2022 |
Solís, Francisco Javier Toledo; Fernandes, Jorge M O; Sarropoulou, Elena; Monzón, Ignacio Fernández Noncoding RNAs in fish physiology and development: miRNAs as a cornerstone in gene networks Incollection Cellular and Molecular Approaches in Fish Biology, pp. 105–159, Elsevier, 2022, ISBN: 978-0-12-822273-7. @incollection{toledo_solis_noncoding_2022, title = {Noncoding RNAs in fish physiology and development: miRNAs as a cornerstone in gene networks}, author = {Francisco Javier Toledo Solís and Jorge M O Fernandes and Elena Sarropoulou and Ignacio Fernández Monzón}, url = {https://linkinghub.elsevier.com/retrieve/pii/B9780128222737000124}, doi = {10.1016/B978-0-12-822273-7.00012-4}, isbn = {978-0-12-822273-7}, year = {2022}, date = {2022-01-01}, urldate = {2022-02-17}, booktitle = {Cellular and Molecular Approaches in Fish Biology}, pages = {105--159}, publisher = {Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Kaitetzidou, Elisavet; Gilfillan, Gregor D; Antonopoulou, Efthimia; Sarropoulou, Elena Sex-biased dynamics of three-spined stickleback (Gasterosteus aculeatus) gene expression patterns Journal Article Genomics, 114 (1), pp. 266–277, 2022, ISSN: 08887543. @article{kaitetzidou_sex-biased_2022b, title = {Sex-biased dynamics of three-spined stickleback (Gasterosteus aculeatus) gene expression patterns}, author = {Elisavet Kaitetzidou and Gregor D Gilfillan and Efthimia Antonopoulou and Elena Sarropoulou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Kaitetzidou-Genomics-3.pdf https://linkinghub.elsevier.com/retrieve/pii/S0888754321004377}, doi = {10.1016/j.ygeno.2021.12.010}, issn = {08887543}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {Genomics}, volume = {114}, number = {1}, pages = {266--277}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
García-Pérez, Isabel; Molsosa-Solanas, Anna; Perelló-Amorós, Miquel; Sarropoulou, Elena; Blasco, Josefina; Gutiérrez, Joaquim; de la serrana, Daniel Garcia The Emerging Role of Long Non-Coding RNAs in Development and Function of Gilthead Sea Bream (Sparus aurata) Fast Skeletal Muscle Journal Article Cells, 11 (3), pp. 428, 2022, ISSN: 2073-4409. @article{garcia-perez_emerging_2022, title = {The Emerging Role of Long Non-Coding RNAs in Development and Function of Gilthead Sea Bream (Sparus aurata) Fast Skeletal Muscle}, author = {Isabel García-Pérez and Anna Molsosa-Solanas and Miquel Perelló-Amorós and Elena Sarropoulou and Josefina Blasco and Joaquim Gutiérrez and Daniel Garcia de la serrana}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/03/2022-Garcia-Perez-CELLS-13.pdf https://www.mdpi.com/2073-4409/11/3/428}, doi = {10.3390/cells11030428}, issn = {2073-4409}, year = {2022}, date = {2022-01-01}, urldate = {2022-03-11}, journal = {Cells}, volume = {11}, number = {3}, pages = {428}, abstract = {Long non-coding RNAs (lncRNAs) are an emerging group of ncRNAs that can modulate gene expression at the transcriptional or translational levels. In the present work, previously published transcriptomic data were used to identify lncRNAs expressed in gilthead sea bream skeletal muscle, and their transcription levels were studied under different physiological conditions. Two hundred and ninety lncRNAs were identified and, based on transcriptomic differences between juveniles and adults, a total of seven lncRNAs showed potential to be important for muscle development. Our data suggest that the downregulation of most of the studied lncRNAs might be linked to increased myoblast proliferation, while their upregulation might be necessary for differentiation. However, with these data, as it is not possible to propose a formal mechanism to explain their effect, bioinformatic analysis suggests two possible mechanisms. First, the lncRNAs may act as sponges of myoblast proliferation inducers microRNAs (miRNAs) such as miR-206, miR-208, and miR-133 (binding energy MEF textless −25.0 kcal). Secondly, lncRNA20194 had a strong predicted interaction towards the myod1 mRNA (ndG = −0.17) that, based on the positive correlation between the two genes, might promote its function. Our study represents the first characterization of lncRNAs in gilthead sea bream fast skeletal muscle and provides evidence regarding their involvement in muscle development.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Long non-coding RNAs (lncRNAs) are an emerging group of ncRNAs that can modulate gene expression at the transcriptional or translational levels. In the present work, previously published transcriptomic data were used to identify lncRNAs expressed in gilthead sea bream skeletal muscle, and their transcription levels were studied under different physiological conditions. Two hundred and ninety lncRNAs were identified and, based on transcriptomic differences between juveniles and adults, a total of seven lncRNAs showed potential to be important for muscle development. Our data suggest that the downregulation of most of the studied lncRNAs might be linked to increased myoblast proliferation, while their upregulation might be necessary for differentiation. However, with these data, as it is not possible to propose a formal mechanism to explain their effect, bioinformatic analysis suggests two possible mechanisms. First, the lncRNAs may act as sponges of myoblast proliferation inducers microRNAs (miRNAs) such as miR-206, miR-208, and miR-133 (binding energy MEF textless −25.0 kcal). Secondly, lncRNA20194 had a strong predicted interaction towards the myod1 mRNA (ndG = −0.17) that, based on the positive correlation between the two genes, might promote its function. Our study represents the first characterization of lncRNAs in gilthead sea bream fast skeletal muscle and provides evidence regarding their involvement in muscle development. |
Papadaki, Maria; Kaitetzidou, Elisavet; Papadakis, Ioannis E; Sfakianakis, Dimitris G; Papandroulakis, Nikos; Mylonas, Constantinos C; Sarropoulou, Elena Temperature-Biased miRNA Expression Patterns during European Sea Bass (Dicentrarchus labrax) Development Journal Article International Journal of Molecular Sciences, 23 (19), pp. 11164, 2022, ISSN: 1422-0067. @article{papadaki_temperature-biased_2022, title = {Temperature-Biased miRNA Expression Patterns during European Sea Bass (Dicentrarchus labrax) Development}, author = {Maria Papadaki and Elisavet Kaitetzidou and Ioannis E Papadakis and Dimitris G Sfakianakis and Nikos Papandroulakis and Constantinos C Mylonas and Elena Sarropoulou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/09/2022-Papadaki-IJMS-65.pdf https://www.mdpi.com/1422-0067/23/19/11164}, doi = {10.3390/ijms231911164}, issn = {1422-0067}, year = {2022}, date = {2022-01-01}, urldate = {2022-09-27}, journal = {International Journal of Molecular Sciences}, volume = {23}, number = {19}, pages = {11164}, abstract = {Environmental effects and, particularly, temperature changes have been demonstrated to influence the activity, function, and well-being of teleosts. Temperature may change seasonally in the wild, and in captivity under aquaculture operations. Moreover, climate change is expected to shift temperature profiles worldwide. MicroRNAs (miRNA) are important temperature-sensitive gene-expression regulators acting at the post-transcriptional level. They are known to be key regulators in development, reproduction, and immune responses. Therefore, early larval development of the European sea bass (Dicentrarchus labrax), one of the most extensively cultured species in Mediterranean aquaculture, was investigated at early rearing temperatures, i.e., 15, 17.5, and 20 °C, in regard to the impact of temperatures on miRNAs through sncRNA high-throughput sequencing but also at the phenotypic level in terms of growth, sex, vision, and skeletal deformities. Expression profiling revealed stage- and temperature-specific miRNA expression targeting genes with roles in reproduction and immune response mainly at the flexion and all-fins stages. Similar stage- and temperature-specific results were also observed concerning the number of rod cells and lower jaw elongation. The present work presents for the first time highly promising results on the influence of early rearing temperature at the post-transcriptional level during European sea bass development, with a putative impact on reproduction and immune response, as well as regarding teleost vision and larval development.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Environmental effects and, particularly, temperature changes have been demonstrated to influence the activity, function, and well-being of teleosts. Temperature may change seasonally in the wild, and in captivity under aquaculture operations. Moreover, climate change is expected to shift temperature profiles worldwide. MicroRNAs (miRNA) are important temperature-sensitive gene-expression regulators acting at the post-transcriptional level. They are known to be key regulators in development, reproduction, and immune responses. Therefore, early larval development of the European sea bass (Dicentrarchus labrax), one of the most extensively cultured species in Mediterranean aquaculture, was investigated at early rearing temperatures, i.e., 15, 17.5, and 20 °C, in regard to the impact of temperatures on miRNAs through sncRNA high-throughput sequencing but also at the phenotypic level in terms of growth, sex, vision, and skeletal deformities. Expression profiling revealed stage- and temperature-specific miRNA expression targeting genes with roles in reproduction and immune response mainly at the flexion and all-fins stages. Similar stage- and temperature-specific results were also observed concerning the number of rod cells and lower jaw elongation. The present work presents for the first time highly promising results on the influence of early rearing temperature at the post-transcriptional level during European sea bass development, with a putative impact on reproduction and immune response, as well as regarding teleost vision and larval development. |
2021 |
Hermi, Fatma; Gómez-Abellán, Victoria; Pérez-Oliva, Ana B; García-Moreno, Diana; López-Muñoz, Azucena; Sarropoulou, Elena; Arizcun, Marta; Ridha, Oueslati; Mulero, Victoriano; Sepulcre, María P Developmental & Comparative Immunology, 114 , pp. 103803, 2021, ISSN: 0145305X. @article{hermi_molecular_2021, title = {The molecular, functional and phylogenetic characterization of PGE2 receptors reveals their different roles in the immune response of the teleost fish gilthead seabream (Sparus aurata L.)}, author = {Fatma Hermi and Victoria Gómez-Abellán and Ana B Pérez-Oliva and Diana García-Moreno and Azucena López-Muñoz and Elena Sarropoulou and Marta Arizcun and Oueslati Ridha and Victoriano Mulero and María P Sepulcre}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0145305X2030358X}, doi = {10.1016/j.dci.2020.103803}, issn = {0145305X}, year = {2021}, date = {2021-01-01}, urldate = {2020-08-23}, journal = {Developmental & Comparative Immunology}, volume = {114}, pages = {103803}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Makridis, Pavlos; Kokou, Fotini; Bournakas, Christos; Papandroulakis, Nikos; Sarropoulou, Elena Microorganisms, 9 (1), pp. 128, 2021, ISSN: 2076-2607. @article{makridis_isolation_2021, title = {Isolation of Phaeobacter sp. from Larvae of Atlantic Bonito (Sarda sarda) in a Mesocosmos Unit, and Its Use for the Rearing of European Seabass Larvae (Dicentrarchus labrax L.)}, author = {Pavlos Makridis and Fotini Kokou and Christos Bournakas and Nikos Papandroulakis and Elena Sarropoulou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021_2-Makridis-MICROORGANISMS.pdf https://www.mdpi.com/2076-2607/9/1/128}, doi = {10.3390/microorganisms9010128}, issn = {2076-2607}, year = {2021}, date = {2021-01-01}, urldate = {2021-02-02}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {128}, abstract = {The target of this study was to use indigenous probiotic bacteria in the rearing of seabass larvae. A Phaeobacter sp. strain isolated from bonito yolk-sac larvae (Sarda sarda) and identified by amplification of 16S rDNA showed in vitro inhibition against Vibrio anguillarum. This Phaeobacter sp. strain was used in the rearing of seabass larvae (Dicentrarchus labrax L.) in a large-scale trial. The survival of seabass after 60 days of rearing and the specific growth rate at the late exponential growth phase were significantly higher in the treatment receiving probiotics (p textless 0.05). Microbial community richness as determined by denaturing gradient gel electrophoresis (DGGE) showed an increase in bacterial diversity with fish development. Changes associated with the administration of probiotics were observed 11 and 18 days after hatching but were not apparent after probiotic administration stopped. In a small challenge experiment, seabass larvae from probiotic treatment showed increased survival (p textless 0.05) after experimental infection with a mild pathogen (Vibrio harveyi). Overall, our results showed that the use of an indigenous probiotic strain had a beneficial impact on larval rearing in industry-like conditions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The target of this study was to use indigenous probiotic bacteria in the rearing of seabass larvae. A Phaeobacter sp. strain isolated from bonito yolk-sac larvae (Sarda sarda) and identified by amplification of 16S rDNA showed in vitro inhibition against Vibrio anguillarum. This Phaeobacter sp. strain was used in the rearing of seabass larvae (Dicentrarchus labrax L.) in a large-scale trial. The survival of seabass after 60 days of rearing and the specific growth rate at the late exponential growth phase were significantly higher in the treatment receiving probiotics (p textless 0.05). Microbial community richness as determined by denaturing gradient gel electrophoresis (DGGE) showed an increase in bacterial diversity with fish development. Changes associated with the administration of probiotics were observed 11 and 18 days after hatching but were not apparent after probiotic administration stopped. In a small challenge experiment, seabass larvae from probiotic treatment showed increased survival (p textless 0.05) after experimental infection with a mild pathogen (Vibrio harveyi). Overall, our results showed that the use of an indigenous probiotic strain had a beneficial impact on larval rearing in industry-like conditions. |
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. |
2020 |
Papadaki, Maria; Kaitetzidou, Elisavet; Mylonas, Constantinos C; Sarropoulou, Elena Non-coding RNA Expression Patterns of Two Different Teleost Gonad Maturation Stages Journal Article Marine Biotechnology, 22 (5), pp. 683–695, 2020, ISSN: 1436-2228, 1436-2236. @article{papadaki_non-coding_2020, title = {Non-coding RNA Expression Patterns of Two Different Teleost Gonad Maturation Stages}, author = {Maria Papadaki and Elisavet Kaitetzidou and Constantinos C Mylonas and Elena Sarropoulou}, url = {http://link.springer.com/10.1007/s10126-020-09991-2 https://imbbc.hcmr.gr/wp-content/uploads/2020/10/Papadaki-2020-MBTE-pre-print.pdf}, doi = {10.1007/s10126-020-09991-2}, issn = {1436-2228, 1436-2236}, year = {2020}, date = {2020-10-01}, urldate = {2020-10-05}, journal = {Marine Biotechnology}, volume = {22}, number = {5}, pages = {683--695}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2019 |
Kaitetzidou, Elisavet; Katsiadaki, Ioanna; Lagnel, Jacques; Antonopoulou, Efthimia; Sarropoulou, Elena Unravelling paralogous gene expression dynamics during three-spined stickleback embryogenesis Journal Article Scientific Reports, 9 (1), pp. 3752, 2019, ISSN: 2045-2322. @article{kaitetzidou_unravelling_2019, title = {Unravelling paralogous gene expression dynamics during three-spined stickleback embryogenesis}, author = {Elisavet Kaitetzidou and Ioanna Katsiadaki and Jacques Lagnel and Efthimia Antonopoulou and Elena Sarropoulou}, url = {http://www.nature.com/articles/s41598-019-40127-2}, doi = {10.1038/s41598-019-40127-2}, issn = {2045-2322}, year = {2019}, date = {2019-12-01}, urldate = {2020-08-21}, journal = {Scientific Reports}, volume = {9}, number = {1}, pages = {3752}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sarropoulou, Elena; Kaitetzidou, Elizabet; Papandroulakis, Nikos; Tsalafouta, Aleka; Pavlidis, Michalis Inventory of European Sea Bass (Dicentrarchus labrax) sncRNAs Vital During Early Teleost Development Journal Article Frontiers in Genetics, 10 , pp. 657, 2019, ISSN: 1664-8021. @article{sarropoulou_inventory_2019, title = {Inventory of European Sea Bass (Dicentrarchus labrax) sncRNAs Vital During Early Teleost Development}, author = {Elena Sarropoulou and Elizabet Kaitetzidou and Nikos Papandroulakis and Aleka Tsalafouta and Michalis Pavlidis}, url = {https://www.frontiersin.org/article/10.3389/fgene.2019.00657/full}, doi = {10.3389/fgene.2019.00657}, issn = {1664-8021}, year = {2019}, date = {2019-07-01}, urldate = {2020-08-21}, journal = {Frontiers in Genetics}, volume = {10}, pages = {657}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2018 |
Pauletto, Marianna; Manousaki, Tereza; Ferraresso, Serena; Babbucci, Massimiliano; Tsakogiannis, Alexandros; Louro, Bruno; Vitulo, Nicola; Quoc, Viet Ha; Carraro, Roberta; Bertotto, Daniela; Franch, Rafaella; Maroso, Francesco; Aslam, Muhammad L; Sonesson, Anna K; Simionati, Barbara; Malacrida, Giorgio; Cestaro, Alessandro; Caberlotto, Stefano; Sarropoulou, Elena; Mylonas, Costantinos C; Power, Deborah M; Patarnello, Tomaso; Canario, Adelino V M; Tsigenopoulos, Costas; Bargelloni, Luca Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish Journal Article Communications Biology, 1 (1), pp. 119, 2018, ISSN: 2399-3642. @article{pauletto_genomic_2018, title = {Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish}, author = {Marianna Pauletto and Tereza Manousaki and Serena Ferraresso and Massimiliano Babbucci and Alexandros Tsakogiannis and Bruno Louro and Nicola Vitulo and Viet Ha Quoc and Roberta Carraro and Daniela Bertotto and Rafaella Franch and Francesco Maroso and Muhammad L Aslam and Anna K Sonesson and Barbara Simionati and Giorgio Malacrida and Alessandro Cestaro and Stefano Caberlotto and Elena Sarropoulou and Costantinos C Mylonas and Deborah M Power and Tomaso Patarnello and Adelino V M Canario and Costas Tsigenopoulos and Luca Bargelloni}, url = {http://www.nature.com/articles/s42003-018-0122-7}, doi = {10.1038/s42003-018-0122-7}, issn = {2399-3642}, year = {2018}, date = {2018-12-01}, urldate = {2020-08-21}, journal = {Communications Biology}, volume = {1}, number = {1}, pages = {119}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Roufidou, Chrysoula; Feidantsis, Konstantinos; Mente, Eleni; Sarropoulou, Elena; Antonopoulou, Efthimia Mediterranean Marine Science, 19 (2), pp. 240–247, 2018, ISSN: 1791-6763, 1108-393X, (BIODIV). @article{roufidou_heat_2018, title = {Heat shock protein (HSP) expression and mitogen-activated protein kinase (MAPK) phosphorylation during early embryonic developmental stages of the Gilthead sea bream (Sparus aurata)}, author = {Chrysoula Roufidou and Konstantinos Feidantsis and Eleni Mente and Elena Sarropoulou and Efthimia Antonopoulou}, url = {https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/14088}, doi = {10.12681/mms.14088}, issn = {1791-6763, 1108-393X}, year = {2018}, date = {2018-06-01}, urldate = {2022-01-17}, journal = {Mediterranean Marine Science}, volume = {19}, number = {2}, pages = {240--247}, abstract = {Both heat shock proteins (HSPs), which have key roles in vital cell functions, as well as members of the mitogen-activated protein kinases (MAPKs), which adjust gene expression by transducing cellular signals to the nucleus, are necessary for normal embryonic development in vertebrates. Therefore, protein expression levels of HSP70 and HSP90 and the activation of members of the MAPK protein family, such as p38 MAPK, ERKs, and JNKs were studied in the early developmental stages of the Gilthead sea bream, Sparus aurata Linnaeus, 1758. The protein expression of HSP70 and the phosphorylation ratio of JNKs remained at equal levels at all examined developmental stages, while the other examined proteins exhibited a differential profile. HSP90 levels were mostly increased at the 16-cell stage and towards the morula stages, and the lowest values were observed at the two- to four-cell and one-half epiboly stages. While p38 MAPK phosphorylation ratio exhibited increased values mostly in the early developmental stages, the opposite was observed concerning ERK phosphorylation ratio, where increased values were observed in the later embryonic stages (high blastula to one-half epiboly stages). These differential profiles of the examined protein expression levels highlight the importance of these proteins during embryogenesis and pave the way for further research to unveil their distinct role in early development.}, note = {BIODIV}, keywords = {}, pubstate = {published}, tppubtype = {article} } Both heat shock proteins (HSPs), which have key roles in vital cell functions, as well as members of the mitogen-activated protein kinases (MAPKs), which adjust gene expression by transducing cellular signals to the nucleus, are necessary for normal embryonic development in vertebrates. Therefore, protein expression levels of HSP70 and HSP90 and the activation of members of the MAPK protein family, such as p38 MAPK, ERKs, and JNKs were studied in the early developmental stages of the Gilthead sea bream, Sparus aurata Linnaeus, 1758. The protein expression of HSP70 and the phosphorylation ratio of JNKs remained at equal levels at all examined developmental stages, while the other examined proteins exhibited a differential profile. HSP90 levels were mostly increased at the 16-cell stage and towards the morula stages, and the lowest values were observed at the two- to four-cell and one-half epiboly stages. While p38 MAPK phosphorylation ratio exhibited increased values mostly in the early developmental stages, the opposite was observed concerning ERK phosphorylation ratio, where increased values were observed in the later embryonic stages (high blastula to one-half epiboly stages). These differential profiles of the examined protein expression levels highlight the importance of these proteins during embryogenesis and pave the way for further research to unveil their distinct role in early development. |
Kokkari, C; Sarropoulou, E; Bastias, R; Mandalakis, M; Katharios, P Isolation and characterization of a novel bacteriophage infecting Vibrio alginolyticus Journal Article Archives of Microbiology, 200 (5), pp. 707–718, 2018, ISSN: 03028933, (Publisher: Springer Verlag). @article{kokkari_isolation_2018, title = {Isolation and characterization of a novel bacteriophage infecting Vibrio alginolyticus}, author = {C Kokkari and E Sarropoulou and R Bastias and M Mandalakis and P Katharios}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85040930909&doi=10.1007%2fs00203-018-1480-8&partnerID=40&md5=b22268a55a9ed98e93e66d4448fbe221}, doi = {10.1007/s00203-018-1480-8}, issn = {03028933}, year = {2018}, date = {2018-01-01}, journal = {Archives of Microbiology}, volume = {200}, number = {5}, pages = {707--718}, abstract = {Vibrio alginolyticus is a common marine bacterium implicated in disease outbreaks in marine farmed fish and invertebrates. Due to the inappropriate use of antibiotics in aquaculture, alternative therapies have been proposed. One of the most promising options is the use of lytic bacteriophages to control pathogenic bacteria. This work describes the isolation and characterization of a lytic phage (VEN) against a V. alginolyticus strain (V2) isolated from a disease outbreak in common dentex (Dentex dentex) cultured at the Hellenic Centre for Marine Research (HCMR) in Crete, Greece. The bacteriophage is morphologically similar to phages from Podoviridae family and remained stable for 1 year at 4 °C and over 1 h when kept at 50 °C. VEN was able to lyse the host bacteria at several multiplicity of infection (MOI) (0.1–100) in liquid cultures. However, it was unable to infect other V. alginolyticus strains. Its genome consists of 44,603 bp with a GC content of 43.5%, while sequence analysis revealed the presence of 54 potential ORFs with a T7-like genomic organization. Almost 65% of the predicted ORFs presented homology with proteins of the vibriophages Vc1 and phi-A318 infecting Vibrio cyclitrophicus and Vibrio alginolyticus, respectively. Phylogenetic analysis applying the amino acid sequence of the large terminase subunit confirmed the close relationship of these phages. Furthermore, the comparison of the RNA polymerase of these phages revealed that the motifs A, B and C related to the catalytic activity and the recognition loop related to promotor identification were also conserved. VEN has an obligate lytic life cycle demonstrated by experimental data and genomic analysis. These results suggest that VEN may provide a good candidate to control recurrent diseases caused by V. alginolyticus at HCMR. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.}, note = {Publisher: Springer Verlag}, keywords = {}, pubstate = {published}, tppubtype = {article} } Vibrio alginolyticus is a common marine bacterium implicated in disease outbreaks in marine farmed fish and invertebrates. Due to the inappropriate use of antibiotics in aquaculture, alternative therapies have been proposed. One of the most promising options is the use of lytic bacteriophages to control pathogenic bacteria. This work describes the isolation and characterization of a lytic phage (VEN) against a V. alginolyticus strain (V2) isolated from a disease outbreak in common dentex (Dentex dentex) cultured at the Hellenic Centre for Marine Research (HCMR) in Crete, Greece. The bacteriophage is morphologically similar to phages from Podoviridae family and remained stable for 1 year at 4 °C and over 1 h when kept at 50 °C. VEN was able to lyse the host bacteria at several multiplicity of infection (MOI) (0.1–100) in liquid cultures. However, it was unable to infect other V. alginolyticus strains. Its genome consists of 44,603 bp with a GC content of 43.5%, while sequence analysis revealed the presence of 54 potential ORFs with a T7-like genomic organization. Almost 65% of the predicted ORFs presented homology with proteins of the vibriophages Vc1 and phi-A318 infecting Vibrio cyclitrophicus and Vibrio alginolyticus, respectively. Phylogenetic analysis applying the amino acid sequence of the large terminase subunit confirmed the close relationship of these phages. Furthermore, the comparison of the RNA polymerase of these phages revealed that the motifs A, B and C related to the catalytic activity and the recognition loop related to promotor identification were also conserved. VEN has an obligate lytic life cycle demonstrated by experimental data and genomic analysis. These results suggest that VEN may provide a good candidate to control recurrent diseases caused by V. alginolyticus at HCMR. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature. |
Tsalafouta, A; Sarropoulou, E; Papandroulakis, N; Pavlidis, M Marine Biotechnology, 20 (5), pp. 611–622, 2018, ISSN: 14362228, (Publisher: Springer New York LLC). @article{tsalafouta_characterization_2018, title = {Characterization and Expression Dynamics of Key Genes Involved in the Gilthead Sea Bream (Sparus aurata) Cortisol Stress Response during Early Ontogeny}, author = {A Tsalafouta and E Sarropoulou and N Papandroulakis and M Pavlidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85048276185&doi=10.1007%2fs10126-018-9833-5&partnerID=40&md5=806b6e065e80bbd391d7c165a62a1c5d}, doi = {10.1007/s10126-018-9833-5}, issn = {14362228}, year = {2018}, date = {2018-01-01}, journal = {Marine Biotechnology}, volume = {20}, number = {5}, pages = {611--622}, abstract = {The present study identified and characterized six key genes involved in the hypothalamic-pituitary-interrenal (HPI) axis of gilthead sea bream (Sparus aurata), a commercially important European aquaculture species. The key genes involved in the HPI axis for which gene structure and synteny analysis was carried out, comprised of two functional forms of glucocorticoid receptors (GR), as well as three forms of pro-opiomelanocortin (POMC) genes and one form of mineralocorticoid receptor (MR) gene. To explore their functional roles during development but also in the stress response, the expression profiles of gr1, gr2, mr, pomc_aI, pomc_aII, and pomc_β were examined during early ontogeny and after an acute stress challenge. The acute stress challenge was applied at the stage of full formation of all fins, where whole body cortisol was also measured. Both the cortisol and the molecular data implied that sea bream larvae at the stage of the full formation of all fins at 45 dph are capable of a response to stress of a similar profile as observed in adult fish. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.}, note = {Publisher: Springer New York LLC}, keywords = {}, pubstate = {published}, tppubtype = {article} } The present study identified and characterized six key genes involved in the hypothalamic-pituitary-interrenal (HPI) axis of gilthead sea bream (Sparus aurata), a commercially important European aquaculture species. The key genes involved in the HPI axis for which gene structure and synteny analysis was carried out, comprised of two functional forms of glucocorticoid receptors (GR), as well as three forms of pro-opiomelanocortin (POMC) genes and one form of mineralocorticoid receptor (MR) gene. To explore their functional roles during development but also in the stress response, the expression profiles of gr1, gr2, mr, pomc_aI, pomc_aII, and pomc_β were examined during early ontogeny and after an acute stress challenge. The acute stress challenge was applied at the stage of full formation of all fins, where whole body cortisol was also measured. Both the cortisol and the molecular data implied that sea bream larvae at the stage of the full formation of all fins at 45 dph are capable of a response to stress of a similar profile as observed in adult fish. © 2018, Springer Science+Business Media, LLC, part of Springer Nature. |
Machado, A M; Sarropoulou, E; Castro, L F C; Vasconcelos, V; Cunha, I Marine Genomics, 2018, ISSN: 18747787, (Publisher: Elsevier B.V.). @article{machado_important_2018, title = {An important resource for understanding bio-adhesion mechanisms: Cement gland transcriptomes of two goose barnacles, Pollicipes pollicipes and Lepas anatifera (Cirripedia, Thoracica)}, author = {A M Machado and E Sarropoulou and L F C Castro and V Vasconcelos and I Cunha}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85056582867&doi=10.1016%2fj.margen.2018.11.001&partnerID=40&md5=86d2c2f77ab6834e7327de1080fc495f}, doi = {10.1016/j.margen.2018.11.001}, issn = {18747787}, year = {2018}, date = {2018-01-01}, journal = {Marine Genomics}, abstract = {Barnacles are sessile organisms globally distributed in marine and estuarine environments. The production of protein-based adhesives by cement glands is crucial for these organisms and plays a vital role in substrate attachment, thus inspiring biotechnological applications. Moreover, barnacles belong to bio-fouling communities, whose fixation onto man-made surfaces is of interest in terms of control and imposes an enormous economic cost on maritime industries. Here, we generated the first de novo assembly of cement gland transcriptomes of Pollicipes pollicipes (rocky-shore goose barnacle) and Lepas anatifera (pelagic goose barnacle) (Cirripedia, Thoracica), to generate molecular resources for understanding the bio-adhesion process in Cirripedia and to provide data for biotechnology. Via the Illumina next-generation sequencing technology, a total of 43.7 and 40.2 million (M) paired-end (PE) clean reads were obtained for P. pollicipes (PP) and L. anatifera (LA), respectively. De novo assemblies resulted in 116,377 transcripts for PP and 94,143 for LA, with N50 s of 1181 and 1028 bp, respectively. The Benchmarking Universal Single-Copy Orthologs (BUSCO) showed 78.7% (PP) and 91.7% (LA) of transcriptome completeness, in terms of expected gene content, for the Arthropoda phylum in each species. These results represent a substantial resource for expanding the knowledge on Cirripedia adhesion mechanisms and for contributions to the gene annotation of Crustacea where molecular resources are presently insufficient. © 2018 Elsevier B.V.}, note = {Publisher: Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Barnacles are sessile organisms globally distributed in marine and estuarine environments. The production of protein-based adhesives by cement glands is crucial for these organisms and plays a vital role in substrate attachment, thus inspiring biotechnological applications. Moreover, barnacles belong to bio-fouling communities, whose fixation onto man-made surfaces is of interest in terms of control and imposes an enormous economic cost on maritime industries. Here, we generated the first de novo assembly of cement gland transcriptomes of Pollicipes pollicipes (rocky-shore goose barnacle) and Lepas anatifera (pelagic goose barnacle) (Cirripedia, Thoracica), to generate molecular resources for understanding the bio-adhesion process in Cirripedia and to provide data for biotechnology. Via the Illumina next-generation sequencing technology, a total of 43.7 and 40.2 million (M) paired-end (PE) clean reads were obtained for P. pollicipes (PP) and L. anatifera (LA), respectively. De novo assemblies resulted in 116,377 transcripts for PP and 94,143 for LA, with N50 s of 1181 and 1028 bp, respectively. The Benchmarking Universal Single-Copy Orthologs (BUSCO) showed 78.7% (PP) and 91.7% (LA) of transcriptome completeness, in terms of expected gene content, for the Arthropoda phylum in each species. These results represent a substantial resource for expanding the knowledge on Cirripedia adhesion mechanisms and for contributions to the gene annotation of Crustacea where molecular resources are presently insufficient. © 2018 Elsevier B.V. |
2017 |
Kokou, F; Sarropoulou, E; Cotou, E; Kentouri, M; Alexis, M; Rigos, G Fish and Shellfish Immunology, 64 , pp. 111–121, 2017, ISSN: 10504648, (Publisher: Academic Press). @article{kokou_effects_2017, title = {Effects of graded dietary levels of soy protein concentrate supplemented with methionine and phosphate on the immune and antioxidant responses of gilthead sea bream (Sparus aurata L.)}, author = {F Kokou and E Sarropoulou and E Cotou and M Kentouri and M Alexis and G Rigos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85015366036&doi=10.1016%2fj.fsi.2017.03.017&partnerID=40&md5=248a8c59f873e9dfc679de05a6cbcdfb}, doi = {10.1016/j.fsi.2017.03.017}, issn = {10504648}, year = {2017}, date = {2017-01-01}, journal = {Fish and Shellfish Immunology}, volume = {64}, pages = {111--121}, abstract = {The effects of a dietary soy protein concentrate (SPC) as a fish meal (FM) substitute, on selected innate immune responses, the oxidative status, hepatic and intestinal morphology of gilthead sea bream, Sparus aurata, were evaluated after a three-month feeding trial. Isonitrogenous (45% crude protein) and isoenergetic (23 kJ/g gross energy) diets with 20% (SPC20), 40% (SPC40) and 60% (SPC60) of SPC inclusion, supplemented with methionine and phosphate, were evaluated against a diet containing FM as the sole protein source. Diets were allocated in triplicate groups of 26-g fish (8 kg m−3/tank) and administered for three months. Immune responses were evaluated by performing immunological assays in blood (respiratory burst activity) and serum (myeloperoxidase content, bacteriolytic and lysozyme activity), as well as by gene expression analysis of immune-associated genes (MHCIIα, β2m, CSF-1R, NCCRP-1, TGF-β1, HSP70) in the head kidney and distal intestine. In addition, oxidative stress was evaluated by measuring the activity of liver enzymes associated with the antioxidant system. The respiratory burst activity of blood was significantly decreased in the SPC40 group, while serum myeloperoxidase content and bacteriolytic and lysozyme activities were affected. Significantly higher expression levels of NCCRP-1 and HSP70 were found in SPC60 head kidneys, while increased intestinal MHCIIα and NCCRP-1 transcripts were observed in SPC40. Hepatic antioxidant enzyme activity of glutathione reductase and glutathione-S-transferase was significantly enhanced in the SPC40 and SPC60 groups, while superoxide dismutase activity was increased only in the SPC40 group. Moreover, increased lipid accumulation in the enterocytes of the distal intestine was observed in the SPC60 group. Overall, a three-month feeding period with diets over 40% of dietary SPC inclusion as a FM substitute, indicated increases on immune and antioxidant enzyme responses, suggesting the dietary SPC levels that gilthead sea bream can tolerate. © 2017 Elsevier Ltd}, note = {Publisher: Academic Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } The effects of a dietary soy protein concentrate (SPC) as a fish meal (FM) substitute, on selected innate immune responses, the oxidative status, hepatic and intestinal morphology of gilthead sea bream, Sparus aurata, were evaluated after a three-month feeding trial. Isonitrogenous (45% crude protein) and isoenergetic (23 kJ/g gross energy) diets with 20% (SPC20), 40% (SPC40) and 60% (SPC60) of SPC inclusion, supplemented with methionine and phosphate, were evaluated against a diet containing FM as the sole protein source. Diets were allocated in triplicate groups of 26-g fish (8 kg m−3/tank) and administered for three months. Immune responses were evaluated by performing immunological assays in blood (respiratory burst activity) and serum (myeloperoxidase content, bacteriolytic and lysozyme activity), as well as by gene expression analysis of immune-associated genes (MHCIIα, β2m, CSF-1R, NCCRP-1, TGF-β1, HSP70) in the head kidney and distal intestine. In addition, oxidative stress was evaluated by measuring the activity of liver enzymes associated with the antioxidant system. The respiratory burst activity of blood was significantly decreased in the SPC40 group, while serum myeloperoxidase content and bacteriolytic and lysozyme activities were affected. Significantly higher expression levels of NCCRP-1 and HSP70 were found in SPC60 head kidneys, while increased intestinal MHCIIα and NCCRP-1 transcripts were observed in SPC40. Hepatic antioxidant enzyme activity of glutathione reductase and glutathione-S-transferase was significantly enhanced in the SPC40 and SPC60 groups, while superoxide dismutase activity was increased only in the SPC40 group. Moreover, increased lipid accumulation in the enterocytes of the distal intestine was observed in the SPC60 group. Overall, a three-month feeding period with diets over 40% of dietary SPC inclusion as a FM substitute, indicated increases on immune and antioxidant enzyme responses, suggesting the dietary SPC levels that gilthead sea bream can tolerate. © 2017 Elsevier Ltd |
Katharios, P; Kalatzis, P G; Kokkari, C; Sarropoulou, E; Middelboe, M Isolation and characterization of a N4-like lytic bacteriophage infecting Vibrio splendidus, a pathogen of fish and bivalves Journal Article PLoS ONE, 12 (12), pp. e0190083, 2017, ISSN: 19326203, (Publisher: Public Library of Science). @article{katharios_isolation_2017, title = {Isolation and characterization of a N4-like lytic bacteriophage infecting Vibrio splendidus, a pathogen of fish and bivalves}, author = {P Katharios and P G Kalatzis and C Kokkari and E Sarropoulou and M Middelboe}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85039803769&doi=10.1371%2fjournal.pone.0190083&partnerID=40&md5=764cc6c742f2f2111527fd680e4aa5b2}, doi = {10.1371/journal.pone.0190083}, issn = {19326203}, year = {2017}, date = {2017-01-01}, journal = {PLoS ONE}, volume = {12}, number = {12}, pages = {e0190083}, abstract = {A novel virulent bacteriophage, vB_VspP_pVa5, infecting a strain of Vibrio splendidus was isolated from a sea-cage aquaculture farm in Greece, and characterized using microbiological methods and genomic analysis. Bacteriophage vB_VspP_pVa5 is a N4-like podovirus with an icosahedral head measuring 85 nm in length and a short non-contractile tail. The phage had a narrow host range infecting only the bacterial host, a latent period of 30 min and a burst size of 24 virions per infected bacterium. Its genome size was 78,145 bp and genomic analysis identified 107 densely-packed genes, 40 of which could be annotated. In addition to the very large virion encapsulated DNA-dependent RNA polymerase which is the signature of the N4-like genus, an interesting feature of the novel phage is the presence of a self-splicing group I intron in the thymidylate synthase gene. A tRNAStop interrupted by a 2.5kb open reading frame–containing area was also identified. The absence of genes related to lysogeny along with the high efficacy observed during in vitro cell lysis trials, indicate that the vB_VspP_pVa5 is a potential candidate component in a bacteriophage cocktail suitable for the biological control of V. splendidus in aquaculture. © 2017 Katharios et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.}, note = {Publisher: Public Library of Science}, keywords = {}, pubstate = {published}, tppubtype = {article} } A novel virulent bacteriophage, vB_VspP_pVa5, infecting a strain of Vibrio splendidus was isolated from a sea-cage aquaculture farm in Greece, and characterized using microbiological methods and genomic analysis. Bacteriophage vB_VspP_pVa5 is a N4-like podovirus with an icosahedral head measuring 85 nm in length and a short non-contractile tail. The phage had a narrow host range infecting only the bacterial host, a latent period of 30 min and a burst size of 24 virions per infected bacterium. Its genome size was 78,145 bp and genomic analysis identified 107 densely-packed genes, 40 of which could be annotated. In addition to the very large virion encapsulated DNA-dependent RNA polymerase which is the signature of the N4-like genus, an interesting feature of the novel phage is the presence of a self-splicing group I intron in the thymidylate synthase gene. A tRNAStop interrupted by a 2.5kb open reading frame–containing area was also identified. The absence of genes related to lysogeny along with the high efficacy observed during in vitro cell lysis trials, indicate that the vB_VspP_pVa5 is a potential candidate component in a bacteriophage cocktail suitable for the biological control of V. splendidus in aquaculture. © 2017 Katharios et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
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. |
Kaitetzidou, E; Ludwig, A; Gessner, J; Sarropoulou, E Expression patterns of atlantic sturgeon (Acipenser oxyrinchus) during embryonic development Journal Article G3: Genes, Genomes, Genetics, 7 (2), pp. 533–542, 2017, ISSN: 21601836, (Publisher: Genetics Society of America). @article{kaitetzidou_expression_2017, title = {Expression patterns of atlantic sturgeon (Acipenser oxyrinchus) during embryonic development}, author = {E Kaitetzidou and A Ludwig and J Gessner and E Sarropoulou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85012900590&doi=10.1534%2fg3.116.036699&partnerID=40&md5=a55f7b655c7c43f35caf4131f17e4438}, doi = {10.1534/g3.116.036699}, issn = {21601836}, year = {2017}, date = {2017-01-01}, journal = {G3: Genes, Genomes, Genetics}, volume = {7}, number = {2}, pages = {533--542}, abstract = {During teleost ontogeny the larval and embryonic stages are key stages, since failure during this period of tissue differentiation may cause malformations, developmental delays, poor growth, and massive mortalities. Despite the rapid advances in sequencing technologies, the molecular backgrounds of the development of economically important but endangered fish species like the Atlantic sturgeon (Acipenser oxyrinchus) have not yet been thoroughly investigated. The current study examines the differential expression of transcripts involved in embryonic development of the Atlantic sturgeon. Addressing this goal, a reference transcriptome comprising eight stages was generated using an Illumina HiSequation 2500 platform. The constructed de novo assembly counted to 441,092 unfiltered and 179,564 filtered transcripts. Subsequently, the expression profile of four developmental stages ranging from early (gastrula) to late stages of prelarval development [2 d posthatching (dph)] were investigated applying an Illumina MiSeq platform. Differential expression analysis revealed distinct expression patterns among stages, especially between the two early and the two later stages. Transcripts upregulated at the two early stages were mainly enriched in transcripts linked to developmental processes, while transcripts expressed at the last two stages were mainly enriched in transcripts important to muscle contraction. Furthermore, important stagespecific expression has been detected for the hatching stage with transcripts enriched in molecule transport, and for the 2 dph stage with transcripts enriched in visual perception and lipid digestion. Our investigation represents a significant contribution to the understanding of Atlantic sturgeon embryonic development, and transcript characterization along with the differential expression results will significantly contribute to sturgeon research and aquaculture. © 2017 Kaitetzidou et al.}, note = {Publisher: Genetics Society of America}, keywords = {}, pubstate = {published}, tppubtype = {article} } During teleost ontogeny the larval and embryonic stages are key stages, since failure during this period of tissue differentiation may cause malformations, developmental delays, poor growth, and massive mortalities. Despite the rapid advances in sequencing technologies, the molecular backgrounds of the development of economically important but endangered fish species like the Atlantic sturgeon (Acipenser oxyrinchus) have not yet been thoroughly investigated. The current study examines the differential expression of transcripts involved in embryonic development of the Atlantic sturgeon. Addressing this goal, a reference transcriptome comprising eight stages was generated using an Illumina HiSequation 2500 platform. The constructed de novo assembly counted to 441,092 unfiltered and 179,564 filtered transcripts. Subsequently, the expression profile of four developmental stages ranging from early (gastrula) to late stages of prelarval development [2 d posthatching (dph)] were investigated applying an Illumina MiSeq platform. Differential expression analysis revealed distinct expression patterns among stages, especially between the two early and the two later stages. Transcripts upregulated at the two early stages were mainly enriched in transcripts linked to developmental processes, while transcripts expressed at the last two stages were mainly enriched in transcripts important to muscle contraction. Furthermore, important stagespecific expression has been detected for the hatching stage with transcripts enriched in molecule transport, and for the 2 dph stage with transcripts enriched in visual perception and lipid digestion. Our investigation represents a significant contribution to the understanding of Atlantic sturgeon embryonic development, and transcript characterization along with the differential expression results will significantly contribute to sturgeon research and aquaculture. © 2017 Kaitetzidou et al. |
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. |
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. |
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). |
Nagasawa, Kazue; Sarropoulou, Elena; Edvardsen, Vigdis; Fernandes, Jorge M O Substantial downregulation of myogenic transcripts in skeletal muscle of Atlantic cod during the spawning period. Journal Article PLoS ONE, 11 (2), pp. e0148374, 2016, ISSN: 1932-6203. @article{nagasawa_substantial_2016, title = {Substantial downregulation of myogenic transcripts in skeletal muscle of Atlantic cod during the spawning period.}, author = {Kazue Nagasawa and Elena Sarropoulou and Vigdis Edvardsen and Jorge M O Fernandes}, url = {https://dx.plos.org/10.1371/journal.pone.0148374}, doi = {DOI:10.1371/journal.pone.014837}, issn = {1932-6203}, year = {2016}, date = {2016-01-01}, journal = {PLoS ONE}, volume = {11}, number = {2}, pages = {e0148374}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sarropoulou, Elena; Adamidou, Styliani; Karacostas, Ioannis; Kokou, Fotini Sample size matters in dietary gene expression studies - a case study in the gilthead sea bream (Sparus aurata L.) Journal Article Aquaculture Reports, 3 , pp. 82–87, 2016. @article{sarropoulou_sample_2016, title = {Sample size matters in dietary gene expression studies - a case study in the gilthead sea bream (Sparus aurata L.)}, author = {Elena Sarropoulou and Styliani Adamidou and Ioannis Karacostas and Fotini Kokou}, url = {http://www.sciencedirect.com/science/article/pii/S2352513415300326}, doi = {doi:10.1016/j.aqrep.2015.12.004}, year = {2016}, date = {2016-01-01}, journal = {Aquaculture Reports}, volume = {3}, pages = {82--87}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Georgiou, S; Alami-Durante, H; Power, D M; Sarropoulou, E; Mamuris, Z; Moutou, K A Cell and Tissue Research, 363 (2), pp. 541–554, 2016, ISSN: 0302766X, (Publisher: Springer Verlag). @article{georgiou_transient_2016, title = {Transient up- and down-regulation of expression of myosin light chain 2 and myostatin mRNA mark the changes from stratified hyperplasia to muscle fiber hypertrophy in larvae of gilthead sea bream (Sparus aurata L.)}, author = {S Georgiou and H Alami-Durante and D M Power and E Sarropoulou and Z Mamuris and K A Moutou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84956950356&doi=10.1007%2fs00441-015-2254-0&partnerID=40&md5=e35128d4a27fb8161b4a2ef30b1c3b19}, doi = {10.1007/s00441-015-2254-0}, issn = {0302766X}, year = {2016}, date = {2016-01-01}, journal = {Cell and Tissue Research}, volume = {363}, number = {2}, pages = {541--554}, abstract = {Hyperplasia and hypertrophy are the two mechanisms by which muscle develops and grows. We study these two mechanisms, during the early development of white muscle in Sparus aurata, by means of histology and the expression of structural and regulatory genes. A clear stage of stratified hyperplasia was identified early in the development of gilthead sea bream but ceased by 35 dph when hypertrophy took over. Mosaic recruitment of new white fibers began as soon as 60 dph. The genes mlc2a and mlc2b were expressed at various levels during the main phases of hyperplasia and hypertrophy. The genes myog and mlc2a were significantly up-regulated during the intensive stratified formation of new fibers and their expression was significantly correlated. Expression of mstn1 and igf1 increased at 35 dph, appeared to regulate the hyperplasia-to-hypertrophy transition, and may have stimulated the expression of mlc2a, mlc2b and col1a1 at the onset of mosaic hyperplasia. The up-regulation of mstn1 at transitional phases in muscle development indicates a dual regulatory role of myostatin in fish larval muscle growth. © 2015, Springer-Verlag Berlin Heidelberg.}, note = {Publisher: Springer Verlag}, keywords = {}, pubstate = {published}, tppubtype = {article} } Hyperplasia and hypertrophy are the two mechanisms by which muscle develops and grows. We study these two mechanisms, during the early development of white muscle in Sparus aurata, by means of histology and the expression of structural and regulatory genes. A clear stage of stratified hyperplasia was identified early in the development of gilthead sea bream but ceased by 35 dph when hypertrophy took over. Mosaic recruitment of new white fibers began as soon as 60 dph. The genes mlc2a and mlc2b were expressed at various levels during the main phases of hyperplasia and hypertrophy. The genes myog and mlc2a were significantly up-regulated during the intensive stratified formation of new fibers and their expression was significantly correlated. Expression of mstn1 and igf1 increased at 35 dph, appeared to regulate the hyperplasia-to-hypertrophy transition, and may have stimulated the expression of mlc2a, mlc2b and col1a1 at the onset of mosaic hyperplasia. The up-regulation of mstn1 at transitional phases in muscle development indicates a dual regulatory role of myostatin in fish larval muscle growth. © 2015, Springer-Verlag Berlin Heidelberg. |
Samaras, A; Dimitroglou, A; Sarropoulou, E; Papaharisis, L; Kottaras, L; Pavlidis, M Scientific Reports, 6 , 2016, ISSN: 20452322, (Publisher: Nature Publishing Group). @article{samaras_repeatability_2016, title = {Repeatability of cortisol stress response in the European sea bass (Dicentrarchus labrax) and transcription differences between individuals with divergent responses}, author = {A Samaras and A Dimitroglou and E Sarropoulou and L Papaharisis and L Kottaras and M Pavlidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84990048823&doi=10.1038%2fsrep34858&partnerID=40&md5=2f8fdd5e3716b42be506c888bf96f144}, doi = {10.1038/srep34858}, issn = {20452322}, year = {2016}, date = {2016-01-01}, journal = {Scientific Reports}, volume = {6}, abstract = {Understanding the stress responses of organisms is of importance in the performance and welfare of farmed animals, including fish. Especially fish in aquaculture commonly face stressors, and better knowledge of their responses may assist in proper husbandry and selection of breeding stocks. European sea bass (Dicentrarchus labrax), a species with high cortisol concentrations, is of major importance in this respect. The main objectives of the present study were to assess the repeatability and consistency of cortisol stress response and to identify differences in liver transcription profiles of European sea bass individuals, showing a consistent low (LR) or high (HR) cortisol response. The progeny of six full sib families was used, and sampled for plasma cortisol after an acute stress challenge once per month, for four consecutive months. Results suggest that cortisol responsiveness was a repeatable trait with LR and HR fish showing low or high resting, free and post-stress cortisol concentrations respectively. Finally, the liver transcription profiles of LR and HR fish showed some important differences, indicating differential hepatic regulation between these divergent phenotypes. These transcription differences were related to various metabolic and immunological processes, with 169 transcripts being transcribed exclusively in LR fish and 161 exclusively in HR fish. © 2016 The Author(s).}, note = {Publisher: Nature Publishing Group}, keywords = {}, pubstate = {published}, tppubtype = {article} } Understanding the stress responses of organisms is of importance in the performance and welfare of farmed animals, including fish. Especially fish in aquaculture commonly face stressors, and better knowledge of their responses may assist in proper husbandry and selection of breeding stocks. European sea bass (Dicentrarchus labrax), a species with high cortisol concentrations, is of major importance in this respect. The main objectives of the present study were to assess the repeatability and consistency of cortisol stress response and to identify differences in liver transcription profiles of European sea bass individuals, showing a consistent low (LR) or high (HR) cortisol response. The progeny of six full sib families was used, and sampled for plasma cortisol after an acute stress challenge once per month, for four consecutive months. Results suggest that cortisol responsiveness was a repeatable trait with LR and HR fish showing low or high resting, free and post-stress cortisol concentrations respectively. Finally, the liver transcription profiles of LR and HR fish showed some important differences, indicating differential hepatic regulation between these divergent phenotypes. These transcription differences were related to various metabolic and immunological processes, with 169 transcripts being transcribed exclusively in LR fish and 161 exclusively in HR fish. © 2016 The Author(s). |
2015 |
Consortium, The FAANG; Andersson, Leif; Archibald, Alan L; Bottema, Cynthia D; Brauning, Rudiger; Burgess, Shane C; Burt, Dave W; Casas, Eduardo; Cheng, Hans H; Clarke, Laura; Couldrey, Christine; Dalrymple, Brian P; Elsik, Christine G; Foissac, Sylvain; Giuffra, Elisabetta; Groenen, Martien A; Hayes, Ben J; Huang, LuSheng S; Khatib, Hassan; Kijas, James W; Kim, Heebal; Lunney, Joan K; McCarthy, Fiona M; McEwan, John C; Moore, Stephen; Nanduri, Bindu; Notredame, Cedric; Palti, Yniv; Plastow, Graham S; Reecy, James M; Rohrer, Gary A; Sarropoulou, Elena; Schmidt, Carl J; Silverstein, Jeffrey; Tellam, Ross L; Tixier-Boichard, Michele; Tosser-Klopp, Gwenola; Tuggle, Christopher K; Vilkki, Johanna; White, Stephen N; Zhao, Shuhong; Zhou, Huaijun Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project Journal Article Genome Biology, 16 (1), pp. 57, 2015, ISSN: 1474-760X. @article{the_faang_consortium_coordinated_2015, title = {Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project}, author = {The FAANG Consortium and Leif Andersson and Alan L Archibald and Cynthia D Bottema and Rudiger Brauning and Shane C Burgess and Dave W Burt and Eduardo Casas and Hans H Cheng and Laura Clarke and Christine Couldrey and Brian P Dalrymple and Christine G Elsik and Sylvain Foissac and Elisabetta Giuffra and Martien A Groenen and Ben J Hayes and LuSheng S Huang and Hassan Khatib and James W Kijas and Heebal Kim and Joan K Lunney and Fiona M McCarthy and John C McEwan and Stephen Moore and Bindu Nanduri and Cedric Notredame and Yniv Palti and Graham S Plastow and James M Reecy and Gary A Rohrer and Elena Sarropoulou and Carl J Schmidt and Jeffrey Silverstein and Ross L Tellam and Michele Tixier-Boichard and Gwenola Tosser-Klopp and Christopher K Tuggle and Johanna Vilkki and Stephen N White and Shuhong Zhao and Huaijun Zhou}, url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0622-4}, doi = {10.1186/s13059-015-0622-4}, issn = {1474-760X}, year = {2015}, date = {2015-12-01}, urldate = {2020-08-17}, journal = {Genome Biology}, volume = {16}, number = {1}, pages = {57}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kaitetzidou, E; Chatzifotis, S; Antonopoulou, E; Sarropoulou, E Identification, Phylogeny, and Function of fabp2 Paralogs in Two Non-Model Teleost Fish Species Journal Article Marine Biotechnology, 17 (5), pp. 663–677, 2015, ISSN: 14362228, (Publisher: Springer New York LLC). @article{kaitetzidou_identification_2015, title = {Identification, Phylogeny, and Function of fabp2 Paralogs in Two Non-Model Teleost Fish Species}, author = {E Kaitetzidou and S Chatzifotis and E Antonopoulou and E Sarropoulou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84939566208&doi=10.1007%2fs10126-015-9648-6&partnerID=40&md5=7ed4057e28f0af24da6033ebec855acb}, doi = {10.1007/s10126-015-9648-6}, issn = {14362228}, year = {2015}, date = {2015-01-01}, journal = {Marine Biotechnology}, volume = {17}, number = {5}, pages = {663--677}, abstract = {Intestinal fatty-acid-binding protein (IFABP or FABP2) is a cytosolic transporter of long-chain fatty acids, which is mainly expressed in cells of intestinal tissue. Fatty acids in teleosts are an important source of energy for growth, reproduction, and swimming and a main ingredient in the yolk sac of embryos and larvae. The fabp2 paralogs, fabp2a and fabp2b, were identified for 26 teleost fish species including the paralogs for the two non-model teleost fish species, namely the gilthead sea bream (Sparus aurata) and the European sea bass (Dicentrarchus labrax). Despite the high similarity of fabp2 paralogs, as well as the identical organization in four exons, paralogs were mapped to different chromosomes/linkage groups supporting the hypothesis that the identified transcripts are true paralogs originating from a single ancestor gene after genome duplication. This was also confirmed by phylogenetic analysis using fabp2 sequences of 26 teleosts and by synteny analysis carried out with ten teleosts. Differential expression analysis of the gilthead sea bream and European sea bass fabp2 paralogs in the intestine after fasting and refeeding experiment further revealed their altered implication in metabolism. Additional expression studies in seven developmental stages of the two species detected fabp2 paralogs relatively early in the embryonic development as well as possible complementary or separated roles of the paralogs. The identification and characterization of the two fabp2 paralogs will contribute significantly to the understanding of the fabp2 evolution as well as of the divergences in fatty acid metabolism. © 2015, Springer Science+Business Media New York.}, note = {Publisher: Springer New York LLC}, keywords = {}, pubstate = {published}, tppubtype = {article} } Intestinal fatty-acid-binding protein (IFABP or FABP2) is a cytosolic transporter of long-chain fatty acids, which is mainly expressed in cells of intestinal tissue. Fatty acids in teleosts are an important source of energy for growth, reproduction, and swimming and a main ingredient in the yolk sac of embryos and larvae. The fabp2 paralogs, fabp2a and fabp2b, were identified for 26 teleost fish species including the paralogs for the two non-model teleost fish species, namely the gilthead sea bream (Sparus aurata) and the European sea bass (Dicentrarchus labrax). Despite the high similarity of fabp2 paralogs, as well as the identical organization in four exons, paralogs were mapped to different chromosomes/linkage groups supporting the hypothesis that the identified transcripts are true paralogs originating from a single ancestor gene after genome duplication. This was also confirmed by phylogenetic analysis using fabp2 sequences of 26 teleosts and by synteny analysis carried out with ten teleosts. Differential expression analysis of the gilthead sea bream and European sea bass fabp2 paralogs in the intestine after fasting and refeeding experiment further revealed their altered implication in metabolism. Additional expression studies in seven developmental stages of the two species detected fabp2 paralogs relatively early in the embryonic development as well as possible complementary or separated roles of the paralogs. The identification and characterization of the two fabp2 paralogs will contribute significantly to the understanding of the fabp2 evolution as well as of the divergences in fatty acid metabolism. © 2015, Springer Science+Business Media New York. |
Kokou, F; Sarropoulou, E; Cotou, E; Rigos, G; Henry, M; Alexis, M; Kentouri, M Journal of the World Aquaculture Society, 46 (2), pp. 115–128, 2015, ISSN: 08938849, (Publisher: Blackwell Publishing Inc.). @article{kokou_effects_2015, title = {Effects of fish meal replacement by a soybean protein on growth, histology, selected immune and oxidative status markers of gilthead sea bream, Sparus aurata}, author = {F Kokou and E Sarropoulou and E Cotou and G Rigos and M Henry and M Alexis and M Kentouri}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84925962477&doi=10.1111%2fjwas.12181&partnerID=40&md5=8968f20ba7b477a763db252568770b94}, doi = {10.1111/jwas.12181}, issn = {08938849}, year = {2015}, date = {2015-01-01}, journal = {Journal of the World Aquaculture Society}, volume = {46}, number = {2}, pages = {115--128}, abstract = {The purpose of the trial was to study the impact of a 6-mo dietary administration of soybean protein on growth, liver and intestine morphology, immune response, and oxidative stress in gilthead sea bream. The immune response was evaluated by performing immunological assays in blood, head kidney (HK), or serum (respiratory burst activity [RBA], myeloperoxidase content and bacteriolytic activity) and gene expression analysis of immune-associated genes (MHCIIα [major histocompatibility complex IIα], β2m [β-2-microglobulin], CSF-1R [colony-stimulating factor-1 receptor], NCCRP-1 [nonspecific cytotoxic cell receptor protein 1], TGF-β1 [transforming growth factor beta-1], and HSP70 [heat-shock protein 70]) in HK and intestine. Oxidative stress was evaluated by measuring the activity of liver enzymes associated with antioxidant system. The soybean protein was administrated in the diets at 20, 40, and 60% levels and its effects were evaluated compared with a fish meal diet. Growth and feed efficiency were affected negatively from 40% level. Increased RBA and expression levels of TGF-β1 and β2m were found in HK only at 40% level. In intestine, at 60% level CSF-1R expression was upregulated and some signs of inflammation were evident. In liver, at 60% level lipid accumulation in hepatocytes was observed and enzyme activity was increased. Dietary administration of soybean protein indicated changes from 40% in growth and immune response, and exerted an antioxidative effect at 60% level. © by the World Aquaculture Society 2015.}, note = {Publisher: Blackwell Publishing Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The purpose of the trial was to study the impact of a 6-mo dietary administration of soybean protein on growth, liver and intestine morphology, immune response, and oxidative stress in gilthead sea bream. The immune response was evaluated by performing immunological assays in blood, head kidney (HK), or serum (respiratory burst activity [RBA], myeloperoxidase content and bacteriolytic activity) and gene expression analysis of immune-associated genes (MHCIIα [major histocompatibility complex IIα], β2m [β-2-microglobulin], CSF-1R [colony-stimulating factor-1 receptor], NCCRP-1 [nonspecific cytotoxic cell receptor protein 1], TGF-β1 [transforming growth factor beta-1], and HSP70 [heat-shock protein 70]) in HK and intestine. Oxidative stress was evaluated by measuring the activity of liver enzymes associated with antioxidant system. The soybean protein was administrated in the diets at 20, 40, and 60% levels and its effects were evaluated compared with a fish meal diet. Growth and feed efficiency were affected negatively from 40% level. Increased RBA and expression levels of TGF-β1 and β2m were found in HK only at 40% level. In intestine, at 60% level CSF-1R expression was upregulated and some signs of inflammation were evident. In liver, at 60% level lipid accumulation in hepatocytes was observed and enzyme activity was increased. Dietary administration of soybean protein indicated changes from 40% in growth and immune response, and exerted an antioxidative effect at 60% level. © by the World Aquaculture Society 2015. |
Kaitetzidou, E; Xiang, J; Antonopoulou, E; Tsigenopoulos, C S; Sarropoulou, E Dynamics of gene expression patterns during early development of the European seabass (Dicentrarchus labrax) Journal Article Physiological Genomics, 47 (5), pp. 158–169, 2015, ISSN: 10948341, (Publisher: American Physiological Society). @article{kaitetzidou_dynamics_2015, title = {Dynamics of gene expression patterns during early development of the European seabass (Dicentrarchus labrax)}, author = {E Kaitetzidou and J Xiang and E Antonopoulou and C S Tsigenopoulos and E Sarropoulou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84930978495&doi=10.1152%2fphysiolgenomics.00001.2015&partnerID=40&md5=ac0e811b8dd4948aca47662547595ee0}, doi = {10.1152/physiolgenomics.00001.2015}, issn = {10948341}, year = {2015}, date = {2015-01-01}, journal = {Physiological Genomics}, volume = {47}, number = {5}, pages = {158--169}, abstract = {Larval and embryonic stages are the most critical period in the life cycle of marine fish. Key developmental events occur early in development and are influenced by external parameters like stress, temperature, salinity, and photoperiodism. Any failure may cause malformations, developmental delays, poor growth, and massive mortalities. Advanced understanding of molecular processes underlying marine larval development may lead to superior larval rearing conditions. Today, the new sequencing and bioinformatic methods allow transcriptome screens comprising messenger (mRNA) and microRNA (miRNA) with the scope of detecting differential expression for any species of interest. In the present study, we applied Illumina technology to investigate the transcriptome of early developmental stages of the European seabass (Dicentrarchus labrax). The European seabass, in its natural environment, is a euryhaline species and has shown high adaptation processes in early life phases. During its embryonic and larval phases the European seabass lives in a marine environment and as a juvenile it migrates to coastal zones, estuaries, and lagoons. Investigating the dynamics of gene expression in its early development may shed light on factors promoting phenotypic plasticity and may also contribute to the improvement and advancement of rearing methods of the European seabass, a species of high economic importance in European and Mediterranean aquaculture. We present the identification, characterization, and expression of mRNA and miRNA, comprising paralogous genes and differentially spliced transcripts from early developmental stages of the European seabass. We further investigated the detection of possible interactions of miRNA with mRNA. © 2015 the American Physiological Society.}, note = {Publisher: American Physiological Society}, keywords = {}, pubstate = {published}, tppubtype = {article} } Larval and embryonic stages are the most critical period in the life cycle of marine fish. Key developmental events occur early in development and are influenced by external parameters like stress, temperature, salinity, and photoperiodism. Any failure may cause malformations, developmental delays, poor growth, and massive mortalities. Advanced understanding of molecular processes underlying marine larval development may lead to superior larval rearing conditions. Today, the new sequencing and bioinformatic methods allow transcriptome screens comprising messenger (mRNA) and microRNA (miRNA) with the scope of detecting differential expression for any species of interest. In the present study, we applied Illumina technology to investigate the transcriptome of early developmental stages of the European seabass (Dicentrarchus labrax). The European seabass, in its natural environment, is a euryhaline species and has shown high adaptation processes in early life phases. During its embryonic and larval phases the European seabass lives in a marine environment and as a juvenile it migrates to coastal zones, estuaries, and lagoons. Investigating the dynamics of gene expression in its early development may shed light on factors promoting phenotypic plasticity and may also contribute to the improvement and advancement of rearing methods of the European seabass, a species of high economic importance in European and Mediterranean aquaculture. We present the identification, characterization, and expression of mRNA and miRNA, comprising paralogous genes and differentially spliced transcripts from early developmental stages of the European seabass. We further investigated the detection of possible interactions of miRNA with mRNA. © 2015 the American Physiological Society. |
Bazakos, C; Manioudaki, M E; Sarropoulou, E; Spano, T; Kalaitzis, P 454 pyrosequencing of olive (Olea europaea L.) transcriptome in response to salinity Journal Article PLoS ONE, 10 (11), 2015, ISSN: 19326203, (Publisher: Public Library of Science). @article{bazakos_454_2015, title = {454 pyrosequencing of olive (Olea europaea L.) transcriptome in response to salinity}, author = {C Bazakos and M E Manioudaki and E Sarropoulou and T Spano and P Kalaitzis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84956690252&doi=10.1371%2fjournal.pone.0143000&partnerID=40&md5=15ddad48a1b8bba2022eeac05d0dac9d}, doi = {10.1371/journal.pone.0143000}, issn = {19326203}, year = {2015}, date = {2015-01-01}, journal = {PLoS ONE}, volume = {10}, number = {11}, abstract = {Olive (Olea europaea L.) is one of the most important crops in the Mediterranean region. The expansion of cultivation in areas irrigated with low quality and saline water has negative effects on growth and productivity however the investigation of the molecular basis of salt tolerance in olive trees has been only recently initiated. To this end, we investigated the molecular response of cultivar Kalamon to salinity stress using next-generation sequencing technology to explore the transcriptome profile of olive leaves and roots and identify differentially expressed genes that are related to salt tolerance response. Out of 291,958 obtained trimmed reads, 28,270 unique transcripts were identified of which 35%are annotated, a percentage that is comparable to similar reports on non-model plants. Among the 1,624 clusters in roots that comprise more than one read, 24 were differentially expressed comprising 9 down- and 15 up-regulated genes. Respectively, inleaves, among the 2,642 clusters, 70 were identified as differentially expressed, with 14 down- and 56 up-regulated genes. Using nextgeneration sequencing technology we were able to identify salt-response-related transcripts. Furthermore we provide an annotated transcriptome of olive as well as expression data, which are both significant tools for further molecular studies in olive. © 2015 Bazakos et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.}, note = {Publisher: Public Library of Science}, keywords = {}, pubstate = {published}, tppubtype = {article} } Olive (Olea europaea L.) is one of the most important crops in the Mediterranean region. The expansion of cultivation in areas irrigated with low quality and saline water has negative effects on growth and productivity however the investigation of the molecular basis of salt tolerance in olive trees has been only recently initiated. To this end, we investigated the molecular response of cultivar Kalamon to salinity stress using next-generation sequencing technology to explore the transcriptome profile of olive leaves and roots and identify differentially expressed genes that are related to salt tolerance response. Out of 291,958 obtained trimmed reads, 28,270 unique transcripts were identified of which 35%are annotated, a percentage that is comparable to similar reports on non-model plants. Among the 1,624 clusters in roots that comprise more than one read, 24 were differentially expressed comprising 9 down- and 15 up-regulated genes. Respectively, inleaves, among the 2,642 clusters, 70 were identified as differentially expressed, with 14 down- and 56 up-regulated genes. Using nextgeneration sequencing technology we were able to identify salt-response-related transcripts. Furthermore we provide an annotated transcriptome of olive as well as expression data, which are both significant tools for further molecular studies in olive. © 2015 Bazakos et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
2014 |
Angosto, Diego; Montero, Jana; López-Muñoz, Azucena; Alcaraz-Pérez, Francisca; Bird, Steve; Sarropoulou, Elena; Abellán, Emilia; Meseguer, José; Sepulcre, María P; Mulero, Victoriano Identification and functional characterization of a new IL-1 family member, IL-1Fm2, in most evolutionarily advanced fish Journal Article Innate Immunity, 20 (5), pp. 487–500, 2014, ISSN: 1753-4259, 1753-4267. @article{angosto_identification_2014, title = {Identification and functional characterization of a new IL-1 family member, IL-1Fm2, in most evolutionarily advanced fish}, author = {Diego Angosto and Jana Montero and Azucena López-Muñoz and Francisca Alcaraz-Pérez and Steve Bird and Elena Sarropoulou and Emilia Abellán and José Meseguer and María P Sepulcre and Victoriano Mulero}, url = {http://journals.sagepub.com/doi/10.1177/1753425913501011}, doi = {10.1177/1753425913501011}, issn = {1753-4259, 1753-4267}, year = {2014}, date = {2014-07-01}, urldate = {2020-08-18}, journal = {Innate Immunity}, volume = {20}, number = {5}, pages = {487--500}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Tsigenopoulos, C S; Louro, B; Chatziplis, D; Lagnel, J; Vogiatzi, E; Loukovitis, D; Franch, R; Sarropoulou, E; Power, D M; Patarnello, T; Mylonas, C C; Magoulas, A; Bargelloni, L; Canario, A; Kotoulas, G Second generation genetic linkage map for the gilthead sea bream Sparus aurata L. Journal Article Marine Genomics, 18 (PA), pp. 77–82, 2014, ISSN: 18747787, (Publisher: Elsevier B.V.). @article{tsigenopoulos_second_2014, title = {Second generation genetic linkage map for the gilthead sea bream Sparus aurata L.}, author = {C S Tsigenopoulos and B Louro and D Chatziplis and J Lagnel and E Vogiatzi and D Loukovitis and R Franch and E Sarropoulou and D M Power and T Patarnello and C C Mylonas and A Magoulas and L Bargelloni and A Canario and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84922896860&doi=10.1016%2fj.margen.2014.09.008&partnerID=40&md5=c3bdc2b59c298f1c4d2cf093183db7ab}, doi = {10.1016/j.margen.2014.09.008}, issn = {18747787}, year = {2014}, date = {2014-01-01}, journal = {Marine Genomics}, volume = {18}, number = {PA}, pages = {77--82}, abstract = {An updated second linkage map was constructed for the gilthead sea bream, Sparus aurata L., a fish species of great economic importance for the Mediterranean aquaculture industry. In contrast to the first linkage map which mainly consisted of genomic microsatellites (SSRs), the new linkage map is highly enriched with SSRs found in Expressed Sequence Tags (EST-SSRs), which greatly facilitates comparative mapping with other teleosts. The new map consists of 321 genetic markers in 27 linkage groups (LGs): 232 genomic microsatellites, 85 EST-SSRs and 4 SNPs; of those, 13 markers were linked to LGs but were not ordered. Eleven markers (5 SSRs, 5 EST-SSRs and 1 SNP) are not assigned to any LG. The total length of the sex-averaged map is 1769.7. cM, 42% longer than the previously published one, and the number of markers in each LG ranges from 2 to 30. The inter-marker distance varies from 0 to 75.6. cM, with an average of 5.75. cM. The male and female maps have a length of 1349.2 and 2172.1. cM, respectively, and the average distance between markers is 4.38 and 7.05. cM, respectively. Comparative mapping with the three-spined stickleback (Gasterosteus acuulatus) chromosomes and scaffolds showed conserved synteny with 132 S. aurata markers (42.9% of those mapped) having a hit on the stickleback genome. © 2014 Elsevier B.V.}, note = {Publisher: Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } An updated second linkage map was constructed for the gilthead sea bream, Sparus aurata L., a fish species of great economic importance for the Mediterranean aquaculture industry. In contrast to the first linkage map which mainly consisted of genomic microsatellites (SSRs), the new linkage map is highly enriched with SSRs found in Expressed Sequence Tags (EST-SSRs), which greatly facilitates comparative mapping with other teleosts. The new map consists of 321 genetic markers in 27 linkage groups (LGs): 232 genomic microsatellites, 85 EST-SSRs and 4 SNPs; of those, 13 markers were linked to LGs but were not ordered. Eleven markers (5 SSRs, 5 EST-SSRs and 1 SNP) are not assigned to any LG. The total length of the sex-averaged map is 1769.7. cM, 42% longer than the previously published one, and the number of markers in each LG ranges from 2 to 30. The inter-marker distance varies from 0 to 75.6. cM, with an average of 5.75. cM. The male and female maps have a length of 1349.2 and 2172.1. cM, respectively, and the average distance between markers is 4.38 and 7.05. cM, respectively. Comparative mapping with the three-spined stickleback (Gasterosteus acuulatus) chromosomes and scaffolds showed conserved synteny with 132 S. aurata markers (42.9% of those mapped) having a hit on the stickleback genome. © 2014 Elsevier B.V. |
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. |
Manousaki, Tereza; Tsakogiannis, Alexandros; Lagnel, Jacques; Sarropoulou, Elena; Xiang, Jenny Z; Papandroulakis, Nikos; Mylonas, Constantinos C; Tsigenopoulos, Costas S The sex-specific transcriptome of the hermaphrodite sparid sharpsnout seabream (Diplodus puntazzo) Journal Article BMC genomics, 15 (1), pp. 655, 2014, (Publisher: BioMed Central). @article{manousaki_sex-specific_2014, title = {The sex-specific transcriptome of the hermaphrodite sparid sharpsnout seabream (Diplodus puntazzo)}, author = {Tereza Manousaki and Alexandros Tsakogiannis and Jacques Lagnel and Elena Sarropoulou and Jenny Z Xiang and Nikos Papandroulakis and Constantinos C Mylonas and Costas S Tsigenopoulos}, year = {2014}, date = {2014-01-01}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {655}, note = {Publisher: BioMed Central}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sarropoulou, E; Moghadam, H K; Papandroulakis, N; de la Gandara, F; AO, Garcia; Makridis, P The Atlantic bonito (Sarda sarda, Bloch 1793) transcriptome and detection of differential expression during larvae development Journal Article PLoS ONE, 9 (2), pp. e87744, 2014. @article{sarropoulou_atlantic_2014, title = {The Atlantic bonito (Sarda sarda, Bloch 1793) transcriptome and detection of differential expression during larvae development}, author = {E Sarropoulou and H K Moghadam and N Papandroulakis and F de la Gandara and Garcia AO and P Makridis}, doi = {https://doi.org/10.1371/journal.pone.0087744}, year = {2014}, date = {2014-01-01}, journal = {PLoS ONE}, volume = {9}, number = {2}, pages = {e87744}, abstract = {The Atlantic bonito (Sarda sarda, Bloch 1793) belongs to the important marine fish species with a wide geographical distribution covering the Atlantic Ocean, the Mediterranean and its bordering seas. Aquaculture practices for this species are still in their infancies and scientific studies are seldom undertaken, mainly because of difficulties in sampling. Thus for small tuna species like the Atlantic bonito only little is known about its biology and regarding the molecular background even less information is available. In the production of marine fish it is known that the most critical period is the larval stages, as high growth rates as well as significant developmental changes take place. In this study we have investigated the transcriptome of the Atlantic bonito of five larvae stages applying Illumina sequencing technology. For non-model species like aquaculture species, transcriptome analysis of RNA samples from individuals using Illumina sequencing technology is technically efficient and cost effective. In the present study a total number of 169,326,711 paired-end reads with a read length of 100 base pairs were generated resulting in a reference transcriptome of 68,220 contigs with an average length of 2054 base pairs. For differential expression analyses single end reads were obtained from different developmental stages and mapped to the constructed reference transcriptome. Differential expression analyses revealed in total 18,657 differentially expressed transcripts and were assigned to five distinguished groups. Each of the five clusters shows stage specific gene expression. We present for the first time in the Atlantic bonito an extensive RNA-Seq based characterization of its transcriptome as well as significant information on differential expression among five developmental larvae stages. The generated transcripts, including SNP and microsatellite information for candidate molecular markers and gene expression information will be a valuable resource for future genetic and molecular studies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Atlantic bonito (Sarda sarda, Bloch 1793) belongs to the important marine fish species with a wide geographical distribution covering the Atlantic Ocean, the Mediterranean and its bordering seas. Aquaculture practices for this species are still in their infancies and scientific studies are seldom undertaken, mainly because of difficulties in sampling. Thus for small tuna species like the Atlantic bonito only little is known about its biology and regarding the molecular background even less information is available. In the production of marine fish it is known that the most critical period is the larval stages, as high growth rates as well as significant developmental changes take place. In this study we have investigated the transcriptome of the Atlantic bonito of five larvae stages applying Illumina sequencing technology. For non-model species like aquaculture species, transcriptome analysis of RNA samples from individuals using Illumina sequencing technology is technically efficient and cost effective. In the present study a total number of 169,326,711 paired-end reads with a read length of 100 base pairs were generated resulting in a reference transcriptome of 68,220 contigs with an average length of 2054 base pairs. For differential expression analyses single end reads were obtained from different developmental stages and mapped to the constructed reference transcriptome. Differential expression analyses revealed in total 18,657 differentially expressed transcripts and were assigned to five distinguished groups. Each of the five clusters shows stage specific gene expression. We present for the first time in the Atlantic bonito an extensive RNA-Seq based characterization of its transcriptome as well as significant information on differential expression among five developmental larvae stages. The generated transcripts, including SNP and microsatellite information for candidate molecular markers and gene expression information will be a valuable resource for future genetic and molecular studies. |
Sánchez-Hernández, M; Arizcun, M; García-Alcázar, A; Sarropoulou, E; Mulero, V; García-Ayala, A Fish granulocytes express a constitutively active androgen receptor variant Journal Article Developmental and Comparative Immunology, 45 (1), pp. 115–122, 2014, ISSN: 0145305X, (Publisher: Elsevier Ltd). @article{sanchez-hernandez_fish_2014, title = {Fish granulocytes express a constitutively active androgen receptor variant}, author = {M Sánchez-Hernández and M Arizcun and A García-Alcázar and E Sarropoulou and V Mulero and A García-Ayala}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84896022881&doi=10.1016%2fj.dci.2014.01.024&partnerID=40&md5=1a2e59d11552c3d737a8182dfc5733ff}, doi = {10.1016/j.dci.2014.01.024}, issn = {0145305X}, year = {2014}, date = {2014-01-01}, journal = {Developmental and Comparative Immunology}, volume = {45}, number = {1}, pages = {115--122}, abstract = {In humans, alternative splicing of androgen receptor (AR) is usually involved in some diseases. However, our knowledge about the presence of AR variants in other species and its importance for immunity is scant. Here, we report the identification of a constitutively active AR variant lacking the ligand-binding domain (LBD), ARδLBD, in the fish gilthead seabream. ARδLBD is expressed in the testis and the head-kidney (HK), and its expression varies with the reproductive stage and is correlated with plasma testosterone (T). In addition, ARδLBD is expressed in acidophilic granulocytes (AGs), which are the functional equivalent of mammalian neutrophils, but not in macrophages, and its expression is modulated by both T and immune stimuli. Notably, AR and ARδLBD were able to interact, being the activity of AR dominant at all concentrations tested of the ligand. These results reveal a new mechanism for the regulation of neutrophil biology in vertebrates and explain the conflicting results that suggest that androgens are less important than AR in human and mouse neutrophil homeostasis. © 2014 Elsevier Ltd.}, note = {Publisher: Elsevier Ltd}, keywords = {}, pubstate = {published}, tppubtype = {article} } In humans, alternative splicing of androgen receptor (AR) is usually involved in some diseases. However, our knowledge about the presence of AR variants in other species and its importance for immunity is scant. Here, we report the identification of a constitutively active AR variant lacking the ligand-binding domain (LBD), ARδLBD, in the fish gilthead seabream. ARδLBD is expressed in the testis and the head-kidney (HK), and its expression varies with the reproductive stage and is correlated with plasma testosterone (T). In addition, ARδLBD is expressed in acidophilic granulocytes (AGs), which are the functional equivalent of mammalian neutrophils, but not in macrophages, and its expression is modulated by both T and immune stimuli. Notably, AR and ARδLBD were able to interact, being the activity of AR dominant at all concentrations tested of the ligand. These results reveal a new mechanism for the regulation of neutrophil biology in vertebrates and explain the conflicting results that suggest that androgens are less important than AR in human and mouse neutrophil homeostasis. © 2014 Elsevier Ltd. |
2013 |
Fernández, Carmen García; Roufidou, Chrysoula; Antonopoulou, Efthimia; Sarropoulou, Elena Expression of Developmental-Stage-Specific Genes in the Gilthead Sea Bream Sparus aurata L. Journal Article Marine Biotechnology, 15 (3), pp. 313–320, 2013, ISSN: 1436-2228, 1436-2236. @article{fernandez_expression_2013, title = {Expression of Developmental-Stage-Specific Genes in the Gilthead Sea Bream Sparus aurata L.}, author = {Carmen García Fernández and Chrysoula Roufidou and Efthimia Antonopoulou and Elena Sarropoulou}, url = {http://link.springer.com/10.1007/s10126-012-9486-8}, doi = {10.1007/s10126-012-9486-8}, issn = {1436-2228, 1436-2236}, year = {2013}, date = {2013-06-01}, urldate = {2020-08-18}, journal = {Marine Biotechnology}, volume = {15}, number = {3}, pages = {313--320}, abstract = {The mechanism of early fish development as well as the control of egg quality is of great importance for the ability of the oocyte to develop after fertilization. Embryonic development is initially regulated by maternally provided mRNAs and later by the zygotic genome. Maternal mRNAs have an important role in initiating processes crucial to patterning the developing fish embryo. Furthermore, it has been shown that maternal RNA plays an important role in egg quality. The identification and characterization of candidate maternal genes in non-model fish species with important aquaculture interest like the gilthead sea bream Sparus aurata L. is of importance for future studies related to egg quality. The broodstock of the gilthead sea bream produces large quantities of eggs with a high and non-controllable quality variation. In the present study, we have studied the gene expression of 16 genes (gapdh 1 and 2, cathepsin D, L, S and Z, erk1, jnk1, p38 alpha and p38 delta, ppar alpha, beta and gamma, tubulin beta, ferritin M, cyclinA2) of different functional categories in seven developmental stages. The 16 genes were chosen based on their putative involvement in egg quality and regulation of early development. In total, 11 showed a characteristic gene expression pattern pinpointing to the possible function as maternal genes and thus may function as molecular biomarker for egg quality. © 2012 Springer Science+Business Media New York.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The mechanism of early fish development as well as the control of egg quality is of great importance for the ability of the oocyte to develop after fertilization. Embryonic development is initially regulated by maternally provided mRNAs and later by the zygotic genome. Maternal mRNAs have an important role in initiating processes crucial to patterning the developing fish embryo. Furthermore, it has been shown that maternal RNA plays an important role in egg quality. The identification and characterization of candidate maternal genes in non-model fish species with important aquaculture interest like the gilthead sea bream Sparus aurata L. is of importance for future studies related to egg quality. The broodstock of the gilthead sea bream produces large quantities of eggs with a high and non-controllable quality variation. In the present study, we have studied the gene expression of 16 genes (gapdh 1 and 2, cathepsin D, L, S and Z, erk1, jnk1, p38 alpha and p38 delta, ppar alpha, beta and gamma, tubulin beta, ferritin M, cyclinA2) of different functional categories in seven developmental stages. The 16 genes were chosen based on their putative involvement in egg quality and regulation of early development. In total, 11 showed a characteristic gene expression pattern pinpointing to the possible function as maternal genes and thus may function as molecular biomarker for egg quality. © 2012 Springer Science+Business Media New York. |
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. |
Georgiou, S; Sarropoulou, E; Power, D M; Alami-Durante, H; Mamuris, Z; Moutou, K A Expression of skeletal myosin light chain 2 in gilthead sea bream (Sparus aurata, L): regulation and correlation to growth markers. Journal Article Communications in agricultural and applied biological sciences, 78 (4), pp. 151–152, 2013, ISSN: 13791176. @article{georgiou_expression_2013, title = {Expression of skeletal myosin light chain 2 in gilthead sea bream (Sparus aurata, L): regulation and correlation to growth markers.}, author = {S Georgiou and E Sarropoulou and D M Power and H Alami-Durante and Z Mamuris and K A Moutou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84907261013&partnerID=40&md5=7f81a5029f4904421dda9a9d89cd818d}, issn = {13791176}, year = {2013}, date = {2013-01-01}, journal = {Communications in agricultural and applied biological sciences}, volume = {78}, number = {4}, pages = {151--152}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2012 |
Sarropoulou, Elena; Fernandes, Jorge; Liu, Zhanjiang John GIA 2011: Genomics in Aquaculture 2011 Symposium Journal Article Marine Biotechnology, 14 (5), pp. 513–514, 2012, ISSN: 1436-2228, 1436-2236. @article{sarropoulou_gia_2012, title = {GIA 2011: Genomics in Aquaculture 2011 Symposium}, author = {Elena Sarropoulou and Jorge Fernandes and Zhanjiang John Liu}, url = {http://link.springer.com/10.1007/s10126-012-9468-x}, doi = {10.1007/s10126-012-9468-x}, issn = {1436-2228, 1436-2236}, year = {2012}, date = {2012-10-01}, urldate = {2020-08-18}, journal = {Marine Biotechnology}, volume = {14}, number = {5}, pages = {513--514}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sarropoulou, E; Galindo-Villegas, J; García-Alcázar, A; Kasapidis, P; Mulero, V Characterization of European Sea Bass Transcripts by RNA SEQ After Oral Vaccine Against V. anguillarum Journal Article Marine Biotechnology, 14 (5), pp. 634–642, 2012, ISSN: 14362228. @article{sarropoulou_characterization_2012, title = {Characterization of European Sea Bass Transcripts by RNA SEQ After Oral Vaccine Against V. anguillarum}, author = {E Sarropoulou and J Galindo-Villegas and A García-Alcázar and P Kasapidis and V Mulero}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84865444000&doi=10.1007%2fs10126-012-9466-z&partnerID=40&md5=9c0f09c470e3b9a06d0ec9930b4c3a42}, doi = {10.1007/s10126-012-9466-z}, issn = {14362228}, year = {2012}, date = {2012-01-01}, journal = {Marine Biotechnology}, volume = {14}, number = {5}, pages = {634--642}, abstract = {The European sea bass (Dicentrarchus labrax) is, along with the gilthead sea bream (Sparus aurata), one of the most extensively cultured species in European aquaculture productions. Massive mortalities may be caused by bacterial or viral infections in intensive aquaculture production. Evaluation of the efficacy of an oral vaccine against Vibrio anguillarum (Aquavac Vibrio Oral) in sea bass revealed specific immune gene expression profiles in the gut as well as protection of fish. In the present study, we performed RNA SEQ in two different tissues: the hind gut and the head kidney. For each tissue, one control sample (where a sample presents a pool of four to five individuals) and one sample after oral vaccine against V. anguillarum were submitted to 454 next-generation sequencing. In total, 269,043 sequences were obtained, 143,007 for head kidney and 125,036 for gut. The read lengths ranged from 40 to 706 bp with an average length of 348 bp. The total number of clustered sequences for head kidney is accounting to 49,089 ( 34 %) and for gut to 71,676 ( 57 %). Differential expression was detected for 496 transcripts in head kidney and for 336 in gut. The results not only enrich the present collection of expressed sequence tag sequences including rare transcripts like leukocyte immune-type receptors, cullin, or supervillin but also show the efficacy of oral vaccination against V. anguillarum. © 2012 Springer Science+Business Media, LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The European sea bass (Dicentrarchus labrax) is, along with the gilthead sea bream (Sparus aurata), one of the most extensively cultured species in European aquaculture productions. Massive mortalities may be caused by bacterial or viral infections in intensive aquaculture production. Evaluation of the efficacy of an oral vaccine against Vibrio anguillarum (Aquavac Vibrio Oral) in sea bass revealed specific immune gene expression profiles in the gut as well as protection of fish. In the present study, we performed RNA SEQ in two different tissues: the hind gut and the head kidney. For each tissue, one control sample (where a sample presents a pool of four to five individuals) and one sample after oral vaccine against V. anguillarum were submitted to 454 next-generation sequencing. In total, 269,043 sequences were obtained, 143,007 for head kidney and 125,036 for gut. The read lengths ranged from 40 to 706 bp with an average length of 348 bp. The total number of clustered sequences for head kidney is accounting to 49,089 ( 34 %) and for gut to 71,676 ( 57 %). Differential expression was detected for 496 transcripts in head kidney and for 336 in gut. The results not only enrich the present collection of expressed sequence tag sequences including rare transcripts like leukocyte immune-type receptors, cullin, or supervillin but also show the efficacy of oral vaccination against V. anguillarum. © 2012 Springer Science+Business Media, LLC. |
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. |
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 |
Sarropoulou, Elena; Fernandes, Jorge M O Comparative genomics in teleost species: Knowledge transfer by linking the genomes of model and non-model fish species Journal Article Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 6 (1), pp. 92–102, 2011, ISSN: 1744117X. @article{sarropoulou_comparative_2011, title = {Comparative genomics in teleost species: Knowledge transfer by linking the genomes of model and non-model fish species}, author = {Elena Sarropoulou and Jorge M O Fernandes}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1744117X10000808}, doi = {10.1016/j.cbd.2010.09.003}, issn = {1744117X}, year = {2011}, date = {2011-03-01}, urldate = {2020-08-17}, journal = {Comparative Biochemistry and Physiology Part D: Genomics and Proteomics}, volume = {6}, number = {1}, pages = {92--102}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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. |
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. |
Bazakos, C; Manioudaki, M; Therios, I; Voyiatzis, D; Kafetzopoulos, D; Sarropoulou, E; Awada, T; Kalaitzis, P Gene expression analysis of olive tree (Olea europaea L.) in response to salt stress Journal Article Acta Horticulturae, 924 , pp. 47 – 54, 2011. @article{bazakos_gene_2011, title = {Gene expression analysis of olive tree (Olea europaea L.) in response to salt stress}, author = {C Bazakos and M Manioudaki and I Therios and D Voyiatzis and D Kafetzopoulos and E Sarropoulou and T Awada and P Kalaitzis}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84863628601&partnerID=40&md5=6239b9328cfd9d75254d0b952742ca31}, year = {2011}, date = {2011-01-01}, journal = {Acta Horticulturae}, volume = {924}, pages = {47 -- 54}, abstract = {Olive (Olea europaea L.) is one of the most significant crops in the Mediterranean region. The expansion in cultivation of olive to areas irrigated with low quality water, mostly saline, limits growth and productivity. Although a number of studies have been conducted on the effects of salinity on olive growth, the molecular basis of salt tolerance has not been investigated. A five-month salt stress experiment was set up with one-year-old plants of the cultivar ’Kalamon’, which exhibits tolerance to salinity. A custom olive cDNA microarray, composed of 1,121 cDNAs, was constructed and used for comparative transcriptome analysis of salt-treated and untreated roots. In addition, the expression profiles of selected cDNAs were further analyzed. Salt stress-related cDNA homologues through nucleotide bioinformatic analyses have been found.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Olive (Olea europaea L.) is one of the most significant crops in the Mediterranean region. The expansion in cultivation of olive to areas irrigated with low quality water, mostly saline, limits growth and productivity. Although a number of studies have been conducted on the effects of salinity on olive growth, the molecular basis of salt tolerance has not been investigated. A five-month salt stress experiment was set up with one-year-old plants of the cultivar ’Kalamon’, which exhibits tolerance to salinity. A custom olive cDNA microarray, composed of 1,121 cDNAs, was constructed and used for comparative transcriptome analysis of salt-treated and untreated roots. In addition, the expression profiles of selected cDNAs were further analyzed. Salt stress-related cDNA homologues through nucleotide bioinformatic analyses have been found. |
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 |
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 |
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 |
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. |
2007 |
Psochiou, Eleni; Sarropoulou, Elena; Mamuris, Zissis; Moutou, Katerina A Sequence analysis and tissue expression pattern of Sparus aurata chymotrypsinogens and trypsinogen Journal Article Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 147 (3), pp. 367–377, 2007, ISSN: 10964959. @article{psochiou_sequence_2007, title = {Sequence analysis and tissue expression pattern of Sparus aurata chymotrypsinogens and trypsinogen}, author = {Eleni Psochiou and Elena Sarropoulou and Zissis Mamuris and Katerina A Moutou}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1096495907000772}, doi = {10.1016/j.cbpb.2007.01.020}, issn = {10964959}, year = {2007}, date = {2007-07-01}, urldate = {2020-08-18}, journal = {Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology}, volume = {147}, number = {3}, pages = {367--377}, abstract = {Two apparently full-length cDNA clones encoding chymotrypsinogens I and II (CHTRI, 1022 bp; CHTRII, 909 bp) and one cDNA clone encoding trypsinogen II (TRPII, 848 bp) were isolated from a cDNA library prepared from gilthead sea bream (Sparus aurata) liver. The deduced amino acid sequences of the isolated cDNAs contain highly conserved residues essential for serine protease catalytic activity and conformational maintenance. The deduced amino acid sequences of CHTRI and CHTRII are 261 aa and 277 aa long, respectively, and share only 61% identity. Sea bream CHTRII appears to be the longest of all known teleostean chymotrypsinogen forms and contains a high number of methionine residues. Compared with CHTRI, CHTRII is more hydrophobic and has a lower isoelectric point. On the other hand, deduced amino acid sequence of TRPII is 241 aa long and has a signal peptide of thirteen amino acid residues and an activation peptide of seven amino acids long. In contrast to CHTRI and CHTRII, TRPII has a low isoelectric point (4.95), which makes it anionic at neutral pH. Northern blot analysis revealed that liver is the major transcription site for all zymogens. As expected, all zymogen transcripts were detected in parts of the digestive tract (stomach, pyloric caeca, anterior and posterior intestine) and pyloric caeca presented the most intense expression. In all tissues and amongst all zymogens, TRPII constitutive expression was the highest. © 2007 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Two apparently full-length cDNA clones encoding chymotrypsinogens I and II (CHTRI, 1022 bp; CHTRII, 909 bp) and one cDNA clone encoding trypsinogen II (TRPII, 848 bp) were isolated from a cDNA library prepared from gilthead sea bream (Sparus aurata) liver. The deduced amino acid sequences of the isolated cDNAs contain highly conserved residues essential for serine protease catalytic activity and conformational maintenance. The deduced amino acid sequences of CHTRI and CHTRII are 261 aa and 277 aa long, respectively, and share only 61% identity. Sea bream CHTRII appears to be the longest of all known teleostean chymotrypsinogen forms and contains a high number of methionine residues. Compared with CHTRI, CHTRII is more hydrophobic and has a lower isoelectric point. On the other hand, deduced amino acid sequence of TRPII is 241 aa long and has a signal peptide of thirteen amino acid residues and an activation peptide of seven amino acids long. In contrast to CHTRI and CHTRII, TRPII has a low isoelectric point (4.95), which makes it anionic at neutral pH. Northern blot analysis revealed that liver is the major transcription site for all zymogens. As expected, all zymogen transcripts were detected in parts of the digestive tract (stomach, pyloric caeca, anterior and posterior intestine) and pyloric caeca presented the most intense expression. In all tissues and amongst all zymogens, TRPII constitutive expression was the highest. © 2007 Elsevier Inc. All rights reserved. |
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. |
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. |
2006 |
Senger, Fabrice; Priat, Catherine; Hitte, Christophe; Sarropoulou, Elena; Franch, Rafaella; Geisler, Robert; Bargelloni, Luca; Power, Deborah; Galibert, Francis The first radiation hybrid map of a perch-like fish: The gilthead seabream (Sparus aurata L) Journal Article Genomics, 87 (6), pp. 793–800, 2006, ISSN: 08887543. @article{senger_first_2006, title = {The first radiation hybrid map of a perch-like fish: The gilthead seabream (Sparus aurata L)}, author = {Fabrice Senger and Catherine Priat and Christophe Hitte and Elena Sarropoulou and Rafaella Franch and Robert Geisler and Luca Bargelloni and Deborah Power and Francis Galibert}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0888754305003411}, doi = {10.1016/j.ygeno.2005.11.019}, issn = {08887543}, year = {2006}, date = {2006-06-01}, urldate = {2020-08-18}, journal = {Genomics}, volume = {87}, number = {6}, pages = {793--800}, abstract = {Among Teleosts, Perciformes are the largest order of fishes and include numerous species of commercial importance. Perciformes also comprise species of primary interest for evolutionary studies and analysis of the sex determination systems and sex chromosome plasticity. Unfortunately, genomics tools and resources for Perciformes remain to be developed. Here, we report the production of a seabream whole-genome radiation hybrid (RH) panel in which quality was ascertained by the construction of a 2-Mb-resolution RH map. The map encompasses 440 markers (288 microsatellites, 82 gene-based markers, and 70 STS) suitable for linkage analysis and comparative mapping studies. Achievement of a RH panel and a whole-genome RH map should contribute to establishing seabream as a fish model among the Perciformes and should be of importance in aquaculture for marker-assisted selection, improvement of growth performance, and disease management. Development of RH maps in a cost-effective manner for other fishes with the described methodology will offer a powerful approach in aquaculture and will provide extended capabilities for comparing vertebrate genome evolution. © 2005 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Among Teleosts, Perciformes are the largest order of fishes and include numerous species of commercial importance. Perciformes also comprise species of primary interest for evolutionary studies and analysis of the sex determination systems and sex chromosome plasticity. Unfortunately, genomics tools and resources for Perciformes remain to be developed. Here, we report the production of a seabream whole-genome radiation hybrid (RH) panel in which quality was ascertained by the construction of a 2-Mb-resolution RH map. The map encompasses 440 markers (288 microsatellites, 82 gene-based markers, and 70 STS) suitable for linkage analysis and comparative mapping studies. Achievement of a RH panel and a whole-genome RH map should contribute to establishing seabream as a fish model among the Perciformes and should be of importance in aquaculture for marker-assisted selection, improvement of growth performance, and disease management. Development of RH maps in a cost-effective manner for other fishes with the described methodology will offer a powerful approach in aquaculture and will provide extended capabilities for comparing vertebrate genome evolution. © 2005 Elsevier Inc. All rights reserved. |
Sarropoulou, E; Power, D M; Mamuris, Z; Moutou, K A The two isoforms of myosin light chain 2 in gilthead sea bream (Sparus aurata); alternative polyadenylation site selection and tissue expression Journal Article Archiv fur Tierzucht, 49 , pp. 92 – 96, 2006. @article{sarropoulou_two_2006, title = {The two isoforms of myosin light chain 2 in gilthead sea bream (Sparus aurata); alternative polyadenylation site selection and tissue expression}, author = {E Sarropoulou and D M Power and Z Mamuris and K A Moutou}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-33646234711&partnerID=40&md5=23611f5ac723b7135b9293effa3d7b06}, year = {2006}, date = {2006-01-01}, journal = {Archiv fur Tierzucht}, volume = {49}, pages = {92 -- 96}, abstract = {Myosin light chain 2 (MLC2) is an essential component of the myosin molecule, with a regulatory role in binding Ca2+. In gilthead sea bream, a MLC2 clone has been isolated and characterized, that encodes for a 170 aa peptide and contains three potential polyadenylation signals in the 3' UTR. In this study, the isolation of three alternative transcripts of the already known MLC2 (isoform A) is reported, along with the isolation and characterization of a second MLC2 isoform (B). All three isoform A transcripts encode the same peptide but differ in the length of their 3' UTRs (284bp, 788bp and 876bp respectively) and are generated by alternative polyadenylation site selection. Transcripts of isoform A were detected both in white and red muscle. MLC2 isoform B encodes also for a 170 aa protein. Isoform B was detected in all tissues examined (red, white, smooth and cardiac muscle, kidney, liver, spleen, brain, gills, epidermis). The differential expression of the two isoforms and of the alternative transcripts of isoform A during development is currently under study, in order to investigate the functional significance and regulation of 3' UTR length in transcription and mRNA turnover rate.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Myosin light chain 2 (MLC2) is an essential component of the myosin molecule, with a regulatory role in binding Ca2+. In gilthead sea bream, a MLC2 clone has been isolated and characterized, that encodes for a 170 aa peptide and contains three potential polyadenylation signals in the 3' UTR. In this study, the isolation of three alternative transcripts of the already known MLC2 (isoform A) is reported, along with the isolation and characterization of a second MLC2 isoform (B). All three isoform A transcripts encode the same peptide but differ in the length of their 3' UTRs (284bp, 788bp and 876bp respectively) and are generated by alternative polyadenylation site selection. Transcripts of isoform A were detected both in white and red muscle. MLC2 isoform B encodes also for a 170 aa protein. Isoform B was detected in all tissues examined (red, white, smooth and cardiac muscle, kidney, liver, spleen, brain, gills, epidermis). The differential expression of the two isoforms and of the alternative transcripts of isoform A during development is currently under study, in order to investigate the functional significance and regulation of 3' UTR length in transcription and mRNA turnover rate. |
Franch, R; Louro, B; Tsalavouta, M; Chatziplis, D; Tsigenopoulos, C S; Sarropoulou, E; Antonello, J; Magoulas, A; Mylonas, C C; Babbucci, M; Patarnello, T; Power, D M; Kotoulas, G; Bargelloni, L A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L. Journal Article Genetics, 174 (2), pp. 851–861, 2006, ISSN: 00166731. @article{franch_genetic_2006, title = {A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L.}, author = {R Franch and B Louro and M Tsalavouta and D Chatziplis and C S Tsigenopoulos and E Sarropoulou and J Antonello and A Magoulas and C C Mylonas and M Babbucci and T Patarnello and D M Power and G Kotoulas and L Bargelloni}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33750471928&doi=10.1534%2fgenetics.106.059014&partnerID=40&md5=5223c21cec86860a04d8be5eff57e24c}, doi = {10.1534/genetics.106.059014}, issn = {00166731}, year = {2006}, date = {2006-01-01}, journal = {Genetics}, volume = {174}, number = {2}, pages = {851--861}, abstract = {The gilthead sea bream (Sparus aurata L.) is a marine fish of great importance for fisheries and aquaculture. It has also a peculiar sex-determination system, being a protandrous hermaphrodite. Here we report the construction of a first-generation genetic linkage map for S. aurata, based on 204 microsatellite markers. Twenty-six linkage groups (LG) were found. The total map length was 1241.9 cM. The ratio between sex-specific map lengths was 1:1.2 (male:female). Comparison with a preliminary radiation hybrid (RH) map reveals a good concordance, as all markers located in a single LG are located in a single RH group, except for Ad-25 and CId-31. Comparison with the Tetraodon nigroviridis genome revealed a considerable number of evolutionary conserved regions (ECRs) between the two species. The mean size of ECRs was 182 bp (sequence identity 60-90%). Forty-one ECRs have a known chromosomal location in the pufferfish genome. Despite the limited number of anchoring points, significant syntenic relationships were found. The linkage map presented here provides a robust comparative framework for QTL analysis in S. aurata and is a step toward the identification of genetic loci involved both in the determination of economically important traits and in the individual timing of sex reversal. Copyright © 2006 by the Genetics Society of America.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The gilthead sea bream (Sparus aurata L.) is a marine fish of great importance for fisheries and aquaculture. It has also a peculiar sex-determination system, being a protandrous hermaphrodite. Here we report the construction of a first-generation genetic linkage map for S. aurata, based on 204 microsatellite markers. Twenty-six linkage groups (LG) were found. The total map length was 1241.9 cM. The ratio between sex-specific map lengths was 1:1.2 (male:female). Comparison with a preliminary radiation hybrid (RH) map reveals a good concordance, as all markers located in a single LG are located in a single RH group, except for Ad-25 and CId-31. Comparison with the Tetraodon nigroviridis genome revealed a considerable number of evolutionary conserved regions (ECRs) between the two species. The mean size of ECRs was 182 bp (sequence identity 60-90%). Forty-one ECRs have a known chromosomal location in the pufferfish genome. Despite the limited number of anchoring points, significant syntenic relationships were found. The linkage map presented here provides a robust comparative framework for QTL analysis in S. aurata and is a step toward the identification of genetic loci involved both in the determination of economically important traits and in the individual timing of sex reversal. Copyright © 2006 by the Genetics Society of America. |
2005 |
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} } |