.2004.09.007&partnerID=40&md5=a65c976ffbb7419b3edd624a3efbeb4d}, doi = {10.1016/j.ympev.2004.09.007}, issn = {10557903}, year = {2005}, date = {2005-01-01}, journal = {Molecular Phylogenetics and Evolution}, volume = {34}, number = {1}, pages = {55--66}, abstract = {The phylogeographic structure of the brown hare (Lepus europaeus) was studied by analysing mtDNA control region sequences of 98 individuals from continental and insular Greece, Bulgaria, Cyprus and northern Israel, together with 44 published sequences from Italy and central Europe. We found two distinct clades separated by an average nucleotide divergence of 6.6%, which may correspond to a Balkan and to an Asia Minor refugium. The estimated time of separation of the two clades was dated back to 105,000- 490,000 years ago. These two clades coexist in the area of northeastern Greece and Bulgaria, most likely as a result of a post-glacial northward expansion. Within the southern Balkan refugium, network analyses showed geographical structuring, which supports the hypothesis of several isolated Late Pleistocene populations. The central European and Italian populations appear to have originated from a non-detected northern Balkan population that was genetically closely related to some northern Greek populations, as a result of postglacial expansion, translocations or a combination of both. Moreover, several cases of ancient and recent translocations by humans were detected, especially for some island populations, while the eastern Aegean islands off the Asia Minor coast were most likely colonized naturally through Late Pleistocene land bridge connection. The genetic analysis presented here provides a framework for designing proper conservation and management guidelines for this species. © 2004 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The phylogeographic structure of the brown hare (Lepus europaeus) was studied by analysing mtDNA control region sequences of 98 individuals from continental and insular Greece, Bulgaria, Cyprus and northern Israel, together with 44 published sequences from Italy and central Europe. We found two distinct clades separated by an average nucleotide divergence of 6.6%, which may correspond to a Balkan and to an Asia Minor refugium. The estimated time of separation of the two clades was dated back to 105,000- 490,000 years ago. These two clades coexist in the area of northeastern Greece and Bulgaria, most likely as a result of a post-glacial northward expansion. Within the southern Balkan refugium, network analyses showed geographical structuring, which supports the hypothesis of several isolated Late Pleistocene populations. The central European and Italian populations appear to have originated from a non-detected northern Balkan population that was genetically closely related to some northern Greek populations, as a result of postglacial expansion, translocations or a combination of both. Moreover, several cases of ancient and recent translocations by humans were detected, especially for some island populations, while the eastern Aegean islands off the Asia Minor coast were most likely colonized naturally through Late Pleistocene land bridge connection. The genetic analysis presented here provides a framework for designing proper conservation and management guidelines for this species. © 2004 Elsevier Inc. All rights reserved. |
Sarropoulou, E; Kotoulas, G; Power, D M; Geisler, R Physiological Genomics, 23 (2), pp. 182–191, 2005, ISSN: 10948341. @article{sarropoulou_gene_2005, title = {Gene expression profiling of gilthead sea bream during early development and detection of stress-related genes by the application of cDNA microarray technology}, author = {E Sarropoulou and G Kotoulas and D M Power and R Geisler}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33745678365&doi=10.1152%2fphysiolgenomics.00139.2005&partnerID=40&md5=497797e3b9a6bc0c8a3554c078ea6805}, doi = {10.1152/physiolgenomics.00139.2005}, issn = {10948341}, year = {2005}, date = {2005-01-01}, journal = {Physiological Genomics}, volume = {23}, number = {2}, pages = {182--191}, abstract = {Large-scale gene expression studies were performed for one of the main European aquaculture species, the gilthead sea bream Sparus auratus L. For this purpose, a cDNA microarray containing 10,176 clones from a cDNA library of mixed embryonic and larval stages was constructed. In addition to its importance for aquaculture, the taxonomic position and the relatively small genome size of sea bream makes it a prospective model for evolutionary biology and comparative genomics. However, so far, no large-scale analysis of gene expression exists for this species. In the present study, gene expression was analyzed in gilthead sea bream during early development, a significant period in the determination of quantitative traits and therefore of considerable interest for aquaculture. Synexpression groups expressed primarily early and late in development were determined and were composed of both known and novel genes. Furthermore, it was possible to identify stress response genes induced by cortisol injections using the cDNA microarray generated. The creation of gene expression profiles for sea bream by microarray hybridization will accelerate identification of candidate genes involved in multifactorial traits and certain regulatory pathways and will also contribute to a better understanding of the genetic background of fish physiology, which may help to improve aquaculture practices. Copyright © 2005 the American Physiological Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Large-scale gene expression studies were performed for one of the main European aquaculture species, the gilthead sea bream Sparus auratus L. For this purpose, a cDNA microarray containing 10,176 clones from a cDNA library of mixed embryonic and larval stages was constructed. In addition to its importance for aquaculture, the taxonomic position and the relatively small genome size of sea bream makes it a prospective model for evolutionary biology and comparative genomics. However, so far, no large-scale analysis of gene expression exists for this species. In the present study, gene expression was analyzed in gilthead sea bream during early development, a significant period in the determination of quantitative traits and therefore of considerable interest for aquaculture. Synexpression groups expressed primarily early and late in development were determined and were composed of both known and novel genes. Furthermore, it was possible to identify stress response genes induced by cortisol injections using the cDNA microarray generated. The creation of gene expression profiles for sea bream by microarray hybridization will accelerate identification of candidate genes involved in multifactorial traits and certain regulatory pathways and will also contribute to a better understanding of the genetic background of fish physiology, which may help to improve aquaculture practices. Copyright © 2005 the American Physiological Society. |
Sarropoulou, Elena; Power, D M; A, Magoulas; Geisler, R; Kotoulas, Giorgios Comparative analysis and characterization of expressed sequence tags in gilthead sea bream (Sparus aurata) liver and embryos. Journal Article Aquaculture, 243 (1-4), pp. 69–81, 2005. @article{sarropoulou_comparative_2005, title = {Comparative analysis and characterization of expressed sequence tags in gilthead sea bream (Sparus aurata) liver and embryos.}, author = {Elena Sarropoulou and D M Power and Magoulas A and R Geisler and Giorgios Kotoulas}, year = {2005}, date = {2005-01-01}, journal = {Aquaculture}, volume = {243}, number = {1-4}, pages = {69--81}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Makridis, P; Martins, S; Tsalavouta, M; Dionisio, L C; Kotoulas, G; Magoulas, A; Dinis, M T Antimicrobial activity in bacteria isolated from Senegalese sole, Solea senegalensis, fed with natural prey Journal Article Aquaculture Research, 36 (16), pp. 1619–1627, 2005, ISSN: 1355557X. @article{makridis_antimicrobial_2005, title = {Antimicrobial activity in bacteria isolated from Senegalese sole, Solea senegalensis, fed with natural prey}, author = {P Makridis and S Martins and M Tsalavouta and L C Dionisio and G Kotoulas and A Magoulas and M T Dinis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-29044440557&doi=10.1111%2fj.1365-2109.2005.01388.x&partnerID=40&md5=64efc6efd5ef382391232a269eb428d1}, doi = {10.1111/j.1365-2109.2005.01388.x}, issn = {1355557X}, year = {2005}, date = {2005-01-01}, journal = {Aquaculture Research}, volume = {36}, number = {16}, pages = {1619--1627}, abstract = {Intestinal bacteria in marine fish may produce antimicrobial substances which inhibit pathogenic bacteria. The aim of this study was to determine the influence of a change of fish diet on the antimicrobial activity of the culturable aerobic gut microflora of Senegalese sole, Solea senegalensis. Pre-adult 15-month-old fish previously fed on an artificial diet, were fed polychaetes (Hediste diversicolor), which form part of the natural diet of Senegalese sole. Samples were taken 0, 3 and 6 weeks after start of the experiment from the stomach, small and large intestine of the fish. The bacterial strains isolated from these samples were sub-cultured to pure cultures and stored at - 80°C. Several biochemical tests were run to obtain some basic phenotypic characteristics of the isolated strains. Amplification and sequencing of 16S rDNA fragments were used to identify the majority of the bacterial strains isolated. The identification by use of this molecular approach gave results in agreement to the phenotypic characterization. Feeding with polychaetes significantly increased (P textless 0.05) the numbers of presumptive Vibrio isolates in the gut. The number of bacterial strains with antimicrobial activity, as determined by two in vitro approaches, was significantly (P textless 0.05) increased by feeding with polychaetes. © 2005 Blackwell Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Intestinal bacteria in marine fish may produce antimicrobial substances which inhibit pathogenic bacteria. The aim of this study was to determine the influence of a change of fish diet on the antimicrobial activity of the culturable aerobic gut microflora of Senegalese sole, Solea senegalensis. Pre-adult 15-month-old fish previously fed on an artificial diet, were fed polychaetes (Hediste diversicolor), which form part of the natural diet of Senegalese sole. Samples were taken 0, 3 and 6 weeks after start of the experiment from the stomach, small and large intestine of the fish. The bacterial strains isolated from these samples were sub-cultured to pure cultures and stored at - 80°C. Several biochemical tests were run to obtain some basic phenotypic characteristics of the isolated strains. Amplification and sequencing of 16S rDNA fragments were used to identify the majority of the bacterial strains isolated. The identification by use of this molecular approach gave results in agreement to the phenotypic characterization. Feeding with polychaetes significantly increased (P textless 0.05) the numbers of presumptive Vibrio isolates in the gut. The number of bacterial strains with antimicrobial activity, as determined by two in vitro approaches, was significantly (P textless 0.05) increased by feeding with polychaetes. © 2005 Blackwell Publishing Ltd. |
Chistiakov, D A; Hellemans, B; Haley, C S; Law, A S; Tsigenopoulos, C S; Kotoulas, G; Bertotto, D; Libertini, A; Volckaert, F A M A microsatellite linkage map of the European sea bass Dicentrarchus labrax L. Journal Article Genetics, 170 (4), pp. 1821–1826, 2005, ISSN: 00166731. @article{chistiakov_microsatellite_2005, title = {A microsatellite linkage map of the European sea bass Dicentrarchus labrax L.}, author = {D A Chistiakov and B Hellemans and C S Haley and A S Law and C S Tsigenopoulos and G Kotoulas and D Bertotto and A Libertini and F A M Volckaert}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-25444490899&doi=10.1534%2fgenetics.104.039719&partnerID=40&md5=8dfc95ab2fdb751d0c70b2f5f1342b11}, doi = {10.1534/genetics.104.039719}, issn = {00166731}, year = {2005}, date = {2005-01-01}, journal = {Genetics}, volume = {170}, number = {4}, pages = {1821--1826}, abstract = {A genetic linkage map of the European sea bass (Dicentrarchus labrax) was constructed from 174 microsatellite markers, including 145 new markers reported in this study. The mapping panel was derived from farmed sea bass from the North Adriatic Sea and consisted of a single family including both parents and 50 full-sib progeny (biparental diploids). A total of 162 microsatellites were mapped in 25 linkage groups. Eleven loci represent type I (coding) markers; 2 loci are located within the peptide Y (linkage group 1) and cytochrome P450 aromatase (linkage group 6) genes. The sex-averaged map spans 814.5 cM of the sea bass genome. The female map covers 905.9 cM, whereas the male map covers only 567.4 cM. The constructed map represents the first linkage map of European sea bass, one of the most important aquaculture species in Europe. Copyright © 2005 by the Genetics Society of America.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A genetic linkage map of the European sea bass (Dicentrarchus labrax) was constructed from 174 microsatellite markers, including 145 new markers reported in this study. The mapping panel was derived from farmed sea bass from the North Adriatic Sea and consisted of a single family including both parents and 50 full-sib progeny (biparental diploids). A total of 162 microsatellites were mapped in 25 linkage groups. Eleven loci represent type I (coding) markers; 2 loci are located within the peptide Y (linkage group 1) and cytochrome P450 aromatase (linkage group 6) genes. The sex-averaged map spans 814.5 cM of the sea bass genome. The female map covers 905.9 cM, whereas the male map covers only 567.4 cM. The constructed map represents the first linkage map of European sea bass, one of the most important aquaculture species in Europe. Copyright © 2005 by the Genetics Society of America. |
2004 |
Kasapidis, P; Planes, S; Laurent, V; Quinta, R; Teia, A; Lenfant, R; Darivianakis, S; Terzoglou, V; Kotoulas, G; Magoulas, A Stock discrimination and temporal and spatial genetic variation of sardine (Sardina pilchardus) in northeastern Atlantic, with a combined analysis of nuclear (microsatellites and allozymes) and mitochondrial DNA markers. Inproceedings Kasapidis, P (Ed.): 2004 ICES Annual Science Conference, 2004. @inproceedings{kasapidis_stock_2004, title = {Stock discrimination and temporal and spatial genetic variation of sardine (Sardina pilchardus) in northeastern Atlantic, with a combined analysis of nuclear (microsatellites and allozymes) and mitochondrial DNA markers.}, author = {P Kasapidis and S Planes and V Laurent and R Quinta and A Teia and R Lenfant and S Darivianakis and V Terzoglou and G Kotoulas and A Magoulas}, editor = {P Kasapidis}, year = {2004}, date = {2004-09-01}, booktitle = {2004 ICES Annual Science Conference}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Chistiakov, D A; Hellemans, B; Tsigenopoulos, C S; Law, A S; Bartley, N; Bertotto, D; Libertini, A; Kotoulas, G; Haley, C S; Volckaert, F A M Development and linkage relationships for new microsatellite markers of the sea bass (Dicentrarchus labrax L.) Journal Article Animal Genetics, 35 (1), pp. 53–57, 2004, ISSN: 02689146. @article{chistiakov_development_2004, title = {Development and linkage relationships for new microsatellite markers of the sea bass (Dicentrarchus labrax L.)}, author = {D A Chistiakov and B Hellemans and C S Tsigenopoulos and A S Law and N Bartley and D Bertotto and A Libertini and G Kotoulas and C S Haley and F A M Volckaert}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-10744228402&doi=10.1046%2fj.1365-2052.2003.01076.x&partnerID=40&md5=04f787b68dff2aecc25e57226b021721}, doi = {10.1046/j.1365-2052.2003.01076.x}, issn = {02689146}, year = {2004}, date = {2004-01-01}, journal = {Animal Genetics}, volume = {35}, number = {1}, pages = {53--57}, abstract = {Twenty-eight polymorphic microsatellites were isolated from the sea bass, Dicentrarchus labrax, using a microsatellite enrichment protocol and selective hybridization with oligonucleotide probes. Analysis for these markers and 11 recently described microsatellites of D. labrax found linkage between 26 loci and revealed eight linkage groups.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Twenty-eight polymorphic microsatellites were isolated from the sea bass, Dicentrarchus labrax, using a microsatellite enrichment protocol and selective hybridization with oligonucleotide probes. Analysis for these markers and 11 recently described microsatellites of D. labrax found linkage between 26 loci and revealed eight linkage groups. |
2003 |
Tsigenopoulos, C S; Hellemans, B; Chistiakov, D A; Libertini, A; Kotoulas, G; Volckaert, F Eleven new microsatellites of the sea bass (Dicentrarchus labrax L.) Journal Article Molecular Ecology Notes, 3 (3), pp. 352–354, 2003, ISSN: 14718278. @article{tsigenopoulos_eleven_2003, title = {Eleven new microsatellites of the sea bass (Dicentrarchus labrax L.)}, author = {C S Tsigenopoulos and B Hellemans and D A Chistiakov and A Libertini and G Kotoulas and F Volckaert}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0041874880&doi=10.1046%2fj.1471-8286.2003.00447.x&partnerID=40&md5=821b63e875e1041a9f4dd3f9e973c928}, doi = {10.1046/j.1471-8286.2003.00447.x}, issn = {14718278}, year = {2003}, date = {2003-01-01}, journal = {Molecular Ecology Notes}, volume = {3}, number = {3}, pages = {352--354}, abstract = {Eleven polymorphic microsatellites were isolated from the sea bass, Dicentrarchus labrax, using a microsatellite enrichment protocol and selective hybridization with an (AC)12 probe. The loci showed different variation patterns in 21 unrelated sea bass individuals, with a mean number of alleles of 8.6 and a mean observed heterozygosity of 0.68. These microsatellite markers should be useful for population genetic analysis and biodiversity studies of sea bass.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Eleven polymorphic microsatellites were isolated from the sea bass, Dicentrarchus labrax, using a microsatellite enrichment protocol and selective hybridization with an (AC)12 probe. The loci showed different variation patterns in 21 unrelated sea bass individuals, with a mean number of alleles of 8.6 and a mean observed heterozygosity of 0.68. These microsatellite markers should be useful for population genetic analysis and biodiversity studies of sea bass. |
Kotoulas, G; Mejuto, J; Tserpes, G; Garcia-Cortes, B; Peristeraki, P; la Serna, De J M; Magoulas, A DNA microsatellite markers in service of swordfish stock-structure analysis in the Atlantic and Mediterranean Journal Article ICCAT Col. Vol. Sci. Papers, 55 (4), pp. 1632–1639, 2003. @article{kotoulas_dna_2003, title = {DNA microsatellite markers in service of swordfish stock-structure analysis in the Atlantic and Mediterranean}, author = {G Kotoulas and J Mejuto and G Tserpes and B Garcia-Cortes and P Peristeraki and J M De la Serna and A Magoulas}, year = {2003}, date = {2003-01-01}, journal = {ICCAT Col. Vol. Sci. Papers}, volume = {55}, number = {4}, pages = {1632--1639}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2002 |
Garnier-Géré, P H; Naciri-Graven, Y; Bougrier, S; Magoulas, A; Héral, M; Kotoulas, G; Hawkins, A; Gérard, A Molecular Ecology, 11 (8), pp. 1499–1514, 2002, ISSN: 09621083. @article{garnier-gere_influences_2002, title = {Influences of triploidy, parentage and genetic diversity on growth of the Pacific oyster Crassostrea gigas reared in contrasting natural environments}, author = {P H Garnier-Géré and Y Naciri-Graven and S Bougrier and A Magoulas and M Héral and G Kotoulas and A Hawkins and A Gérard}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035993750&doi=10.1046%2fj.1365-294X.2002.01531.x&partnerID=40&md5=fda8b0e20f8e19d34fe231f8cfaf81a2}, doi = {10.1046/j.1365-294X.2002.01531.x}, issn = {09621083}, year = {2002}, date = {2002-01-01}, journal = {Molecular Ecology}, volume = {11}, number = {8}, pages = {1499--1514}, abstract = {An increasing number of hypotheses are being proposed to explain the faster growth potential of triploids in molluscs, including their partial sterility or their higher heterozygosity compared to diploids. Triploid advantage however, remains controversial for poorer sites, because of a potential trade-off with survival. These questions were addressed in Crassostrea gigas by deploying meiosis II triploids and their diploid siblings from a single mass spawning of three males and seven females, in two contrasting locations for their trophic resources. One hundred and fifty individuals were sampled at each site after nine months, measured for weight and biochemical composition, and genotyped using three microsatellite and seven allozyme loci. Higher performance was observed at the fastgrowing site for all traits except shell weight, and triploids had greater weights and biochemical contents than diploids at harvest. Triploids also grew faster at the poorer site, and showed similar survival rates to diploids at both sites. Triploids had significantly higher average allozyme and microsatellite diversity. However, they performed better for a wide range of individual heterozygosity values, arguing for an advantage of the triploid state per se, that could be due to positive effects on growth of both sterility of triploids with subsequent resource re-allocation and possible faster transcription with three copies of each gene. Despite evidence of very low or no inbreeding in the diploid sample, positive associations between individual allozyme diversity and growth were detected, which explained little but significant amounts of phenotypic variation. These associations were interpreted as direct effects of allozymes, either alone or including epistatic interactions with other loci. In addition, measures of individual distance (mean-d2) specific to microsatellites, were negatively correlated with growth in diploids, indicating possible effects of outbreeding depression between more distant genomes of parents from distinct populations.}, keywords = {}, pubstate = {published}, tppubtype = {article} } An increasing number of hypotheses are being proposed to explain the faster growth potential of triploids in molluscs, including their partial sterility or their higher heterozygosity compared to diploids. Triploid advantage however, remains controversial for poorer sites, because of a potential trade-off with survival. These questions were addressed in Crassostrea gigas by deploying meiosis II triploids and their diploid siblings from a single mass spawning of three males and seven females, in two contrasting locations for their trophic resources. One hundred and fifty individuals were sampled at each site after nine months, measured for weight and biochemical composition, and genotyped using three microsatellite and seven allozyme loci. Higher performance was observed at the fastgrowing site for all traits except shell weight, and triploids had greater weights and biochemical contents than diploids at harvest. Triploids also grew faster at the poorer site, and showed similar survival rates to diploids at both sites. Triploids had significantly higher average allozyme and microsatellite diversity. However, they performed better for a wide range of individual heterozygosity values, arguing for an advantage of the triploid state per se, that could be due to positive effects on growth of both sterility of triploids with subsequent resource re-allocation and possible faster transcription with three copies of each gene. Despite evidence of very low or no inbreeding in the diploid sample, positive associations between individual allozyme diversity and growth were detected, which explained little but significant amounts of phenotypic variation. These associations were interpreted as direct effects of allozymes, either alone or including epistatic interactions with other loci. In addition, measures of individual distance (mean-d2) specific to microsatellites, were negatively correlated with growth in diploids, indicating possible effects of outbreeding depression between more distant genomes of parents from distinct populations. |
2000 |
Hawkins, A J S; Magoulas, A; Héral, M; Bougrier, S; Naciri-Graven, Y; Day, A J; Kotoulas, G Genetical Research, 76 (3), pp. 273–284, 2000, ISSN: 00166723. @article{hawkins_separate_2000, title = {Separate effects of triploidy, parentage and genomic diversity upon feeding behaviour, metabolic efficiency and net energy balance in the pacific oyster Crassostrea gigas}, author = {A J S Hawkins and A Magoulas and M Héral and S Bougrier and Y Naciri-Graven and A J Day and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034521887&doi=10.1017%2fS0016672300004766&partnerID=40&md5=b1e5a6ea52adb13f396dcec5d01c96d9}, doi = {10.1017/S0016672300004766}, issn = {00166723}, year = {2000}, date = {2000-01-01}, journal = {Genetical Research}, volume = {76}, number = {3}, pages = {273--284}, abstract = {Triploid oysters were induced using cytochalasin B upon retention of either the first (meiosis I triploids) or the second (meiosis II triploids) polar body in embryos from a single cohort derived from mixed parentage. Allozyme and microsatellite assays enabled the confirmation of both parentage and triploidy status in each oyster. Comparison of meiosis I triploids, meiosis II triploids and diploid siblings established that improved physiological performance in triploids was associated with increased allelic variation, rather than with the quantitative dosage effects of ploidy status. An unidentified maternal influence also interacted with genotype. Among full sibs, allelic variation measured as multi-locus enzyme heterozygosity accounted for up to 42% of the variance in physiological performance; significant positive influences were identified upon feeding rate, absorption efficiency, net energy balance and growth efficiency (= net energy balance ÷ energy absorbed). Whilst allelic variation was greater in both meiosis I and meiosis II triploids than in diploid siblings, both allelic variation and net energy balance were highest in triploids induced at meiosis I. This suggests that it may be preferable to induce triploidy by blocking meiosis I, rather than meiosis II as has traditionally been undertaken during commercial breeding programmes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Triploid oysters were induced using cytochalasin B upon retention of either the first (meiosis I triploids) or the second (meiosis II triploids) polar body in embryos from a single cohort derived from mixed parentage. Allozyme and microsatellite assays enabled the confirmation of both parentage and triploidy status in each oyster. Comparison of meiosis I triploids, meiosis II triploids and diploid siblings established that improved physiological performance in triploids was associated with increased allelic variation, rather than with the quantitative dosage effects of ploidy status. An unidentified maternal influence also interacted with genotype. Among full sibs, allelic variation measured as multi-locus enzyme heterozygosity accounted for up to 42% of the variance in physiological performance; significant positive influences were identified upon feeding rate, absorption efficiency, net energy balance and growth efficiency (= net energy balance ÷ energy absorbed). Whilst allelic variation was greater in both meiosis I and meiosis II triploids than in diploid siblings, both allelic variation and net energy balance were highest in triploids induced at meiosis I. This suggests that it may be preferable to induce triploidy by blocking meiosis I, rather than meiosis II as has traditionally been undertaken during commercial breeding programmes. |
Magoulas, A; Kotoulas, G; Gérard, A; Naciri-Graven, Y; Dermitzakis, E; Hawkins, A J S Comparison of genetic variability and parentage in different ploidy classes of the Japanese oyster Crassostrea gigas Journal Article Genetical Research, 76 (3), pp. 261–272, 2000, ISSN: 00166723. @article{magoulas_comparison_2000, title = {Comparison of genetic variability and parentage in different ploidy classes of the Japanese oyster Crassostrea gigas}, author = {A Magoulas and G Kotoulas and A Gérard and Y Naciri-Graven and E Dermitzakis and A J S Hawkins}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034520835&doi=10.1017%2fS0016672300004778&partnerID=40&md5=6f9a177082cb2cf8620b0bf2ba31d383}, doi = {10.1017/S0016672300004778}, issn = {00166723}, year = {2000}, date = {2000-01-01}, journal = {Genetical Research}, volume = {76}, number = {3}, pages = {261--272}, abstract = {Chemical treatments with cytochalasin B were used to induce triploidy in the progeny of a mass fertilization of 3 male and 7 female Crassostrea gigas parents. Triploids were produced either by retention of the first (meiosis I (MI) triploids) or the second (meiosis II (MII) triploids) polar bodies. These animals, together with their diploid siblings, were divided for two experiments. One set was used to compare physiological performance, and the other set deployed to compare growth in two different natural environments. For both experiments, genetic variability in different ploidy classes was estimated using three microsatellite loci and eight allozyme loci. The microsatellite loci were highly polymorphic, allowing independent confirmation of ploidy status and the unambiguous identification of parentage for each oyster. Significant differences in parentage were found between ploidy classes, despite the fact they originated from the same mass fertilization. This indicates that the assumptions of a common genetic background among random samples of animals taken from the same mass fertilization may be generally valid. Knowledge of parentage also allowed the more accurate scoring of allozyme loci. As expected, triploids were found to be significantly more polymorphic than diploids. However, MI triploids were not significantly more polymorphic than MII triploids. MII triploid genotypes were used to estimate recombination rates between loci and their centromeres. These rates varied between 0.29 and 0.71, indicating only moderate chiasma interference.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Chemical treatments with cytochalasin B were used to induce triploidy in the progeny of a mass fertilization of 3 male and 7 female Crassostrea gigas parents. Triploids were produced either by retention of the first (meiosis I (MI) triploids) or the second (meiosis II (MII) triploids) polar bodies. These animals, together with their diploid siblings, were divided for two experiments. One set was used to compare physiological performance, and the other set deployed to compare growth in two different natural environments. For both experiments, genetic variability in different ploidy classes was estimated using three microsatellite loci and eight allozyme loci. The microsatellite loci were highly polymorphic, allowing independent confirmation of ploidy status and the unambiguous identification of parentage for each oyster. Significant differences in parentage were found between ploidy classes, despite the fact they originated from the same mass fertilization. This indicates that the assumptions of a common genetic background among random samples of animals taken from the same mass fertilization may be generally valid. Knowledge of parentage also allowed the more accurate scoring of allozyme loci. As expected, triploids were found to be significantly more polymorphic than diploids. However, MI triploids were not significantly more polymorphic than MII triploids. MII triploid genotypes were used to estimate recombination rates between loci and their centromeres. These rates varied between 0.29 and 0.71, indicating only moderate chiasma interference. |
1998 |
Magoulas, A; Kotoulas, G; Batargias, C; Zouros, E Genetic markers in marine biology and aquaculture research: when to use what Incollection Agnese, J F (Ed.): Genetics and Aquaculture in Africa, pp. 67–78, ORSTOM, Paris, 1998, (Backup Publisher: ORSTOM). @incollection{magoulas_genetic_1998, title = {Genetic markers in marine biology and aquaculture research: when to use what}, author = {A Magoulas and G Kotoulas and C Batargias and E Zouros}, editor = {J F Agnese}, year = {1998}, date = {1998-01-01}, booktitle = {Genetics and Aquaculture in Africa}, pages = {67--78}, publisher = {ORSTOM}, address = {Paris}, note = {Backup Publisher: ORSTOM}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
1997 |
Borsa, P; Naciri, M; Bahri, L; Chikhi, L; de Leon, Garcia F J; Kotoulas, G; Bonhomme, F Vie et Milieu, 47 (4), pp. 295–305, 1997, ISSN: 02408759. @article{borsa_infraspecific_1997, title = {Infraspecific zoogeography of the Mediterranean: population genetic analysis on sixteen Atlanto-Mediterranean species (fishes and invertebrates) [Zoogeographie infra-specifique de la Mer Mediterranee: analyse des donnees genetiques populationnelles sur seize especes atlanto-mediterraneennes (poissons et invertebres)]}, author = {P Borsa and M Naciri and L Bahri and L Chikhi and F J Garcia de Leon and G Kotoulas and F Bonhomme}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0031403021&partnerID=40&md5=84cd00d266e65a028ccbf3c537e40b88}, issn = {02408759}, year = {1997}, date = {1997-01-01}, journal = {Vie et Milieu}, volume = {47}, number = {4}, pages = {295--305}, abstract = {The faunal relationships of the Atlantic and the Mediterranean have been affected by tectonic change in the Miocene, by climate change in the Pleistocene and by hydrological discontinuity. We use a population genetics approach to the biogeography of the Mediterranean marine fauna, in particular to describe the level of recent or present-day exchanges with the Atlantic. The level of genetic differences between populations was estimated from published and unpublished data on sixteen species from the northeastern Atlantic and the Mediterranean. For a majority of species, either tropical or subtropical or boreal fishes, or coastal invertebrates, a moderately strong to strong genetic cline between each side of the Gibraltar strait area was observed. Such a pattern was also observed in a proportion of species between each side of the Sicilian-Tunisian strait. In a limited number of cases, the geographic patterns of population genetic structure however conformed with the expectations from an isolation-by-distance model. The molecular phylogeographic approach in a boreal species, the flounder Platichthys flesus, led to the inferrence of the historical movements of colonisation and geographic isolation of the populations. A similar approach used in a tropical species (the Spanish sardine Sardinella aurita) and a cosmopolitan species (the grey mullet Mugil cephalus) revealed close genetic relationships between Mediterranean and west-tropical Atlantic populations. We analyse the possible implications of these findings to the systematics of the Mediterranean populations and we speculate about the future of boreal species vis-a-vis the present climatic change. We debate on various hypotheses for the maintaining of abrupt genetic clines in the marine environment.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The faunal relationships of the Atlantic and the Mediterranean have been affected by tectonic change in the Miocene, by climate change in the Pleistocene and by hydrological discontinuity. We use a population genetics approach to the biogeography of the Mediterranean marine fauna, in particular to describe the level of recent or present-day exchanges with the Atlantic. The level of genetic differences between populations was estimated from published and unpublished data on sixteen species from the northeastern Atlantic and the Mediterranean. For a majority of species, either tropical or subtropical or boreal fishes, or coastal invertebrates, a moderately strong to strong genetic cline between each side of the Gibraltar strait area was observed. Such a pattern was also observed in a proportion of species between each side of the Sicilian-Tunisian strait. In a limited number of cases, the geographic patterns of population genetic structure however conformed with the expectations from an isolation-by-distance model. The molecular phylogeographic approach in a boreal species, the flounder Platichthys flesus, led to the inferrence of the historical movements of colonisation and geographic isolation of the populations. A similar approach used in a tropical species (the Spanish sardine Sardinella aurita) and a cosmopolitan species (the grey mullet Mugil cephalus) revealed close genetic relationships between Mediterranean and west-tropical Atlantic populations. We analyse the possible implications of these findings to the systematics of the Mediterranean populations and we speculate about the future of boreal species vis-a-vis the present climatic change. We debate on various hypotheses for the maintaining of abrupt genetic clines in the marine environment. |
Borsa, P; Naciri, M; Bahri, L; Chikhi, L; de Leon, Garcia F J; Kotoulas, G; Bonhomme, F Infraspecific zoogeography of the Mediterranean: population genetic analysis on sixteen Atlanto-Mediterranean species (fishes and invertebrates) Journal Article Vie et Milieu, 47 , pp. 295 – 305, 1997. @article{borsa_infraspecific_1997-1, title = {Infraspecific zoogeography of the Mediterranean: population genetic analysis on sixteen Atlanto-Mediterranean species (fishes and invertebrates)}, author = {P Borsa and M Naciri and L Bahri and L Chikhi and F J Garcia de Leon and G Kotoulas and F Bonhomme}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0031403021&partnerID=40&md5=84cd00d266e65a028ccbf3c537e40b88}, year = {1997}, date = {1997-01-01}, journal = {Vie et Milieu}, volume = {47}, pages = {295 -- 305}, abstract = {The faunal relationships of the Atlantic and the Mediterranean have been affected by tectonic change in the Miocene, by climate change in the Pleistocene and by hydrological discontinuity. We use a population genetics approach to the biogeography of the Mediterranean marine fauna, in particular to describe the level of recent or present-day exchanges with the Atlantic. The level of genetic differences between populations was estimated from published and unpublished data on sixteen species from the northeastern Atlantic and the Mediterranean. For a majority of species, either tropical or subtropical or boreal fishes, or coastal invertebrates, a moderately strong to strong genetic cline between each side of the Gibraltar strait area was observed. Such a pattern was also observed in a proportion of species between each side of the Sicilian-Tunisian strait. In a limited number of cases, the geographic patterns of population genetic structure however conformed with the expectations from an isolation-by-distance model. The molecular phylogeographic approach in a boreal species, the flounder Platichthys flesus, led to the inferrence of the historical movements of colonisation and geographic isolation of the populations. A similar approach used in a tropical species (the Spanish sardine Sardinella aurita) and a cosmopolitan species (the grey mullet Mugil cephalus) revealed close genetic relationships between Mediterranean and west-tropical Atlantic populations. We analyse the possible implications of these findings to the systematics of the Mediterranean populations and we speculate about the future of boreal species vis-a-vis the present climatic change. We debate on various hypotheses for the maintaining of abrupt genetic clines in the marine environment.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The faunal relationships of the Atlantic and the Mediterranean have been affected by tectonic change in the Miocene, by climate change in the Pleistocene and by hydrological discontinuity. We use a population genetics approach to the biogeography of the Mediterranean marine fauna, in particular to describe the level of recent or present-day exchanges with the Atlantic. The level of genetic differences between populations was estimated from published and unpublished data on sixteen species from the northeastern Atlantic and the Mediterranean. For a majority of species, either tropical or subtropical or boreal fishes, or coastal invertebrates, a moderately strong to strong genetic cline between each side of the Gibraltar strait area was observed. Such a pattern was also observed in a proportion of species between each side of the Sicilian-Tunisian strait. In a limited number of cases, the geographic patterns of population genetic structure however conformed with the expectations from an isolation-by-distance model. The molecular phylogeographic approach in a boreal species, the flounder Platichthys flesus, led to the inferrence of the historical movements of colonisation and geographic isolation of the populations. A similar approach used in a tropical species (the Spanish sardine Sardinella aurita) and a cosmopolitan species (the grey mullet Mugil cephalus) revealed close genetic relationships between Mediterranean and west-tropical Atlantic populations. We analyse the possible implications of these findings to the systematics of the Mediterranean populations and we speculate about the future of boreal species vis-a-vis the present climatic change. We debate on various hypotheses for the maintaining of abrupt genetic clines in the marine environment. |
1996 |
Zouros, E; Thiriot-Quievreux, C; Kotoulas, G Genetical Research, 68 (2), pp. 109–116, 1996, ISSN: 00166723. @article{zouros_negative_1996, title = {The negative correlation between somatic aneuploidy and growth in the oyster Crassostrea gigas and implications for the effects of induced polyploidization}, author = {E Zouros and C Thiriot-Quievreux and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0029827355&partnerID=40&md5=521daa399a6f0c6e7a91a097fde9d06d}, issn = {00166723}, year = {1996}, date = {1996-01-01}, journal = {Genetical Research}, volume = {68}, number = {2}, pages = {109--116}, abstract = {This study extends previous observations that chromosome loss in somatic cells of juveniles of the pacific oyster Crassostrea gigas is associated with reduced growth rate. All four studies designed to examine this association (two using random population samples and two using full sibs) produced the same result. This consistent effect appears to be unrelated with the commonly, but not consistently, observed correlation between degree of allozyme heterozygosity and growth. We propose that the inverse relationship between aneuploidy and growth is due to the unmasking of deleterious recessive genes caused by 'progressive haploidization' of somatic cells. Because unmasking of deleterious recessive genes by random chromosome loss is unlikely in polyploid cells, this hypothesis may also provide an explanation for the observation that artificially produced polyploid shellfish usually grow at faster rates than normal diploid ones.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study extends previous observations that chromosome loss in somatic cells of juveniles of the pacific oyster Crassostrea gigas is associated with reduced growth rate. All four studies designed to examine this association (two using random population samples and two using full sibs) produced the same result. This consistent effect appears to be unrelated with the commonly, but not consistently, observed correlation between degree of allozyme heterozygosity and growth. We propose that the inverse relationship between aneuploidy and growth is due to the unmasking of deleterious recessive genes caused by 'progressive haploidization' of somatic cells. Because unmasking of deleterious recessive genes by random chromosome loss is unlikely in polyploid cells, this hypothesis may also provide an explanation for the observation that artificially produced polyploid shellfish usually grow at faster rates than normal diploid ones. |
1995 |
Kotoulas, Georgios; Magoulas, Antonios; Tsimenides, N; Zouros, E Marked mitochondrial DNA differences between Mediterranean and Atlantic populations of the swordfish, Xiphias gladius Journal Article Molecular Ecology, 4 (4), pp. 473–482, 1995, ISSN: 09621083. @article{kotoulas_marked_1995, title = {Marked mitochondrial DNA differences between Mediterranean and Atlantic populations of the swordfish, Xiphias gladius}, author = {Georgios Kotoulas and Antonios Magoulas and N Tsimenides and E Zouros}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0028874118&doi=10.1111%2fj.1365-294X.1995.tb00241.x&partnerID=40&md5=529a83d003e7708c8e88bcf66c58b29e}, doi = {10.1111/j.1365-294X.1995.tb00241.x}, issn = {09621083}, year = {1995}, date = {1995-01-01}, journal = {Molecular Ecology}, volume = {4}, number = {4}, pages = {473--482}, abstract = {Restriction analysis of mitochondrial DNA (mtDNA) from 204 individuals of swordfish (Xiphias gladius) revealed no differentiation among samples from three sites in the Mediterranean Sea (Greece, Italy, Spain), but a high degree of differentiation between Mediterranean samples and a sample from the Gulf of Guinea. A fifth sample from the Atlantic side of the Straits of Gibraltar (Tarifa) consisted mostly of mitotypes that are common in the Mediterranean, but contained several of mtDNA types of the Guinea sample not found in the Mediterranean. We conclude that, in spite of free migration of swordfish across the Straits of Gibraltar, little genetic exchange occurs between the populations inhabiting the Mediterranean Sea and the tropical Atlantic ocean. This is the first evidence of genetic differentiation among geographic populations of this highly mobile species that supports a world‐wide fishery. Copyright © 1995, Wiley Blackwell. All rights reserved}, keywords = {}, pubstate = {published}, tppubtype = {article} } Restriction analysis of mitochondrial DNA (mtDNA) from 204 individuals of swordfish (Xiphias gladius) revealed no differentiation among samples from three sites in the Mediterranean Sea (Greece, Italy, Spain), but a high degree of differentiation between Mediterranean samples and a sample from the Gulf of Guinea. A fifth sample from the Atlantic side of the Straits of Gibraltar (Tarifa) consisted mostly of mitotypes that are common in the Mediterranean, but contained several of mtDNA types of the Guinea sample not found in the Mediterranean. We conclude that, in spite of free migration of swordfish across the Straits of Gibraltar, little genetic exchange occurs between the populations inhabiting the Mediterranean Sea and the tropical Atlantic ocean. This is the first evidence of genetic differentiation among geographic populations of this highly mobile species that supports a world‐wide fishery. Copyright © 1995, Wiley Blackwell. All rights reserved |
Kotoulas, G; Bonhomme, F; Borsa, P Genetic structure of the common sole Solea vulgaris at different geographic scales Journal Article Marine Biology, 122 (3), pp. 361–375, 1995, ISSN: 00253162, (Publisher: Springer-Verlag). @article{kotoulas_genetic_1995, title = {Genetic structure of the common sole Solea vulgaris at different geographic scales}, author = {G Kotoulas and F Bonhomme and P Borsa}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0029414659&doi=10.1007%2fBF00350869&partnerID=40&md5=efae5e82aeadebd78b94d317e2406129}, doi = {10.1007/BF00350869}, issn = {00253162}, year = {1995}, date = {1995-01-01}, journal = {Marine Biology}, volume = {122}, number = {3}, pages = {361--375}, abstract = {The genetic structure of the flatfish Solea vulgaris was investigated on several spatial scales and at the temporal level through analysis of electrophoretic variation at 8 to 12 polymorphic enzyme loci. No differentiation was apparent at the temporal scale. Some differentiation was detected at and above the regional scale. Isolation by distance was evidenced by the significant correlation between genetic and geographic distances, and by the consistency of the results of multiple-locus correspondence analysis with geographic sampling patterns. The analysis suggested that the geographic unit of population structure (i.e. a geographical area corresponding to a panmictic or nearly panmictic population) lies within a radius of the order of 100 km. The isolation-by-distance pattern in S. vulgaris contrasted with the known genetic structures of other flatfish species of the northeastern Atlantic and Mediterranean in a way that may be related to the range of their respective temperature tolerances for eggs and larvae. © 1995 Springer-Verlag.}, note = {Publisher: Springer-Verlag}, keywords = {}, pubstate = {published}, tppubtype = {article} } The genetic structure of the flatfish Solea vulgaris was investigated on several spatial scales and at the temporal level through analysis of electrophoretic variation at 8 to 12 polymorphic enzyme loci. No differentiation was apparent at the temporal scale. Some differentiation was detected at and above the regional scale. Isolation by distance was evidenced by the significant correlation between genetic and geographic distances, and by the consistency of the results of multiple-locus correspondence analysis with geographic sampling patterns. The analysis suggested that the geographic unit of population structure (i.e. a geographical area corresponding to a panmictic or nearly panmictic population) lies within a radius of the order of 100 km. The isolation-by-distance pattern in S. vulgaris contrasted with the known genetic structures of other flatfish species of the northeastern Atlantic and Mediterranean in a way that may be related to the range of their respective temperature tolerances for eggs and larvae. © 1995 Springer-Verlag. |
1993 |
Magoulas, A; Kotoulas, G; Tsimenides, N; Zouros, E; la Serna, De J M; Metrio, De G Genetic structure of swordfish (Xiphias gladius) populations of the Mediterranean and the eastern side of the Atlantic: analysis by mitochondrial DNA markers Journal Article ICCAT Collective Volume of Scientific Papers, XL , pp. 126–136, 1993. @article{magoulas_genetic_1993, title = {Genetic structure of swordfish (Xiphias gladius) populations of the Mediterranean and the eastern side of the Atlantic: analysis by mitochondrial DNA markers}, author = {A Magoulas and G Kotoulas and N Tsimenides and E Zouros and J M De la Serna and G De Metrio}, year = {1993}, date = {1993-01-01}, journal = {ICCAT Collective Volume of Scientific Papers}, volume = {XL}, pages = {126--136}, keywords = {}, pubstate = {published}, tppubtype = {article} } |