2025
Holm, Johanna B; Paragkamian, Savvas; Humphreys, Mike; Chatterjee, Apaala; Yarwood, Stephanie; Gaimaro, Josh; Stavroulaki, Melanthia; Tsaparis, Dimitris; Plaitis, Manolis; Kasapidis, Panagiotis; Darivianakis, Stelios; Kotoulas, Georgios; Magoulas, Antonios; Oulas, Anastasis; Kyrpiotakis, Zacharias; Pavlidis, Pavlos; Hoopen, Petra Ten; Cochrane, Guy; Kooistra, Wiebe H C F; Schriml, Jason R; Schriml, Bronwen E; Lagkouvardos, Ilias; Gkorezis, Panos; Davies, Neil; Laney, Christine; Stanish, Lee; Sutton, Granger; Tighe, Scott; Mizrachi, Ilene Karsch; Parks, Donovan; Yilmaz, Pelin; Carey, Chelsea; Buttigieg, Pier; Goldstein, Philip; Pafilis, Evangelos; Schriml, Lynn M
First island-wide, single-day soil collection study on Crete reveals environmental drivers of microbial diversity Journal Article
In: Environmental Microbiome, vol. 20, no. 1, pp. 94, 2025, ISSN: 2524-6372.
@article{holm_first_2025,
title = {First island-wide, single-day soil collection study on Crete reveals environmental drivers of microbial diversity},
author = {Johanna B Holm and Savvas Paragkamian and Mike Humphreys and Apaala Chatterjee and Stephanie Yarwood and Josh Gaimaro and Melanthia Stavroulaki and Dimitris Tsaparis and Manolis Plaitis and Panagiotis Kasapidis and Stelios Darivianakis and Georgios Kotoulas and Antonios Magoulas and Anastasis Oulas and Zacharias Kyrpiotakis and Pavlos Pavlidis and Petra Ten Hoopen and Guy Cochrane and Wiebe H C F Kooistra and Jason R Schriml and Bronwen E Schriml and Ilias Lagkouvardos and Panos Gkorezis and Neil Davies and Christine Laney and Lee Stanish and Granger Sutton and Scott Tighe and Ilene Karsch Mizrachi and Donovan Parks and Pelin Yilmaz and Chelsea Carey and Pier Buttigieg and Philip Goldstein and Evangelos Pafilis and Lynn M Schriml},
url = {https://environmentalmicrobiome.biomedcentral.com/articles/10.1186/s40793-025-00752-z
/wp-content/uploads/2025/09/2025-Holm-Paragkamian-EnvMicro-46.pdf},
doi = {10.1186/s40793-025-00752-z},
issn = {2524-6372},
year = {2025},
date = {2025-09-04},
urldate = {2025-09-08},
journal = {Environmental Microbiome},
volume = {20},
number = {1},
pages = {94},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2024
Gioti, Anastasia; Theodosopoulou, Danai; Bravakos, Panos; Magoulas, Antonios; Kotoulas, Georgios
The bioinformatics landscape in environmental omics: Lessons from a national ELIXIR survey Journal Article
In: iScience, vol. 27, no. 6, pp. 110062, 2024, ISSN: 25890042.
@article{gioti_bioinformatics_2024,
title = {The bioinformatics landscape in environmental omics: Lessons from a national ELIXIR survey},
author = {Anastasia Gioti and Danai Theodosopoulou and Panos Bravakos and Antonios Magoulas and Georgios Kotoulas},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/06/2024-Gioti-iScience-26.pdf
https://linkinghub.elsevier.com/retrieve/pii/S2589004224012872},
doi = {10.1016/j.isci.2024.110062},
issn = {25890042},
year = {2024},
date = {2024-06-08},
urldate = {2024-06-10},
journal = {iScience},
volume = {27},
number = {6},
pages = {110062},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Katirtzoglou, Aikaterini; Tsaparis, Dimitris; Kolios, Evangelos; Magoulas, Antonios; Mylonas, Constantinos C; Fakriadis, Ioannis; Manousaki, Tereza; Tsigenopoulos, Costas S
In: Frontiers in Fish Science, vol. 2, pp. 1356313, 2024, ISSN: 2813-9097.
@article{katirtzoglou_population_2024,
title = {Population genomic analysis of the greater amberjack (\textit{Seriola dumerili}) in the Mediterranean and the Northeast Atlantic, based on SNPs, microsatellites, and mitochondrial DNA sequences},
author = {Aikaterini Katirtzoglou and Dimitris Tsaparis and Evangelos Kolios and Antonios Magoulas and Constantinos C Mylonas and Ioannis Fakriadis and Tereza Manousaki and Costas S Tsigenopoulos},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/03/2024-Kaitirtzoglou-frish-14.pdf
https://www.frontiersin.org/articles/10.3389/frish.2024.1356313/full},
doi = {10.3389/frish.2024.1356313},
issn = {2813-9097},
year = {2024},
date = {2024-03-14},
urldate = {2024-03-14},
journal = {Frontiers in Fish Science},
volume = {2},
pages = {1356313},
abstract = {The greater amberjack (
Seriola dumerili
) has attracted considerable economic interest since the 1990s because it possesses traits that distinguish it as a promising candidate in aquaculture. However, the challenges of its successful rearing, combined with the need to develop proper management practices, underline the importance of research into the genetic diversity of both wild and farmed stocks. We aimed to decipher the genetic structure of
S. dumerili
in the Eastern Mediterranean and the Northeast Atlantic using three types of genetic markers (mitochondrial control region sequences, microsatellites, and single nucleotide polymorphisms, or SNPs) to evaluate the population genetic structure of the species. The results were compared to those of previous studies of the species focusing on the Central Mediterranean and confirmed the presence of two divergent mtDNA haplogroups distributed without any detectable geographical structuring within the Mediterranean and the Atlantic. However, population analyses of the genetic structure of the species using either 10 microsatellites or a set of 1,051 SNP markers suggest that the species forms three genetically distinct groups, one in the Mediterranean and two in the Atlantic. The latter has so far not been reported in the Northeast Atlantic, and that this differentiation refers to samples from the Canary Islands is surprising. Fifteen candidate outlier SNP loci were identified in the data set, one located within the
tead1a
/TEF-1A gene, which has been associated with temperature acclimation of the medaka. This work enriches our knowledge of the genetic diversity of wild populations of the greater amberjack in the Mediterranean and the Northeast Atlantic and attempts to investigate signs of local adaptation toward a better understanding of the species distribution patterns. Future studies should be conducted to investigate the genomic regions associated with temperature acclimation in marine organisms that have to adapt to the ongoing climate change pressures, such as sea temperature rise, in order to survive.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The greater amberjack (
Seriola dumerili
) has attracted considerable economic interest since the 1990s because it possesses traits that distinguish it as a promising candidate in aquaculture. However, the challenges of its successful rearing, combined with the need to develop proper management practices, underline the importance of research into the genetic diversity of both wild and farmed stocks. We aimed to decipher the genetic structure of
S. dumerili
in the Eastern Mediterranean and the Northeast Atlantic using three types of genetic markers (mitochondrial control region sequences, microsatellites, and single nucleotide polymorphisms, or SNPs) to evaluate the population genetic structure of the species. The results were compared to those of previous studies of the species focusing on the Central Mediterranean and confirmed the presence of two divergent mtDNA haplogroups distributed without any detectable geographical structuring within the Mediterranean and the Atlantic. However, population analyses of the genetic structure of the species using either 10 microsatellites or a set of 1,051 SNP markers suggest that the species forms three genetically distinct groups, one in the Mediterranean and two in the Atlantic. The latter has so far not been reported in the Northeast Atlantic, and that this differentiation refers to samples from the Canary Islands is surprising. Fifteen candidate outlier SNP loci were identified in the data set, one located within the
tead1a
/TEF-1A gene, which has been associated with temperature acclimation of the medaka. This work enriches our knowledge of the genetic diversity of wild populations of the greater amberjack in the Mediterranean and the Northeast Atlantic and attempts to investigate signs of local adaptation toward a better understanding of the species distribution patterns. Future studies should be conducted to investigate the genomic regions associated with temperature acclimation in marine organisms that have to adapt to the ongoing climate change pressures, such as sea temperature rise, in order to survive.
Seriola dumerili
) has attracted considerable economic interest since the 1990s because it possesses traits that distinguish it as a promising candidate in aquaculture. However, the challenges of its successful rearing, combined with the need to develop proper management practices, underline the importance of research into the genetic diversity of both wild and farmed stocks. We aimed to decipher the genetic structure of
S. dumerili
in the Eastern Mediterranean and the Northeast Atlantic using three types of genetic markers (mitochondrial control region sequences, microsatellites, and single nucleotide polymorphisms, or SNPs) to evaluate the population genetic structure of the species. The results were compared to those of previous studies of the species focusing on the Central Mediterranean and confirmed the presence of two divergent mtDNA haplogroups distributed without any detectable geographical structuring within the Mediterranean and the Atlantic. However, population analyses of the genetic structure of the species using either 10 microsatellites or a set of 1,051 SNP markers suggest that the species forms three genetically distinct groups, one in the Mediterranean and two in the Atlantic. The latter has so far not been reported in the Northeast Atlantic, and that this differentiation refers to samples from the Canary Islands is surprising. Fifteen candidate outlier SNP loci were identified in the data set, one located within the
tead1a
/TEF-1A gene, which has been associated with temperature acclimation of the medaka. This work enriches our knowledge of the genetic diversity of wild populations of the greater amberjack in the Mediterranean and the Northeast Atlantic and attempts to investigate signs of local adaptation toward a better understanding of the species distribution patterns. Future studies should be conducted to investigate the genomic regions associated with temperature acclimation in marine organisms that have to adapt to the ongoing climate change pressures, such as sea temperature rise, in order to survive.
Skaraki, Katerina; Pavloudi, Christina; Dailianis, Thanos; Lagnel, Jacques; Pantazidou, Adriani; Magoulas, Antonios; Kotoulas, Georgios
Microbial diversity in four Mediterranean irciniid sponges Journal Article
In: Biodiversity Data Journal, vol. 12, pp. e114809, 2024, ISSN: 1314-2828, 1314-2836.
@article{skaraki_microbial_2024,
title = {Microbial diversity in four Mediterranean irciniid sponges},
author = {Katerina Skaraki and Christina Pavloudi and Thanos Dailianis and Jacques Lagnel and Adriani Pantazidou and Antonios Magoulas and Georgios Kotoulas},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/02/2024-Skaraki-BioDDJ-6.pdf
https://bdj.pensoft.net/article/114809/},
doi = {10.3897/BDJ.12.e114809},
issn = {1314-2828, 1314-2836},
year = {2024},
date = {2024-02-01},
urldate = {2024-02-05},
journal = {Biodiversity Data Journal},
volume = {12},
pages = {e114809},
abstract = {This paper describes a dataset of microbial communities from four different sponge species:
Ircinia oros
(Schmidt, 1864),
Ircinia variabilis
(Schmidt, 1862),
Sarcotragus spinosulus
Schmidt, 1862 and
Sarcotragus fasciculatus
(Pallas, 1766). The examined sponges all belong to Demospongiae (Class); Keratosa (Subclass); Dictyoceratida (Order); Irciniidae (Family). Samples were collected by scuba diving at depths between 6-14 m from two sampling sites of rocky formations at the northern coast of Crete (Cretan Sea, eastern Mediterranean) and were subjected to metabarcoding for the V5-V6 region of the 16S rRNA gene.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
This paper describes a dataset of microbial communities from four different sponge species:
Ircinia oros
(Schmidt, 1864),
Ircinia variabilis
(Schmidt, 1862),
Sarcotragus spinosulus
Schmidt, 1862 and
Sarcotragus fasciculatus
(Pallas, 1766). The examined sponges all belong to Demospongiae (Class); Keratosa (Subclass); Dictyoceratida (Order); Irciniidae (Family). Samples were collected by scuba diving at depths between 6-14 m from two sampling sites of rocky formations at the northern coast of Crete (Cretan Sea, eastern Mediterranean) and were subjected to metabarcoding for the V5-V6 region of the 16S rRNA gene.
Ircinia oros
(Schmidt, 1864),
Ircinia variabilis
(Schmidt, 1862),
Sarcotragus spinosulus
Schmidt, 1862 and
Sarcotragus fasciculatus
(Pallas, 1766). The examined sponges all belong to Demospongiae (Class); Keratosa (Subclass); Dictyoceratida (Order); Irciniidae (Family). Samples were collected by scuba diving at depths between 6-14 m from two sampling sites of rocky formations at the northern coast of Crete (Cretan Sea, eastern Mediterranean) and were subjected to metabarcoding for the V5-V6 region of the 16S rRNA gene.
2023
Polymenakou, Paraskevi N; Nomikou, Paraskevi; Hannington, Mark; Petersen, Sven; Kilias, Stephanos P; Anastasiou, Thekla I; Papadimitriou, Vasiliki; Zaka, Eleutheria; Kristoffersen, Jon Bent; Lampridou, Danai; Wind, Sandra; Heinath, Verena; Lange, Sabine; Magoulas, Antonios
Taxonomic diversity of microbial communities in sub-seafloor hydrothermal sediments of the active Santorini-Kolumbo volcanic field Journal Article
In: Frontiers in Microbiology, vol. 14, pp. 1188544, 2023, ISSN: 1664-302X.
@article{polymenakou_taxonomic_2023,
title = {Taxonomic diversity of microbial communities in sub-seafloor hydrothermal sediments of the active Santorini-Kolumbo volcanic field},
author = {Paraskevi N Polymenakou and Paraskevi Nomikou and Mark Hannington and Sven Petersen and Stephanos P Kilias and Thekla I Anastasiou and Vasiliki Papadimitriou and Eleutheria Zaka and Jon Bent Kristoffersen and Danai Lampridou and Sandra Wind and Verena Heinath and Sabine Lange and Antonios Magoulas},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/07/2023-Polymenakou-FrontMicro-35.pdf
https://www.frontiersin.org/articles/10.3389/fmicb.2023.1188544/full},
doi = {10.3389/fmicb.2023.1188544},
issn = {1664-302X},
year = {2023},
date = {2023-07-06},
urldate = {2023-07-06},
journal = {Frontiers in Microbiology},
volume = {14},
pages = {1188544},
abstract = {Introduction
Active hydrothermal vents of volcanic origin provide a remarkable manifestation of life on Earth under extreme conditions, which may have consequences for our understanding of habitability on other terrestrial bodies as well.
Methods
Here, we performed for the first time Illumina sequencing of bacterial and archaeal communities on sub-seafloor samples collected from the Santorini-Kolumbo volcanic field. A total of 19 (3-m long) gravity corers were collected and processed for microbial community analysis.
Results
From a total of 6,46,671 produced V4 sequences for all samples, a total of 10,496 different Operational Taxonomic Units (OTUs) were identified that were assigned to 40 bacterial and 9 archaeal phyla and 14 candidate divisions. On average, the most abundant phyla in all samples were Chloroflexi (Chloroflexota) (24.62%), followed by Proteobacteria (Pseudomonadota) (11.29%), Firmicutes (Bacillota) (10.73%), Crenarchaeota (Thermoproteota) (8.55%), and Acidobacteria (Acidobacteriota) (8.07%). At the genus level, a total of 286 known genera and candidate genera were mostly dominated by members of
Bacillus, Thermoflexus, Desulfatiglans, Pseudoalteromonas
, and
Pseudomonas
.
Discussion
In most of the stations, the Chao1 values at the deeper layers were comparable to the surface sediment samples denoting the high diversity in the subsurface of these ecosystems. Heatmap analysis based on the 100 most abundant OTUs, grouped the sampling stations according to their geographical location, placing together the two hottest stations (up to 99°C). This result indicates that this specific area within the active Kolumbo crater create a distinct niche, where microorganisms with adaptation strategies to withstand heat stresses can thrive, such as the endospore-forming Firmicutes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Introduction
Active hydrothermal vents of volcanic origin provide a remarkable manifestation of life on Earth under extreme conditions, which may have consequences for our understanding of habitability on other terrestrial bodies as well.
Methods
Here, we performed for the first time Illumina sequencing of bacterial and archaeal communities on sub-seafloor samples collected from the Santorini-Kolumbo volcanic field. A total of 19 (3-m long) gravity corers were collected and processed for microbial community analysis.
Results
From a total of 6,46,671 produced V4 sequences for all samples, a total of 10,496 different Operational Taxonomic Units (OTUs) were identified that were assigned to 40 bacterial and 9 archaeal phyla and 14 candidate divisions. On average, the most abundant phyla in all samples were Chloroflexi (Chloroflexota) (24.62%), followed by Proteobacteria (Pseudomonadota) (11.29%), Firmicutes (Bacillota) (10.73%), Crenarchaeota (Thermoproteota) (8.55%), and Acidobacteria (Acidobacteriota) (8.07%). At the genus level, a total of 286 known genera and candidate genera were mostly dominated by members of
Bacillus, Thermoflexus, Desulfatiglans, Pseudoalteromonas
, and
Pseudomonas
.
Discussion
In most of the stations, the Chao1 values at the deeper layers were comparable to the surface sediment samples denoting the high diversity in the subsurface of these ecosystems. Heatmap analysis based on the 100 most abundant OTUs, grouped the sampling stations according to their geographical location, placing together the two hottest stations (up to 99°C). This result indicates that this specific area within the active Kolumbo crater create a distinct niche, where microorganisms with adaptation strategies to withstand heat stresses can thrive, such as the endospore-forming Firmicutes.
Active hydrothermal vents of volcanic origin provide a remarkable manifestation of life on Earth under extreme conditions, which may have consequences for our understanding of habitability on other terrestrial bodies as well.
Methods
Here, we performed for the first time Illumina sequencing of bacterial and archaeal communities on sub-seafloor samples collected from the Santorini-Kolumbo volcanic field. A total of 19 (3-m long) gravity corers were collected and processed for microbial community analysis.
Results
From a total of 6,46,671 produced V4 sequences for all samples, a total of 10,496 different Operational Taxonomic Units (OTUs) were identified that were assigned to 40 bacterial and 9 archaeal phyla and 14 candidate divisions. On average, the most abundant phyla in all samples were Chloroflexi (Chloroflexota) (24.62%), followed by Proteobacteria (Pseudomonadota) (11.29%), Firmicutes (Bacillota) (10.73%), Crenarchaeota (Thermoproteota) (8.55%), and Acidobacteria (Acidobacteriota) (8.07%). At the genus level, a total of 286 known genera and candidate genera were mostly dominated by members of
Bacillus, Thermoflexus, Desulfatiglans, Pseudoalteromonas
, and
Pseudomonas
.
Discussion
In most of the stations, the Chao1 values at the deeper layers were comparable to the surface sediment samples denoting the high diversity in the subsurface of these ecosystems. Heatmap analysis based on the 100 most abundant OTUs, grouped the sampling stations according to their geographical location, placing together the two hottest stations (up to 99°C). This result indicates that this specific area within the active Kolumbo crater create a distinct niche, where microorganisms with adaptation strategies to withstand heat stresses can thrive, such as the endospore-forming Firmicutes.
Antoniou, Aglaia; Manousaki, Tereza; Ramírez, Francisco; Cariani, Alessia; Cannas, Rita; Kasapidis, Panagiotis; Magoulas, Antonios; Albo‐Puigserver, Marta; Lloret‐Lloret, Elena; Bellido, Jose Maria; Pennino, Maria Grazia; Follesa, Maria Cristina; Esteban, Antonio; Saraux, Claire; Sbrana, Mario; Spedicato, Maria Teresa; Coll, Marta; Tsigenopoulos, Costas S
Sardines at a junction: Seascape genomics reveals ecological and oceanographic drivers of variation in the textlessspan style= Journal Article
In: Molecular Ecology, pp. mec.16840, 2023, ISSN: 0962-1083, 1365-294X.
@article{antoniou_sardines_2023,
title = {Sardines at a junction: Seascape genomics reveals ecological and oceanographic drivers of variation in the textlessspan style=},
author = {Aglaia Antoniou and Tereza Manousaki and Francisco Ramírez and Alessia Cariani and Rita Cannas and Panagiotis Kasapidis and Antonios Magoulas and Marta Albo‐Puigserver and Elena Lloret‐Lloret and Jose Maria Bellido and Maria Grazia Pennino and Maria Cristina Follesa and Antonio Esteban and Claire Saraux and Mario Sbrana and Maria Teresa Spedicato and Marta Coll and Costas S Tsigenopoulos},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/02/2023-Antoniou-Mol-Eco-9-1.pdf
https://onlinelibrary.wiley.com/doi/10.1111/mec.16840},
doi = {10.1111/mec.16840},
issn = {0962-1083, 1365-294X},
year = {2023},
date = {2023-02-06},
urldate = {2023-02-06},
journal = {Molecular Ecology},
pages = {mec.16840},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2021
Keklikoglou, Kleoniki; Arvanitidis, Christos; Chatzigeorgiou, Georgios; Chatzinikolaou, Eva; Karagiannidis, Efstratios; Koletsa, Triantafyllia; Magoulas, Antonios; Makris, Konstantinos; Mavrothalassitis, George; Papanagnou, Eleni-Dimitra; Papazoglou, Andreas S; Pavloudi, Christina; Trougakos, Ioannis P; Vasileiadou, Katerina; Vogiatzi, Angeliki
Micro-CT for Biological and Biomedical Studies: A Comparison of Imaging Techniques Journal Article
In: vol. 7, no. 9, pp. 172, 2021, ISSN: 2313-433X.
@article{keklikoglou_micro-ct_2021,
title = {Micro-CT for Biological and Biomedical Studies: A Comparison of Imaging Techniques},
author = {Kleoniki Keklikoglou and Christos Arvanitidis and Georgios Chatzigeorgiou and Eva Chatzinikolaou and Efstratios Karagiannidis and Triantafyllia Koletsa and Antonios Magoulas and Konstantinos Makris and George Mavrothalassitis and Eleni-Dimitra Papanagnou and Andreas S Papazoglou and Christina Pavloudi and Ioannis P Trougakos and Katerina Vasileiadou and Angeliki Vogiatzi},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Keklikoglou-jimaging-66-1.pdf
https://www.mdpi.com/2313-433X/7/9/172},
doi = {10.3390/jimaging7090172},
issn = {2313-433X},
year = {2021},
date = {2021-09-01},
urldate = {2021-09-22},
volume = {7},
number = {9},
pages = {172},
abstract = {Several imaging techniques are used in biological and biomedical studies. Micro-computed tomography (micro-CT) is a non-destructive imaging technique that allows the rapid digitisation of internal and external structures of a sample in three dimensions and with great resolution. In this review, the strengths and weaknesses of some common imaging techniques applied in biological and biomedical fields, such as optical microscopy, confocal laser scanning microscopy, and scanning electron microscopy, are presented and compared with the micro-CT technique through five use cases. Finally, the ability of micro-CT to create non-destructively 3D anatomical and morphological data in sub-micron resolution and the necessity to develop complementary methods with other imaging techniques, in order to overcome limitations caused by each technique, is emphasised.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Several imaging techniques are used in biological and biomedical studies. Micro-computed tomography (micro-CT) is a non-destructive imaging technique that allows the rapid digitisation of internal and external structures of a sample in three dimensions and with great resolution. In this review, the strengths and weaknesses of some common imaging techniques applied in biological and biomedical fields, such as optical microscopy, confocal laser scanning microscopy, and scanning electron microscopy, are presented and compared with the micro-CT technique through five use cases. Finally, the ability of micro-CT to create non-destructively 3D anatomical and morphological data in sub-micron resolution and the necessity to develop complementary methods with other imaging techniques, in order to overcome limitations caused by each technique, is emphasised.
Nikolaivits, Efstratios; Siaperas, Romanos; Agrafiotis, Andreas; Ouazzani, Jamal; Magoulas, Antonios; Gioti, Αnastasia; Topakas, Evangelos
In: Science of The Total Environment, vol. 775, pp. 145818, 2021, ISSN: 00489697.
@article{nikolaivits_functional_2021,
title = {Functional and transcriptomic investigation of laccase activity in the presence of PCB29 identifies two novel enzymes and the multicopper oxidase repertoire of a marine-derived fungus},
author = {Efstratios Nikolaivits and Romanos Siaperas and Andreas Agrafiotis and Jamal Ouazzani and Antonios Magoulas and Αnastasia Gioti and Evangelos Topakas},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969721008858},
doi = {10.1016/j.scitotenv.2021.145818},
issn = {00489697},
year = {2021},
date = {2021-06-01},
urldate = {2021-03-17},
journal = {Science of The Total Environment},
volume = {775},
pages = {145818},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bravakos, Panos; Mandalakis, Manolis; Nomikou, Paraskevi; Anastasiou, Thekla I; Kristoffersen, Jon Bent; Stavroulaki, Melanthia; Kilias, Stephanos; Kotoulas, Georgios; Magoulas, Antonios; Polymenakou, Paraskevi N
Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece Journal Article
In: Sci Rep, vol. 11, no. 1, pp. 1336, 2021, ISSN: 2045-2322.
@article{bravakos_genomic_2021,
title = {Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece},
author = {Panos Bravakos and Manolis Mandalakis and Paraskevi Nomikou and Thekla I Anastasiou and Jon Bent Kristoffersen and Melanthia Stavroulaki and Stephanos Kilias and Georgios Kotoulas and Antonios Magoulas and Paraskevi N Polymenakou},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021-Bravakos-SciReport-4.pdf
http://www.nature.com/articles/s41598-020-79359-y},
doi = {10.1038/s41598-020-79359-y},
issn = {2045-2322},
year = {2021},
date = {2021-01-01},
urldate = {2021-02-02},
journal = {Sci Rep},
volume = {11},
number = {1},
pages = {1336},
abstract = {Abstract
Although the rise of antibiotic and multidrug resistant bacteria is one of the biggest current threats to human health, our understanding of the mechanisms involved in antibiotic resistance selection remains scarce. We performed whole genome sequencing of 21
Pseudomonas
strains, previously isolated from an active submarine volcano of Greece, the Kolumbo volcano. Our goal was to identify the genetic basis of the enhanced co-tolerance to antibiotics and acidity of these
Pseudomonas
strains. Pangenome analysis identified 10,908 Gene Clusters (GCs). It revealed that the numbers of phage-related GCs and sigma factors, which both provide the mechanisms of adaptation to environmental stressors, were much higher in the high tolerant
Pseudomonas
strains compared to the rest ones. All identified GCs of these strains were associated with antimicrobial and multidrug resistance. The present study provides strong evidence that the CO
2
-rich seawater of the volcano associated with low pH might be a reservoir of microorganisms carrying multidrug efflux-mediated systems and pumps. We, therefore, suggest further studies of other extreme environments (or ecosystems) and their associated physicochemical parameters (or factors) in the rise of antibiotic resistance.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract
Although the rise of antibiotic and multidrug resistant bacteria is one of the biggest current threats to human health, our understanding of the mechanisms involved in antibiotic resistance selection remains scarce. We performed whole genome sequencing of 21
Pseudomonas
strains, previously isolated from an active submarine volcano of Greece, the Kolumbo volcano. Our goal was to identify the genetic basis of the enhanced co-tolerance to antibiotics and acidity of these
Pseudomonas
strains. Pangenome analysis identified 10,908 Gene Clusters (GCs). It revealed that the numbers of phage-related GCs and sigma factors, which both provide the mechanisms of adaptation to environmental stressors, were much higher in the high tolerant
Pseudomonas
strains compared to the rest ones. All identified GCs of these strains were associated with antimicrobial and multidrug resistance. The present study provides strong evidence that the CO
2
-rich seawater of the volcano associated with low pH might be a reservoir of microorganisms carrying multidrug efflux-mediated systems and pumps. We, therefore, suggest further studies of other extreme environments (or ecosystems) and their associated physicochemical parameters (or factors) in the rise of antibiotic resistance.
Although the rise of antibiotic and multidrug resistant bacteria is one of the biggest current threats to human health, our understanding of the mechanisms involved in antibiotic resistance selection remains scarce. We performed whole genome sequencing of 21
Pseudomonas
strains, previously isolated from an active submarine volcano of Greece, the Kolumbo volcano. Our goal was to identify the genetic basis of the enhanced co-tolerance to antibiotics and acidity of these
Pseudomonas
strains. Pangenome analysis identified 10,908 Gene Clusters (GCs). It revealed that the numbers of phage-related GCs and sigma factors, which both provide the mechanisms of adaptation to environmental stressors, were much higher in the high tolerant
Pseudomonas
strains compared to the rest ones. All identified GCs of these strains were associated with antimicrobial and multidrug resistance. The present study provides strong evidence that the CO
2
-rich seawater of the volcano associated with low pH might be a reservoir of microorganisms carrying multidrug efflux-mediated systems and pumps. We, therefore, suggest further studies of other extreme environments (or ecosystems) and their associated physicochemical parameters (or factors) in the rise of antibiotic resistance.
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
In: GigaScience, vol. 10, no. 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.
High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.
Danis, Theodoros; Papadogiannis, Vasileios; Tsakogiannis, Alexandros; Kristoffersen, Jon B; Golani, Daniel; Tsaparis, Dimitris; Sterioti, Aspasia; Kasapidis, Panagiotis; Kotoulas, Georgios; Magoulas, Antonios; Tsigenopoulos, Costas S; Manousaki, Tereza
Genome Analysis of Lagocephalus sceleratus: Unraveling the Genomic Landscape of a Successful Invader Journal Article
In: Frontiers in Genetics, vol. 12, pp. 2481, 2021, ISSN: 1664-8021.
@article{danis_genome_2021,
title = {Genome Analysis of Lagocephalus sceleratus: Unraveling the Genomic Landscape of a Successful Invader},
author = {Theodoros Danis and Vasileios Papadogiannis and Alexandros Tsakogiannis and Jon B Kristoffersen and Daniel Golani and Dimitris Tsaparis and Aspasia Sterioti and Panagiotis Kasapidis and Georgios Kotoulas and Antonios Magoulas and Costas S Tsigenopoulos and Tereza Manousaki},
url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/01/2021-Danis-FrontGen-84.pdf
https://www.frontiersin.org/article/10.3389/fgene.2021.790850},
doi = {10.3389/fgene.2021.790850},
issn = {1664-8021},
year = {2021},
date = {2021-01-01},
urldate = {2022-01-12},
journal = {Frontiers in Genetics},
volume = {12},
pages = {2481},
abstract = {The Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. The silver-cheeked toadfish (Lagocephalus sceleratus) is a well-known “invasive sprinter” that has invaded and spread, in less than a decade, throughout the Eastern and part of the Western Mediterranean Sea from the Red Sea through the Suez Canal. In this study, we built and analysed the first near-chromosome level genome assembly of L. sceleratus and explored its evolutionary landscape. Through a phylogenomic analysis, we positioned L. sceleratus closer to T. nigroviridis, compared to other members of the family, while gene family evolution analysis revealed that genes associated with the immune response have experienced rapid expansion, providing a genetic basis for studying how L. sceleratus is able to achieve highly successful colonisation. Moreover, we found that voltage-gated sodium channel (NaV 1.4) mutations previously connected to tetrodotoxin resistance in other pufferfishes are not found in L. sceleratus, highlighting the complex evolution of this trait. The high-quality genome assembly built here is expected to set the ground for future studies on the species biology.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. The silver-cheeked toadfish (Lagocephalus sceleratus) is a well-known “invasive sprinter” that has invaded and spread, in less than a decade, throughout the Eastern and part of the Western Mediterranean Sea from the Red Sea through the Suez Canal. In this study, we built and analysed the first near-chromosome level genome assembly of L. sceleratus and explored its evolutionary landscape. Through a phylogenomic analysis, we positioned L. sceleratus closer to T. nigroviridis, compared to other members of the family, while gene family evolution analysis revealed that genes associated with the immune response have experienced rapid expansion, providing a genetic basis for studying how L. sceleratus is able to achieve highly successful colonisation. Moreover, we found that voltage-gated sodium channel (NaV 1.4) mutations previously connected to tetrodotoxin resistance in other pufferfishes are not found in L. sceleratus, highlighting the complex evolution of this trait. The high-quality genome assembly built here is expected to set the ground for future studies on the species biology.
2020
Koutsouveli, Vasiliki; Manousaki, Tereza; Riesgo, Ana; Lagnel, Jacques; Kollias, Spyros; Tsigenopoulos, Costas S; Arvanitidis, Christos; Dounas, Costas; Magoulas, Antonios; Dailianis, Thanos
In: Frontiers in Marine Science, vol. 6, pp. 786, 2020, ISSN: 2296-7745.
@article{koutsouveli_gearing_2020,
title = {Gearing Up for Warmer Times: Transcriptomic Response of Spongia officinalis to Elevated Temperatures Reveals Recruited Mechanisms and Potential for Resilience},
author = {Vasiliki Koutsouveli and Tereza Manousaki and Ana Riesgo and Jacques Lagnel and Spyros Kollias and Costas S Tsigenopoulos and Christos Arvanitidis and Costas Dounas and Antonios Magoulas and Thanos Dailianis},
url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00786/full},
doi = {10.3389/fmars.2019.00786},
issn = {2296-7745},
year = {2020},
date = {2020-01-01},
urldate = {2020-08-06},
journal = {Frontiers in Marine Science},
volume = {6},
pages = {786},
abstract = {The emblematic sponge Spongia officinalis is currently threatened by recurrent mortality incidents in its native habitats. Elevated temperature has been indicated as a major triggering factor, but the molecular mechanisms recruited for the organism’s response to thermal shifts are yet unknown. Here, we experimentally tested the effect of exposure to temperatures of varying intensity and span on its gene expression profile, replicating gradients encountered in the species’ native habitat. Analysis revealed major shifts in the organism’s transcriptomic profile induced by temperatures corresponding to the standard seasonal maximum, triggering processes related to signal transduction, inflammation, and apoptotic pathway. Further elevation of temperature corresponding to local extremes activated further the immune response of the sponge along with protein ubiquitination. Following prolonged exposure, activation of endoplasmic reticulum stress related to accumulation of misfolded proteins and signs of resilience were observed. In the latter condition, categories such as cellular response to stress, wound repair, and diminution of pathological inflammation as also genes related to cell regeneration and cell growth were upregulated. Our results highlight the acknowledged sensitivity of S. officinalis to environmental shifts, providing an insight into the molecular mechanisms involved in the process. Furthermore, they suggest innate capacity for resilience at the current thermal extremes, implying a combination of factors and not temperature per se as the lethal agent. This sheds light on the mechanisms of pressure induced by the ongoing ocean warming trend to coastal sessile invertebrates.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The emblematic sponge Spongia officinalis is currently threatened by recurrent mortality incidents in its native habitats. Elevated temperature has been indicated as a major triggering factor, but the molecular mechanisms recruited for the organism’s response to thermal shifts are yet unknown. Here, we experimentally tested the effect of exposure to temperatures of varying intensity and span on its gene expression profile, replicating gradients encountered in the species’ native habitat. Analysis revealed major shifts in the organism’s transcriptomic profile induced by temperatures corresponding to the standard seasonal maximum, triggering processes related to signal transduction, inflammation, and apoptotic pathway. Further elevation of temperature corresponding to local extremes activated further the immune response of the sponge along with protein ubiquitination. Following prolonged exposure, activation of endoplasmic reticulum stress related to accumulation of misfolded proteins and signs of resilience were observed. In the latter condition, categories such as cellular response to stress, wound repair, and diminution of pathological inflammation as also genes related to cell regeneration and cell growth were upregulated. Our results highlight the acknowledged sensitivity of S. officinalis to environmental shifts, providing an insight into the molecular mechanisms involved in the process. Furthermore, they suggest innate capacity for resilience at the current thermal extremes, implying a combination of factors and not temperature per se as the lethal agent. This sheds light on the mechanisms of pressure induced by the ongoing ocean warming trend to coastal sessile invertebrates.
Polymenakou, Paraskevi N; Nomikou, Paraskevi; Mandalakis, Manolis; Kilias, Stephanos; Kotoulas, Giorgos; Kyrpides, Nikos C; Magoulas, Antonios
Microbial Benthic Communities in the Aegean Sea Book Section
In: Springer Berlin Heidelberg, Berlin, Heidelberg, 2020, (Series Title: The Handbook of Environmental Chemistry).
@incollection{polymenakou_microbial_2020,
title = {Microbial Benthic Communities in the Aegean Sea},
author = {Paraskevi N Polymenakou and Paraskevi Nomikou and Manolis Mandalakis and Stephanos Kilias and Giorgos Kotoulas and Nikos C Kyrpides and Antonios Magoulas},
url = {https://link.springer.com/10.1007/698_2020_685},
doi = {10.1007/698_2020_685},
year = {2020},
date = {2020-01-01},
urldate = {2022-02-17},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
note = {Series Title: The Handbook of Environmental Chemistry},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
Androulakis, Dimitrios N; Dounas, Costas G; Banks, Andrew Clive; Magoulas, Antonios N; Margaris, Dionissios P
In: Sustainability, vol. 12, no. 12, 2020, ISSN: 2071-1050.
@article{androulakis_assessment_2020,
title = {An Assessment of Computational Fluid Dynamics as a Tool to Aid the Design of the HCMR-Artificial-ReefsTM Diving Oasis in the Underwater Biotechnological Park of Crete},
author = {Dimitrios N Androulakis and Costas G Dounas and Andrew Clive Banks and Antonios N Magoulas and Dionissios P Margaris},
url = {https://www.mdpi.com/2071-1050/12/12/4847},
doi = {10.3390/su12124847},
issn = {2071-1050},
year = {2020},
date = {2020-01-01},
journal = {Sustainability},
volume = {12},
number = {12},
abstract = {Since recreational diving activities have increased in recent decades, resulting in additional environmental pressure on the coastal zone, the deployment of artificial reefs as a conservation strategy to divert mass ecotourism from fragile natural reefs has been proposed and realized in many areas of the world. Twelve units of a patented naturoid artificial reef technology developed by the Hellenic Centre for Marine Research (HCMR) were deployed in 2015 in the Underwater Biotechnological Park of Crete (UBPC) in order to create an experimental diving oasis and investigate the potential of achieving this aim for the over-exploited coastal ecosystems of this part of the Eastern Mediterranean. Assessment of the degree of establishment of artificial reefs and their ability to mimic natural ecosystems is often monitored through biological surveys and sampling. The measurement of the chemical, physical, and hydrodynamic characteristics of the water mass surrounding artificial reefs is also essential to fully understand their comparison to natural reefs. In particular, the flow field around reefs has been shown to be one of the most important physical factors in determining suitable conditions for the establishment of a number of key species on reef habitats. However, the combination of biological establishment monitoring and realistic flow-field simulation using computational fluid dynamics as a tool to aid in the design improvement of already existing reef installations has not been fully investigated in previous work. They are often reported separately as either ecological or engineering studies. Therefore, this study examined a full-scale numerical simulation of the field flow around individual already installed naturoid reef shapes, and part of their present arrangement on the sea bottom of the UPBC combined with the field-testing of the functionality of the installed artificial reefs concerning fish species aggregation. The results show that the simulated flow characteristics around the HCMR diving oasis artificial reefs were in good general agreement with the results of former studies, both for flows around a single deployed unit and for flows around a cluster of more than one unit. The results also gave good indications of the performance of individual reef units concerning key desirable characteristics such as downstream shadowing and sediment/nutrient upwelling and resuspension. In particular, they confirmed extended low flow levels (less than 0.3 m/s) and in some cases double vortexes on the downstream side of reef units where observed colonization and habitation of some key fish species had taken place. They also showed how the present distribution of units could be optimized to perform better as an integrated reef cluster. The use of computational fluid dynamics, with field survey data, is therefore suggested as a useful design improvement tool for installed reef structures and their deployment arrangement for recreational diving oases that can aid the sustainable development of the coastal zone.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Since recreational diving activities have increased in recent decades, resulting in additional environmental pressure on the coastal zone, the deployment of artificial reefs as a conservation strategy to divert mass ecotourism from fragile natural reefs has been proposed and realized in many areas of the world. Twelve units of a patented naturoid artificial reef technology developed by the Hellenic Centre for Marine Research (HCMR) were deployed in 2015 in the Underwater Biotechnological Park of Crete (UBPC) in order to create an experimental diving oasis and investigate the potential of achieving this aim for the over-exploited coastal ecosystems of this part of the Eastern Mediterranean. Assessment of the degree of establishment of artificial reefs and their ability to mimic natural ecosystems is often monitored through biological surveys and sampling. The measurement of the chemical, physical, and hydrodynamic characteristics of the water mass surrounding artificial reefs is also essential to fully understand their comparison to natural reefs. In particular, the flow field around reefs has been shown to be one of the most important physical factors in determining suitable conditions for the establishment of a number of key species on reef habitats. However, the combination of biological establishment monitoring and realistic flow-field simulation using computational fluid dynamics as a tool to aid in the design improvement of already existing reef installations has not been fully investigated in previous work. They are often reported separately as either ecological or engineering studies. Therefore, this study examined a full-scale numerical simulation of the field flow around individual already installed naturoid reef shapes, and part of their present arrangement on the sea bottom of the UPBC combined with the field-testing of the functionality of the installed artificial reefs concerning fish species aggregation. The results show that the simulated flow characteristics around the HCMR diving oasis artificial reefs were in good general agreement with the results of former studies, both for flows around a single deployed unit and for flows around a cluster of more than one unit. The results also gave good indications of the performance of individual reef units concerning key desirable characteristics such as downstream shadowing and sediment/nutrient upwelling and resuspension. In particular, they confirmed extended low flow levels (less than 0.3 m/s) and in some cases double vortexes on the downstream side of reef units where observed colonization and habitation of some key fish species had taken place. They also showed how the present distribution of units could be optimized to perform better as an integrated reef cluster. The use of computational fluid dynamics, with field survey data, is therefore suggested as a useful design improvement tool for installed reef structures and their deployment arrangement for recreational diving oases that can aid the sustainable development of the coastal zone.
2019
Manousaki, Tereza; Koutsouveli, Vasiliki; Lagnel, Jacques; Kollias, Spyridon; Tsigenopoulos, Costas S; Arvanitidis, Christos; Magoulas, Antonios; Dounas, Costas; Dailianis, Thanos
A de novo transcriptome assembly for the bath sponge Spongia officinalis, adjusting for microsymbionts Journal Article
In: BMC Research Notes, vol. 12, no. 1, pp. 813, 2019, ISSN: 1756-0500.
@article{manousaki_novo_2019,
title = {A de novo transcriptome assembly for the bath sponge Spongia officinalis, adjusting for microsymbionts},
author = {Tereza Manousaki and Vasiliki Koutsouveli and Jacques Lagnel and Spyridon Kollias and Costas S Tsigenopoulos and Christos Arvanitidis and Antonios Magoulas and Costas Dounas and Thanos Dailianis},
url = {https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4843-6},
doi = {10.1186/s13104-019-4843-6},
issn = {1756-0500},
year = {2019},
date = {2019-12-01},
urldate = {2020-08-06},
journal = {BMC Research Notes},
volume = {12},
number = {1},
pages = {813},
abstract = {Objectives
We report a transcriptome acquisition for the bath sponge Spongia officinalis, a non-model marine organism that hosts rich symbiotic microbial communities. To this end, a pipeline was developed to efficiently separate between bacterial expressed genes from those of eukaryotic origin. The transcriptome was produced to support the assessment of gene expression and, thus, the response of the sponge, to elevated temperatures, replicating conditions currently occurring in its native habitat.
Data description
We describe the assembled transcriptome along with the bioinformatic pipeline used to discriminate between signals of metazoan and prokaryotic origin. The pipeline involves standard read pre-processing steps and incorporates extra analyses to identify and filter prokaryotic reads out of the analysis. The proposed pipeline can be followed to overcome the technical RNASeq problems characteristic for symbiont-rich metazoan organisms with low or non-existent tissue differentiation, such as sponges and cnidarians. At the same time, it can be valuable towards the development of approaches for parallel transcriptomic studies of symbiotic communities and the host.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Objectives
We report a transcriptome acquisition for the bath sponge Spongia officinalis, a non-model marine organism that hosts rich symbiotic microbial communities. To this end, a pipeline was developed to efficiently separate between bacterial expressed genes from those of eukaryotic origin. The transcriptome was produced to support the assessment of gene expression and, thus, the response of the sponge, to elevated temperatures, replicating conditions currently occurring in its native habitat.
Data description
We describe the assembled transcriptome along with the bioinformatic pipeline used to discriminate between signals of metazoan and prokaryotic origin. The pipeline involves standard read pre-processing steps and incorporates extra analyses to identify and filter prokaryotic reads out of the analysis. The proposed pipeline can be followed to overcome the technical RNASeq problems characteristic for symbiont-rich metazoan organisms with low or non-existent tissue differentiation, such as sponges and cnidarians. At the same time, it can be valuable towards the development of approaches for parallel transcriptomic studies of symbiotic communities and the host.
We report a transcriptome acquisition for the bath sponge Spongia officinalis, a non-model marine organism that hosts rich symbiotic microbial communities. To this end, a pipeline was developed to efficiently separate between bacterial expressed genes from those of eukaryotic origin. The transcriptome was produced to support the assessment of gene expression and, thus, the response of the sponge, to elevated temperatures, replicating conditions currently occurring in its native habitat.
Data description
We describe the assembled transcriptome along with the bioinformatic pipeline used to discriminate between signals of metazoan and prokaryotic origin. The pipeline involves standard read pre-processing steps and incorporates extra analyses to identify and filter prokaryotic reads out of the analysis. The proposed pipeline can be followed to overcome the technical RNASeq problems characteristic for symbiont-rich metazoan organisms with low or non-existent tissue differentiation, such as sponges and cnidarians. At the same time, it can be valuable towards the development of approaches for parallel transcriptomic studies of symbiotic communities and the host.
Rizzo, Andrea Luca; Caracausi, Antonio; Chavagnac, Valérie; Nomikou, Paraskevi; Polymenakou, Paraskevi N; Mandalakis, Manolis; Kotoulas, Georgios; Magoulas, Antonios; Castillo, Alain; Lampridou, Danai; Marusczak, Nicolas; Sonke, Jeroen E
Geochemistry of CO2-Rich Gases Venting From Submarine Volcanism: The Case of Kolumbo (Hellenic Volcanic Arc, Greece) Journal Article
In: Frontiers in Earth Science, vol. 7, pp. 60, 2019, ISSN: 2296-6463, (BIODIV).
@article{rizzo_geochemistry_2019,
title = {Geochemistry of CO2-Rich Gases Venting From Submarine Volcanism: The Case of Kolumbo (Hellenic Volcanic Arc, Greece)},
author = {Andrea Luca Rizzo and Antonio Caracausi and Valérie Chavagnac and Paraskevi Nomikou and Paraskevi N Polymenakou and Manolis Mandalakis and Georgios Kotoulas and Antonios Magoulas and Alain Castillo and Danai Lampridou and Nicolas Marusczak and Jeroen E Sonke},
url = {https://www.frontiersin.org/article/10.3389/feart.2019.00060/full},
doi = {10.3389/feart.2019.00060},
issn = {2296-6463},
year = {2019},
date = {2019-04-01},
urldate = {2022-01-17},
journal = {Frontiers in Earth Science},
volume = {7},
pages = {60},
note = {BIODIV},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mandalakis, M; Gavriilidou, A; Polymenakou, P N; Christakis, C A; Nomikou, P; Medvecký, M; Kilias, S P; Kentouri, M; Kotoulas, G; Magoulas, A
Microbial strains isolated from CO2-venting Kolumbo submarine volcano show enhanced co-tolerance to acidity and antibiotics Journal Article
In: Marine Environmental Research, 2019, ISSN: 01411136, (Publisher: Elsevier Ltd).
@article{mandalakis_microbial_2019,
title = {Microbial strains isolated from CO2-venting Kolumbo submarine volcano show enhanced co-tolerance to acidity and antibiotics},
author = {M Mandalakis and A Gavriilidou and P N Polymenakou and C A Christakis and P Nomikou and M Medvecký and S P Kilias and M Kentouri and G Kotoulas and A Magoulas},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85059814164&doi=10.1016%2fj.marenvres.2019.01.002&partnerID=40&md5=69e25c6daab89af12b0091a2c75b0d18},
doi = {10.1016/j.marenvres.2019.01.002},
issn = {01411136},
year = {2019},
date = {2019-01-01},
journal = {Marine Environmental Research},
abstract = {As ocean acidification intensifies, there is growing global concern about the impacts that future pH levels are likely to have on marine life and ecosystems. By analogy, a steep decrease of seawater pH with depth is encountered inside the Kolumbo submarine volcano (northeast Santorini) as a result of natural CO2 venting, making this system ideal for ocean acidification research. Here, we investigated whether the increase of acidity towards deeper layers of Kolumbo crater had any effect on relevant phenotypic traits of bacterial isolates. A total of 31 Pseudomonas strains were isolated from both surface- (SSL) and deep-seawater layers (DSL), with the latter presenting a significantly higher acid tolerance. In particular, the DSL strains were able to cope with H+ levels that were 18 times higher. Similarly, the DSL isolates exhibited a significantly higher tolerance than SSL strains against six commonly used antibiotics and As(III). More importantly, a significant positive correlation was revealed between antibiotics and acid tolerance across the entire set of SSL and DSL isolates. Our findings imply that Pseudomonas species with higher resilience to antibiotics could be favored by the prospect of acidifying oceans. Further studies are required to determine if this feature is universal across marine bacteria and to assess potential ecological impacts. © 2019 Elsevier Ltd},
note = {Publisher: Elsevier Ltd},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
As ocean acidification intensifies, there is growing global concern about the impacts that future pH levels are likely to have on marine life and ecosystems. By analogy, a steep decrease of seawater pH with depth is encountered inside the Kolumbo submarine volcano (northeast Santorini) as a result of natural CO2 venting, making this system ideal for ocean acidification research. Here, we investigated whether the increase of acidity towards deeper layers of Kolumbo crater had any effect on relevant phenotypic traits of bacterial isolates. A total of 31 Pseudomonas strains were isolated from both surface- (SSL) and deep-seawater layers (DSL), with the latter presenting a significantly higher acid tolerance. In particular, the DSL strains were able to cope with H+ levels that were 18 times higher. Similarly, the DSL isolates exhibited a significantly higher tolerance than SSL strains against six commonly used antibiotics and As(III). More importantly, a significant positive correlation was revealed between antibiotics and acid tolerance across the entire set of SSL and DSL isolates. Our findings imply that Pseudomonas species with higher resilience to antibiotics could be favored by the prospect of acidifying oceans. Further studies are required to determine if this feature is universal across marine bacteria and to assess potential ecological impacts. © 2019 Elsevier Ltd
2018
Bounas, Anastasios; Catsadorakis, Giorgos; Logotheti, Annita; Voslamber, Berend; Magoulas, Antonios; Tsaparis, Dimitris
Conservation genetics of a resident population of Greylag Goose (Anser anser) at the southernmost limit of the species’ distribution in Europe Journal Article
In: Avian Research, vol. 9, no. 1, pp. 47, 2018, ISSN: 2053-7166.
@article{bounas_conservation_2018,
title = {Conservation genetics of a resident population of Greylag Goose (Anser anser) at the southernmost limit of the species’ distribution in Europe},
author = {Anastasios Bounas and Giorgos Catsadorakis and Annita Logotheti and Berend Voslamber and Antonios Magoulas and Dimitris Tsaparis},
url = {https://avianres.biomedcentral.com/articles/10.1186/s40657-018-0139-0},
doi = {10.1186/s40657-018-0139-0},
issn = {2053-7166},
year = {2018},
date = {2018-12-01},
urldate = {2020-08-26},
journal = {Avian Research},
volume = {9},
number = {1},
pages = {47},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Polymenakou, Paraskevi; Mandalakis, Manolis; Dailianis, Thanos; Dimitriadis, Charalampos; Medvecky, Matej; Magoulas, Antonios; Gerovasileiou, Vasilis
Preliminary assessment of methanogenic microbial communities in marine caves of Zakynthos Island (Ionian Sea, Greece) Journal Article
In: Mediterranean Marine Science, pp. 284, 2018, ISSN: 1791-6763, 1108-393X.
@article{polymenakou_preliminary_2018,
title = {Preliminary assessment of methanogenic microbial communities in marine caves of Zakynthos Island (Ionian Sea, Greece)},
author = {Paraskevi Polymenakou and Manolis Mandalakis and Thanos Dailianis and Charalampos Dimitriadis and Matej Medvecky and Antonios Magoulas and Vasilis Gerovasileiou},
url = {https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/14374},
doi = {10.12681/mms.14374},
issn = {1791-6763, 1108-393X},
year = {2018},
date = {2018-06-01},
urldate = {2020-08-06},
journal = {Mediterranean Marine Science},
pages = {284},
abstract = {Mediterranean marine caves remain largely unexplored, while particularly limited information is available about the microbial life existing in these unique environments. The present study is a preliminary assessment of the composition of the active anaerobic microbial community colonizing the walls of newly explored systems of underwater caves and small cavities in Zakynthos Island. The interior of these caves is densely coated with egg-shaped, foam-shaped and filamentous biological structures that are characterised by a strong odor of hydrogen sulfide gas. A total of twelve structures scrapped from cave rocks were subjected to anaerobic cultivation for up to 208 days. Strong to moderate methanogenesis was observed in two different types of egg-shaped structures and one foam-like structure. Interestingly, this was observed in experiments that were performed at room temperature (i.e. 25oC) which is substantially lower than those typically considered optimum for methane production (e.g. 35oC). Analysis of the 16S rRNA genes revealed a clear dominance of archaea and bacteria closely related to known methane producers and sulfate reducers, including members of the families Methanomicrobiaceae, Desulfobulbaceae, Desulfobacteraceae, Desulfuromonaceae, Campylobacteraceae, Marinifilaceae, Clostridiaceae, Incertae Sedis – Family I & II. These results show that Mediterranean marine caves can host members of archaea and bacteria with potential biotechnological interest that deserve further investigation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mediterranean marine caves remain largely unexplored, while particularly limited information is available about the microbial life existing in these unique environments. The present study is a preliminary assessment of the composition of the active anaerobic microbial community colonizing the walls of newly explored systems of underwater caves and small cavities in Zakynthos Island. The interior of these caves is densely coated with egg-shaped, foam-shaped and filamentous biological structures that are characterised by a strong odor of hydrogen sulfide gas. A total of twelve structures scrapped from cave rocks were subjected to anaerobic cultivation for up to 208 days. Strong to moderate methanogenesis was observed in two different types of egg-shaped structures and one foam-like structure. Interestingly, this was observed in experiments that were performed at room temperature (i.e. 25oC) which is substantially lower than those typically considered optimum for methane production (e.g. 35oC). Analysis of the 16S rRNA genes revealed a clear dominance of archaea and bacteria closely related to known methane producers and sulfate reducers, including members of the families Methanomicrobiaceae, Desulfobulbaceae, Desulfobacteraceae, Desulfuromonaceae, Campylobacteraceae, Marinifilaceae, Clostridiaceae, Incertae Sedis – Family I & II. These results show that Mediterranean marine caves can host members of archaea and bacteria with potential biotechnological interest that deserve further investigation.
Christakis, C A; Polymenakou, P N; Mandalakis, M; Nomikou, P; Kristoffersen, J B; Lampridou, D; Kotoulas, G; Magoulas, A
Microbial community differentiation between active and inactive sulfide chimneys of the Kolumbo submarine volcano, Hellenic Volcanic Arc Journal Article
In: Extremophiles, vol. 22, no. 1, pp. 13–27, 2018, ISSN: 14310651, (Publisher: Springer Tokyo).
@article{christakis_microbial_2018,
title = {Microbial community differentiation between active and inactive sulfide chimneys of the Kolumbo submarine volcano, Hellenic Volcanic Arc},
author = {C A Christakis and P N Polymenakou and M Mandalakis and P Nomikou and J B Kristoffersen and D Lampridou and G Kotoulas and A Magoulas},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85032008505&doi=10.1007%2fs00792-017-0971-x&partnerID=40&md5=2258d2985b658c3f415f37d92d684597},
doi = {10.1007/s00792-017-0971-x},
issn = {14310651},
year = {2018},
date = {2018-01-01},
journal = {Extremophiles},
volume = {22},
number = {1},
pages = {13--27},
abstract = {Over the last decades, there has been growing interest about the ecological role of hydrothermal sulfide chimneys, their microbial diversity and associated biotechnological potential. Here, we performed dual-index Illumina sequencing of bacterial and archaeal communities on active and inactive sulfide chimneys collected from the Kolumbo hydrothermal field, situated on a geodynamic convergent setting. A total of 15,701 OTUs (operational taxonomic units) were assigned to 56 bacterial and 3 archaeal phyla, 133 bacterial and 16 archaeal classes. Active chimney communities were dominated by OTUs related to thermophilic members of Epsilonproteobacteria, Aquificae and Deltaproteobacteria. Inactive chimney communities were dominated by an OTU closely related to the archaeon Nitrosopumilus sp., and by members of Gammaproteobacteria, Deltaproteobacteria, Planctomycetes and Bacteroidetes. These lineages are closely related to phylotypes typically involved in iron, sulfur, nitrogen, hydrogen and methane cycling. Overall, the inactive sulfide chimneys presented highly diverse and uniform microbial communities, in contrast to the active chimney communities, which were dominated by chemolithoautotrophic and thermophilic lineages. This study represents one of the most comprehensive investigations of microbial diversity in submarine chimneys and elucidates how the dissipation of hydrothermal activity affects the structure of microbial consortia in these extreme ecological niches. © 2017, Springer Japan KK.},
note = {Publisher: Springer Tokyo},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Over the last decades, there has been growing interest about the ecological role of hydrothermal sulfide chimneys, their microbial diversity and associated biotechnological potential. Here, we performed dual-index Illumina sequencing of bacterial and archaeal communities on active and inactive sulfide chimneys collected from the Kolumbo hydrothermal field, situated on a geodynamic convergent setting. A total of 15,701 OTUs (operational taxonomic units) were assigned to 56 bacterial and 3 archaeal phyla, 133 bacterial and 16 archaeal classes. Active chimney communities were dominated by OTUs related to thermophilic members of Epsilonproteobacteria, Aquificae and Deltaproteobacteria. Inactive chimney communities were dominated by an OTU closely related to the archaeon Nitrosopumilus sp., and by members of Gammaproteobacteria, Deltaproteobacteria, Planctomycetes and Bacteroidetes. These lineages are closely related to phylotypes typically involved in iron, sulfur, nitrogen, hydrogen and methane cycling. Overall, the inactive sulfide chimneys presented highly diverse and uniform microbial communities, in contrast to the active chimney communities, which were dominated by chemolithoautotrophic and thermophilic lineages. This study represents one of the most comprehensive investigations of microbial diversity in submarine chimneys and elucidates how the dissipation of hydrothermal activity affects the structure of microbial consortia in these extreme ecological niches. © 2017, Springer Japan KK.
Viret, A; Tsaparis, D; Tsigenopoulos, C S; Berrebi, P; Sabatini, A; Arculeo, M; Fassatoui, C; Magoulas, A; Marengo, M; Morales-Nin, B; Caill-Milly, N; Durieux, E D H
In: PLoS ONE, vol. 13, no. 9, 2018, ISSN: 19326203, (Publisher: Public Library of Science).
@article{viret_absence_2018,
title = {Absence of spatial genetic structure in common dentex (Dentex dentex Linnaeus, 1758) in the Mediterranean Sea as evidenced by nuclear and mitochondrial molecular markers},
author = {A Viret and D Tsaparis and C S Tsigenopoulos and P Berrebi and A Sabatini and M Arculeo and C Fassatoui and A Magoulas and M Marengo and B Morales-Nin and N Caill-Milly and E D H Durieux},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85053134390&doi=10.1371%2fjournal.pone.0203866&partnerID=40&md5=bc629c803f2e5c8490f76f3d27813b81},
doi = {10.1371/journal.pone.0203866},
issn = {19326203},
year = {2018},
date = {2018-01-01},
journal = {PLoS ONE},
volume = {13},
number = {9},
abstract = {The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterranean Sea (17 sites) with an emphasis around Corsica (5 sites), plus one Atlantic Ocean site. This provided an opportunity to examine genetic structuring at local and broader scales to provide science based data for the management of fishing stocks in the region. Two mitochondrial regions were examined (D-loop and COI) along with eight microsatellite loci. The COI data was combined with publicly available sequences and demonstrated past misidentification of common dentex. All markers indicated the absence of population genetic structure from the Bay of Biscay to the eastern Mediterranean Sea. Bayesian approaches, as well as the statistical tests performed on the allelic frequencies from microsatellite loci, indicated low differentiation between samples; there was only a slight (p = 0.05) indication of isolation by distance. Common dentex is a marine fish species with a unique panmictic population in the Mediterranean and likely in the Atlantic Ocean as well. © 2018 Viret et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},
note = {Publisher: Public Library of Science},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterranean Sea (17 sites) with an emphasis around Corsica (5 sites), plus one Atlantic Ocean site. This provided an opportunity to examine genetic structuring at local and broader scales to provide science based data for the management of fishing stocks in the region. Two mitochondrial regions were examined (D-loop and COI) along with eight microsatellite loci. The COI data was combined with publicly available sequences and demonstrated past misidentification of common dentex. All markers indicated the absence of population genetic structure from the Bay of Biscay to the eastern Mediterranean Sea. Bayesian approaches, as well as the statistical tests performed on the allelic frequencies from microsatellite loci, indicated low differentiation between samples; there was only a slight (p = 0.05) indication of isolation by distance. Common dentex is a marine fish species with a unique panmictic population in the Mediterranean and likely in the Atlantic Ocean as well. © 2018 Viret et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Piña, Mery; Colas, Pierre; Cancio, Ibon; Audic, Annie; Bosser, Lucas; Canario, Adelino; Gribbon, Philip; Johnston, Ian A; Kervella, Anne Emmanuelle; Kooistra, Wiebe H C F; Merciecca, Matthieu; Magoulas, Antonios; Nardello, Ilaria; Smith, David; Pade, Nicolas; Robinson, Douglas; Schoen, Antoine; Schultz, Fanny; Kloareg, Bernard
In: Rampelotto, Pabulo H; Trincone, Antonio (Ed.): Grand Challenges in Marine Biotechnology, pp. 405–421, Springer International Publishing, Cham, 2018, ISBN: 978-3-319-69074-2 978-3-319-69075-9, (BIODIV).
@incollection{rampelotto_european_2018,
title = {The European Marine Biological Research Infrastructure Cluster: An Alliance of European Research Infrastructures to Promote the Blue Bioeconomy},
author = {Mery Piña and Pierre Colas and Ibon Cancio and Annie Audic and Lucas Bosser and Adelino Canario and Philip Gribbon and Ian A Johnston and Anne Emmanuelle Kervella and Wiebe H C F Kooistra and Matthieu Merciecca and Antonios Magoulas and Ilaria Nardello and David Smith and Nicolas Pade and Douglas Robinson and Antoine Schoen and Fanny Schultz and Bernard Kloareg},
editor = {Pabulo H Rampelotto and Antonio Trincone},
url = {http://link.springer.com/10.1007/978-3-319-69075-9_10},
isbn = {978-3-319-69074-2 978-3-319-69075-9},
year = {2018},
date = {2018-01-01},
urldate = {2022-01-17},
booktitle = {Grand Challenges in Marine Biotechnology},
pages = {405--421},
publisher = {Springer International Publishing},
address = {Cham},
note = {BIODIV},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
2017
Antoniou, A; Kasapidis, P; Kotoulas, G; Mylonas, C C; Magoulas, A
Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: Insights from genome-wide SNPs and microsatellites Journal Article
In: Journal of Biological Research-Thessaloniki, vol. 24, no. 1, pp. 3, 2017.
@article{antoniou_genetic_2017,
title = {Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: Insights from genome-wide SNPs and microsatellites},
author = {A Antoniou and P Kasapidis and G Kotoulas and C C Mylonas and A Magoulas},
doi = {10.1186/s40709-017-0062-2},
year = {2017},
date = {2017-01-01},
journal = {Journal of Biological Research-Thessaloniki},
volume = {24},
number = {1},
pages = {3},
abstract = {© The Author(s) 2017. Background: Elucidating the patterns of the Atlantic Bluefin tuna [ABFT, Thunnus thynnus (Linnaeus, 1758)] population structure constitutes a challenging task of great importance. Most of the unique challenges stem from its biology, as well as the attributes of the marine realm in which it disperses. Accurate information is urgently needed for stock assessment, and the identification of critical features to the persistence and adaptation of populations in order to formulate and adopt effective strategies for ABFT conservation and management. Conclusions of a great number of ABFT genetic studies on the Mediterranean Sea stock structure are rather controversial and not yet conclusive. In this study, ABFT genomic diversity was investigated in the Mediterranean Sea, which is the most important area for the species' reproduction. Results: Analyzing genome-wide SNPs and microsatellites from ABFT samples collected throughout the Mediterranean Sea did not provide strong evidence of genetic structure, pointing towards the existence of a single panmictic unit. An alternative view would recognize a failure to reject the null hypothesis of a panmictic unit as an effect of the study's sampling design, the type of markers used, and the effectiveness/suitability of analysis methods in respect to the species biological characteristics or any combination of the above. Conclusions: Unravelling the drivers of ABFT population diversity would require the consideration of important aspects of the species spawning behavior for the determination of the appropriate sampling design. Novel approaches and methods of analysis that will bring together experts in genetics/-omics, ecology and oceanography are deemed necessary. Analyzing ABFT genetic data under the discipline of seascape genetics could provide the analysis framework under which major abiotic and biotic forces controlling ABFT recruitment could be identified, elucidating the complicated population dynamics of the species, while multiple and continuous fisheries monitoring should in all cases be considered as a prerequisite in order to achieve efficient and long-term ABFT conservation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© The Author(s) 2017. Background: Elucidating the patterns of the Atlantic Bluefin tuna [ABFT, Thunnus thynnus (Linnaeus, 1758)] population structure constitutes a challenging task of great importance. Most of the unique challenges stem from its biology, as well as the attributes of the marine realm in which it disperses. Accurate information is urgently needed for stock assessment, and the identification of critical features to the persistence and adaptation of populations in order to formulate and adopt effective strategies for ABFT conservation and management. Conclusions of a great number of ABFT genetic studies on the Mediterranean Sea stock structure are rather controversial and not yet conclusive. In this study, ABFT genomic diversity was investigated in the Mediterranean Sea, which is the most important area for the species' reproduction. Results: Analyzing genome-wide SNPs and microsatellites from ABFT samples collected throughout the Mediterranean Sea did not provide strong evidence of genetic structure, pointing towards the existence of a single panmictic unit. An alternative view would recognize a failure to reject the null hypothesis of a panmictic unit as an effect of the study's sampling design, the type of markers used, and the effectiveness/suitability of analysis methods in respect to the species biological characteristics or any combination of the above. Conclusions: Unravelling the drivers of ABFT population diversity would require the consideration of important aspects of the species spawning behavior for the determination of the appropriate sampling design. Novel approaches and methods of analysis that will bring together experts in genetics/-omics, ecology and oceanography are deemed necessary. Analyzing ABFT genetic data under the discipline of seascape genetics could provide the analysis framework under which major abiotic and biotic forces controlling ABFT recruitment could be identified, elucidating the complicated population dynamics of the species, while multiple and continuous fisheries monitoring should in all cases be considered as a prerequisite in order to achieve efficient and long-term ABFT conservation.
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
In: GigaScience, vol. 6, no. 12, pp. 1–13, 2017, ISSN: 2047217X, (Publisher: Oxford University Press).
@article{sarropoulou_full_2017,
title = {Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili},
author = {E Sarropoulou and A Y M Sundaram and E Kaitetzidou and G Kotoulas and G D Gilfillan and N Papandroulakis and C C Mylonas and A Magoulas},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85042364258&doi=10.1093%2fgigascience%2fgix108&partnerID=40&md5=fa6e269b1e6ff57a26c0c9c6efe45226},
doi = {10.1093/gigascience/gix108},
issn = {2047217X},
year = {2017},
date = {2017-01-01},
journal = {GigaScience},
volume = {6},
number = {12},
pages = {1--13},
abstract = {Background: Teleosts of the genus Seriola, commonly known as amberjacks, are of high commercial value in international markets due to their flesh quality and worldwide distribution. The Seriola species of interest to Mediterranean aquaculture is the greater amberjack (Seriola dumerili). This species holds great potential for the aquaculture industry, but in captivity, reproduction has proved to be challenging, and observed growth dysfunction hinders their domestication. Insights into molecular mechanisms may contribute to a better understanding of traits like growth and sex, but investigations to unravel the molecular background of amberjacks have begun only recently. Findings: Illumina HiSeq sequencing generated a high-coverage greater amberjack genome sequence comprising 45 909 scaffolds. Comparative mapping to the Japanese yellowtail (Seriola quinqueriadiata) and to the model species medaka (Oryzias latipes) allowed the generation of in silico groups. Additional gonad transcriptome sequencing identified sex-biased transcripts, including known sex-determining and differentiation genes. Investigation of the muscle transcriptome of slow-growing individuals showed that transcripts involved in oxygen and gas transport were differentially expressed compared with fast/normal-growing individuals. On the other hand, transcripts involved in muscle functions were found to be enriched in fast/normal-growing individuals. Conclusion: The present study provides the first insights into the molecular background of male and female amberjacks and of fast- and slow-growing fish. Therefore, valuable molecular resources have been generated in the form of a first draft genome and a reference transcriptome. Sex-biased genes, which may also have roles in sex determination or differentiation, and genes that may be responsible for slow growth are suggested. © The Author(s) 2017.},
note = {Publisher: Oxford University Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Background: Teleosts of the genus Seriola, commonly known as amberjacks, are of high commercial value in international markets due to their flesh quality and worldwide distribution. The Seriola species of interest to Mediterranean aquaculture is the greater amberjack (Seriola dumerili). This species holds great potential for the aquaculture industry, but in captivity, reproduction has proved to be challenging, and observed growth dysfunction hinders their domestication. Insights into molecular mechanisms may contribute to a better understanding of traits like growth and sex, but investigations to unravel the molecular background of amberjacks have begun only recently. Findings: Illumina HiSeq sequencing generated a high-coverage greater amberjack genome sequence comprising 45 909 scaffolds. Comparative mapping to the Japanese yellowtail (Seriola quinqueriadiata) and to the model species medaka (Oryzias latipes) allowed the generation of in silico groups. Additional gonad transcriptome sequencing identified sex-biased transcripts, including known sex-determining and differentiation genes. Investigation of the muscle transcriptome of slow-growing individuals showed that transcripts involved in oxygen and gas transport were differentially expressed compared with fast/normal-growing individuals. On the other hand, transcripts involved in muscle functions were found to be enriched in fast/normal-growing individuals. Conclusion: The present study provides the first insights into the molecular background of male and female amberjacks and of fast- and slow-growing fish. Therefore, valuable molecular resources have been generated in the form of a first draft genome and a reference transcriptome. Sex-biased genes, which may also have roles in sex determination or differentiation, and genes that may be responsible for slow growth are suggested. © The Author(s) 2017.
2016
Davies, N; Field, D; Gavaghan, D; Holbrook, S J; Planes, S; Troyer, M; Bonsall, M; Claudet, J; Roderick, G; Schmitt, R J; Zettler, L A; Berteaux, V; Bossin, H C; Cabasse, C; Collin, A; Deck, J; Dell, T; Dunne, J; Gates, R; Harfoot, M; Hench, J L; Hopuare, M; Kirch, P; Kotoulas, G; Kosenkov, A; Kusenko, A; Leichter, J J; Lenihan, H; Magoulas, A; Martinez, N; Meyer, C; Stoll, B; Swalla, B; Tartakovsky, D M; Murphy, H T; Turyshev, S; Valdvinos, F; Williams, R; Wood, S
Simulating social-ecological systems: The Island Digital Ecosystem Avatars (IDEA) consortium Journal Article
In: GigaScience, vol. 5, no. 1, 2016, ISSN: 2047217X, (Publisher: BioMed Central Ltd.).
@article{davies_simulating_2016,
title = {Simulating social-ecological systems: The Island Digital Ecosystem Avatars (IDEA) consortium},
author = {N Davies and D Field and D Gavaghan and S J Holbrook and S Planes and M Troyer and M Bonsall and J Claudet and G Roderick and R J Schmitt and L A Zettler and V Berteaux and H C Bossin and C Cabasse and A Collin and J Deck and T Dell and J Dunne and R Gates and M Harfoot and J L Hench and M Hopuare and P Kirch and G Kotoulas and A Kosenkov and A Kusenko and J J Leichter and H Lenihan and A Magoulas and N Martinez and C Meyer and B Stoll and B Swalla and D M Tartakovsky and H T Murphy and S Turyshev and F Valdvinos and R Williams and S Wood},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84991529168&doi=10.1186%2fs13742-016-0118-5&partnerID=40&md5=8cee8d8941e5eaf5d39db97438c349a6},
doi = {10.1186/s13742-016-0118-5},
issn = {2047217X},
year = {2016},
date = {2016-01-01},
journal = {GigaScience},
volume = {5},
number = {1},
abstract = {Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine-terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions. © 2016 Davies et al.},
note = {Publisher: BioMed Central Ltd.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine-terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions. © 2016 Davies et al.
Rizzo, A L; Caracausi, A; Chavagnac, V; Nomikou, P; Polymenakou, P N; Mandalakis, M; Kotoulas, G; Magoulas, A; Castillo, A; Lampridou, D
Kolumbo submarine volcano (Greece): An active window into the Aegean subduction system Journal Article
In: Scientific Reports, vol. 6, 2016, ISSN: 20452322, (Publisher: Nature Publishing Group).
@article{rizzo_kolumbo_2016,
title = {Kolumbo submarine volcano (Greece): An active window into the Aegean subduction system},
author = {A L Rizzo and A Caracausi and V Chavagnac and P Nomikou and P N Polymenakou and M Mandalakis and G Kotoulas and A Magoulas and A Castillo and D Lampridou},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84975454736&doi=10.1038%2fsrep28013&partnerID=40&md5=e24dc2fa03414abaf410e586529f758d},
doi = {10.1038/srep28013},
issn = {20452322},
year = {2016},
date = {2016-01-01},
journal = {Scientific Reports},
volume = {6},
abstract = {Submarine volcanism represents ∼80% of the volcanic activity on Earth and is an important source of mantle-derived gases. These gases are of basic importance for the comprehension of mantle characteristics in areas where subaerial volcanism is missing or strongly modified by the presence of crustal/atmospheric components. Though, the study of submarine volcanism remains a challenge due to their hazardousness and sea-depth. Here, we report 3He/4He measurements in CO2-dominated gases discharged at 500 m below sea level from the high-temperature (∼220 °C) hydrothermal system of the Kolumbo submarine volcano (Greece), located 7 km northeast off Santorini Island in the central part of the Hellenic Volcanic Arc (HVA). We highlight that the mantle below Kolumbo and Santorini has a 3He/4He signature of at least 7.0 Ra (being Ra the 3He/4He ratio of atmospheric He equal to 1.39×10-6), 3 Ra units higher than actually known for gases-rocks from Santorini. This ratio is also the highest measured across the HVA and is indicative of the direct degassing of a Mid-Ocean-Ridge-Basalts (MORB)-like mantle through lithospheric faults. We finally highlight that the degassing of high-temperature fluids with a MORB-like 3He/4He ratio corroborates a vigorous outgassing of mantle-derived volatiles with potential hazard at the Kolumbo submarine volcano.},
note = {Publisher: Nature Publishing Group},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Submarine volcanism represents ∼80% of the volcanic activity on Earth and is an important source of mantle-derived gases. These gases are of basic importance for the comprehension of mantle characteristics in areas where subaerial volcanism is missing or strongly modified by the presence of crustal/atmospheric components. Though, the study of submarine volcanism remains a challenge due to their hazardousness and sea-depth. Here, we report 3He/4He measurements in CO2-dominated gases discharged at 500 m below sea level from the high-temperature (∼220 °C) hydrothermal system of the Kolumbo submarine volcano (Greece), located 7 km northeast off Santorini Island in the central part of the Hellenic Volcanic Arc (HVA). We highlight that the mantle below Kolumbo and Santorini has a 3He/4He signature of at least 7.0 Ra (being Ra the 3He/4He ratio of atmospheric He equal to 1.39×10-6), 3 Ra units higher than actually known for gases-rocks from Santorini. This ratio is also the highest measured across the HVA and is indicative of the direct degassing of a Mid-Ocean-Ridge-Basalts (MORB)-like mantle through lithospheric faults. We finally highlight that the degassing of high-temperature fluids with a MORB-like 3He/4He ratio corroborates a vigorous outgassing of mantle-derived volatiles with potential hazard at the Kolumbo submarine volcano.
Rizzo, A L; Caracausi, A; Chavagnac, V; Nomikou, P; Polymenakou, P N; Mandalakis, M; Kotoulas, Georgios; Magoulas, A; Castillo, A
Kolumbo active seamount (Greece): a window into the Aegean mantle Proceedings Article
In: Nancy, France, 2016, (Publication Title: DINGUE ⋕4, Developments in Noble Gas Understanding and Expertise).
@inproceedings{rizzo_kolumbo_2016-1,
title = {Kolumbo active seamount (Greece): a window into the Aegean mantle},
author = {A L Rizzo and A Caracausi and V Chavagnac and P Nomikou and P N Polymenakou and M Mandalakis and Georgios Kotoulas and A Magoulas and A Castillo},
year = {2016},
date = {2016-01-01},
address = {Nancy, France},
note = {Publication Title: DINGUE ⋕4, Developments in Noble Gas Understanding and Expertise},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Oulas, Anastasis; Polymenakou, Paraskevi N; Seshadri, Rekha; Tripp, James H; Mandalakis, Manolis; Paez-Espino, David A; Pati, Amrita; Chain, Patrick; Nomikou, Paraskevi; Carey, Steven; Kilias, Stephanos; Christakis, Christos; Kotoulas, Georgios; Magoulas, Antonios; Ivanova, Natalia N; Kyrpides, Nikos C
Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology. Journal Article
In: Environmental Microbiology, vol. 18, no. 4, pp. 1122–1136, 2016, ISSN: 1462-2920.
@article{oulas_metagenomic_2016,
title = {Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology.},
author = {Anastasis Oulas and Paraskevi N Polymenakou and Rekha Seshadri and James H Tripp and Manolis Mandalakis and David A Paez-Espino and Amrita Pati and Patrick Chain and Paraskevi Nomikou and Steven Carey and Stephanos Kilias and Christos Christakis and Georgios Kotoulas and Antonios Magoulas and Natalia N Ivanova and Nikos C Kyrpides},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26487573},
doi = {10.1111/1462-2920.13095},
issn = {1462-2920},
year = {2016},
date = {2016-01-01},
journal = {Environmental Microbiology},
volume = {18},
number = {4},
pages = {1122--1136},
abstract = {Hydrothermal vents represent a deep, hot, aphotic biosphere where chemosynthetic primary producers, fuelled by chemicals from Earth's subsurface, form the basis of life. In this study, we examined microbial mats from two distinct volcanic sites within the Hellenic Volcanic Arc (HVA). The HVA is geologically and ecologically unique, with reported emissions of CO2 -saturated fluids at temperatures up to 220°C and a notable absence of macrofauna. Metagenomic data reveals highly complex prokaryotic communities composed of chemolithoautotrophs, some methanotrophs, and to our surprise, heterotrophs capable of anaerobic degradation of aromatic hydrocarbons. Our data suggest that aromatic hydrocarbons may indeed be a significant source of carbon in these sites, and instigate additional research into the nature and origin of these compounds in the HVA. Novel physiology was assigned to several uncultured prokaryotic lineages; most notably, a SAR406 representative is attributed with a role in anaerobic hydrocarbon degradation. This dataset, the largest to date from submarine volcanic ecosystems, constitutes a significant resource of novel genes and pathways with potential biotechnological applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hydrothermal vents represent a deep, hot, aphotic biosphere where chemosynthetic primary producers, fuelled by chemicals from Earth's subsurface, form the basis of life. In this study, we examined microbial mats from two distinct volcanic sites within the Hellenic Volcanic Arc (HVA). The HVA is geologically and ecologically unique, with reported emissions of CO2 -saturated fluids at temperatures up to 220°C and a notable absence of macrofauna. Metagenomic data reveals highly complex prokaryotic communities composed of chemolithoautotrophs, some methanotrophs, and to our surprise, heterotrophs capable of anaerobic degradation of aromatic hydrocarbons. Our data suggest that aromatic hydrocarbons may indeed be a significant source of carbon in these sites, and instigate additional research into the nature and origin of these compounds in the HVA. Novel physiology was assigned to several uncultured prokaryotic lineages; most notably, a SAR406 representative is attributed with a role in anaerobic hydrocarbon degradation. This dataset, the largest to date from submarine volcanic ecosystems, constitutes a significant resource of novel genes and pathways with potential biotechnological applications.
Manousaki, Tereza; Tsakogiannis, Alexandros; Taggart, John B; Palaiokostas, Christos; Tsaparis, Dimitris; Lagnel, Jacques; Chatziplis, Dimitrios; Magoulas, Antonios; Papandroulakis, Nikos; Mylonas, Constantinos C; TSIGENOPOULOS, C. S.
Exploring a nonmodel teleost genome through rad sequencing—linkage mapping in Common Pandora, Pagellus erythrinus and comparative genomic analysis Journal Article
In: G3: Genes, genomes, genetics, vol. 6, no. 3, pp. 509–519, 2016, (Publisher: G3: Genes, Genomes, Genetics).
@article{manousaki_exploring_2016,
title = {Exploring a nonmodel teleost genome through rad sequencing—linkage mapping in Common Pandora, Pagellus erythrinus and comparative genomic analysis},
author = {Tereza Manousaki and Alexandros Tsakogiannis and John B Taggart and Christos Palaiokostas and Dimitris Tsaparis and Jacques Lagnel and Dimitrios Chatziplis and Antonios Magoulas and Nikos Papandroulakis and Constantinos C Mylonas and C. S. TSIGENOPOULOS },
year = {2016},
date = {2016-01-01},
journal = {G3: Genes, genomes, genetics},
volume = {6},
number = {3},
pages = {509--519},
note = {Publisher: G3: Genes, Genomes, Genetics},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2015
Loukovitis, D; Ioannidi, B; Chatziplis, D; Kotoulas, G; Magoulas, A; Tsigenopoulos, C S
In: Mediterranean Marine Science, vol. 16, no. 1, pp. 197–200, 2015, ISSN: 1108393X, (Publisher: Hellenic Centre for Marine Research).
@article{loukovitis_loss_2015,
title = {Loss of genetic variation in Greek hatchery populations of the European sea bass (Dicentrarchus labrax L.) as revealed by microsatellite DNA analysis},
author = {D Loukovitis and B Ioannidi and D Chatziplis and G Kotoulas and A Magoulas and C S Tsigenopoulos},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84924862323&doi=10.12681%2fmms.1033&partnerID=40&md5=d6f2f3b1764f0f707f4f4015dcabe4bb},
doi = {10.12681/mms.1033},
issn = {1108393X},
year = {2015},
date = {2015-01-01},
journal = {Mediterranean Marine Science},
volume = {16},
number = {1},
pages = {197--200},
abstract = {Genetic variation in four reared stocks of European sea bass Dicentrarchus labrax L., originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of three natural populations from Greece and France. The total number of alleles per marker ranged from 8 to 22 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic richness and expected heterozygosity. The genetic differentiation of cultivated samples between them as well as from the wild origin fish was significant, as indicated by Fst analysis. All population pairwise comparisons were statistically significant, except for the pair of the two natural Greek populations. Results of microsatellite DNA analysis herein showed a 37 % reduction of the mean allele number in the hatchery samples compared to the wild ones, suggesting random genetic drift and inbreeding events operating in the hatcheries. Knowledge of the genetic variation in D. labrax cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes.},
note = {Publisher: Hellenic Centre for Marine Research},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Genetic variation in four reared stocks of European sea bass Dicentrarchus labrax L., originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of three natural populations from Greece and France. The total number of alleles per marker ranged from 8 to 22 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic richness and expected heterozygosity. The genetic differentiation of cultivated samples between them as well as from the wild origin fish was significant, as indicated by Fst analysis. All population pairwise comparisons were statistically significant, except for the pair of the two natural Greek populations. Results of microsatellite DNA analysis herein showed a 37 % reduction of the mean allele number in the hatchery samples compared to the wild ones, suggesting random genetic drift and inbreeding events operating in the hatcheries. Knowledge of the genetic variation in D. labrax cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes.
Daskalakis, M I; Rigas, F; Bakolas, A; Magoulas, A; Kotoulas, G; Katsikis, I; Karageorgis, A P; Mavridou, A
Vaterite bio-precipitation induced by Bacillus pumilus isolated from a solutional cave in Paiania, Athens, Greece Journal Article
In: International Biodeterioration and Biodegradation, vol. 99, pp. 73–84, 2015, ISSN: 09648305, (Publisher: Elsevier Ltd).
@article{daskalakis_vaterite_2015,
title = {Vaterite bio-precipitation induced by Bacillus pumilus isolated from a solutional cave in Paiania, Athens, Greece},
author = {M I Daskalakis and F Rigas and A Bakolas and A Magoulas and G Kotoulas and I Katsikis and A P Karageorgis and A Mavridou},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84922670670&doi=10.1016%2fj.ibiod.2014.12.005&partnerID=40&md5=562ec5c40d1639e7fe95fee9946262eb},
doi = {10.1016/j.ibiod.2014.12.005},
issn = {09648305},
year = {2015},
date = {2015-01-01},
journal = {International Biodeterioration and Biodegradation},
volume = {99},
pages = {73--84},
abstract = {In this work, Bacillus pumilus ACA-DC 4061 was selected for its increased capability for biomineralization on marble, under different nutrient media concentrations and temperature conditions. The optimum conditions for the CaCO3 bacterially-induced precipitation were determined with the aid of testing based on the Design of Experiments (DoE). Biomineral (vaterite) precipitation was favored in both the temperatures (25 and 30°C) investigated. Stone loss rate was reduced when the samples were subjected to sonication. Thin sections of the substrate confirmed that vaterite was able to adhere onto the surface. Finally, under non-sterile conditions mimicking an in situ application, B. pumilus ACA-DC 4061 formed a fine layer of calcium carbonate. Therefore, this microorganism showed that vaterite formation may consistently occur under specific conditions and could prove useful as a candidate for on-site applications for stone conservation. © 2014 Elsevier Ltd.},
note = {Publisher: Elsevier Ltd},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In this work, Bacillus pumilus ACA-DC 4061 was selected for its increased capability for biomineralization on marble, under different nutrient media concentrations and temperature conditions. The optimum conditions for the CaCO3 bacterially-induced precipitation were determined with the aid of testing based on the Design of Experiments (DoE). Biomineral (vaterite) precipitation was favored in both the temperatures (25 and 30°C) investigated. Stone loss rate was reduced when the samples were subjected to sonication. Thin sections of the substrate confirmed that vaterite was able to adhere onto the surface. Finally, under non-sterile conditions mimicking an in situ application, B. pumilus ACA-DC 4061 formed a fine layer of calcium carbonate. Therefore, this microorganism showed that vaterite formation may consistently occur under specific conditions and could prove useful as a candidate for on-site applications for stone conservation. © 2014 Elsevier Ltd.
2014
Tsigenopoulos, C S; Louro, B; Chatziplis, D; Lagnel, J; Vogiatzi, E; Loukovitis, D; Franch, R; Sarropoulou, E; Power, D M; Patarnello, T; Mylonas, C C; Magoulas, A; Bargelloni, L; Canario, A; Kotoulas, G
Second generation genetic linkage map for the gilthead sea bream Sparus aurata L. Journal Article
In: Marine Genomics, vol. 18, no. 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.
Daskalakis, M I; Magoulas, A; Kotoulas, G; Katsikis, I; Bakolas, A; Karageorgis, A P; Mavridou, A; Doulia, D; Rigas, F
Cupriavidus metallidurans biomineralization ability and its application as a bioconsolidation enhancer for ornamental marble stone Journal Article
In: Applied Microbiology and Biotechnology, vol. 98, no. 15, pp. 6871–6883, 2014, ISSN: 01757598, (Publisher: Springer Verlag).
@article{daskalakis_cupriavidus_2014,
title = {Cupriavidus metallidurans biomineralization ability and its application as a bioconsolidation enhancer for ornamental marble stone},
author = {M I Daskalakis and A Magoulas and G Kotoulas and I Katsikis and A Bakolas and A P Karageorgis and A Mavridou and D Doulia and F Rigas},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84905058974&doi=10.1007%2fs00253-014-5753-0&partnerID=40&md5=e810152ea01bb2be6c740ba9c5d1b590},
doi = {10.1007/s00253-014-5753-0},
issn = {01757598},
year = {2014},
date = {2014-01-01},
journal = {Applied Microbiology and Biotechnology},
volume = {98},
number = {15},
pages = {6871--6883},
abstract = {Bacterially induced calcium carbonate precipitation of a Cupriavidus metallidurans isolate was investigated to develop an environmentally friendly method for restoration and preservation of ornamental stones. Biomineralization performance was carried out in a growth medium via a Design of Experiments (DoE) approach using, as design factors, the temperature, growth medium concentration, and inoculum concentration. The optimum conditions were determined with the aid of consecutive experiments based on response surface methodology (RSM) and were successfully validated thereafter. Statistical analysis can be utilized as a tool for screening bacterial bioprecipitation as it considerably reduced the experimental time and effort needed for bacterial evaluation. Analytical methods provided an insight to the biomineral characteristics, and sonication tests proved that our isolate could create a solid new layer of vaterite on marble substrate withstanding sonication forces. C. metallidurans ACA-DC 4073 provided a compact vaterite layer on the marble substrate with morphological characteristics that assisted in its differentiation. The latter proved valuable during spraying minimum amount of inoculated media on marble substrate under conditions close to an in situ application. A sufficient and clearly distinguishable layer was identified. © 2014 Springer-Verlag.},
note = {Publisher: Springer Verlag},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bacterially induced calcium carbonate precipitation of a Cupriavidus metallidurans isolate was investigated to develop an environmentally friendly method for restoration and preservation of ornamental stones. Biomineralization performance was carried out in a growth medium via a Design of Experiments (DoE) approach using, as design factors, the temperature, growth medium concentration, and inoculum concentration. The optimum conditions were determined with the aid of consecutive experiments based on response surface methodology (RSM) and were successfully validated thereafter. Statistical analysis can be utilized as a tool for screening bacterial bioprecipitation as it considerably reduced the experimental time and effort needed for bacterial evaluation. Analytical methods provided an insight to the biomineral characteristics, and sonication tests proved that our isolate could create a solid new layer of vaterite on marble substrate withstanding sonication forces. C. metallidurans ACA-DC 4073 provided a compact vaterite layer on the marble substrate with morphological characteristics that assisted in its differentiation. The latter proved valuable during spraying minimum amount of inoculated media on marble substrate under conditions close to an in situ application. A sufficient and clearly distinguishable layer was identified. © 2014 Springer-Verlag.
Vogiatzi, E; Kalogianni, E; Zimmerman, B; Giakoumi, S; Barbieri, R; Paschou, P; Magoulas, A; Tsaparis, D; Poulakakis, N; Tsigenopoulos, CS.
In: Biological Journal of the Linnean Society, vol. 111, pp. 334–349, 2014.
@article{vogiatzi_reduced_2014,
title = {Reduced genetic variation and strong genetic population structure in the freshwater killifish Valencia letourneuxi (Valenciidae) based on nuclear and mitochondrial markers},
author = {E Vogiatzi and E Kalogianni and B Zimmerman and S Giakoumi and R Barbieri and P Paschou and A Magoulas and D Tsaparis and N Poulakakis and CS. Tsigenopoulos},
url = {http://dx.doi.org/10.1111/bij.12206},
doi = {10.1111/bij.12206},
year = {2014},
date = {2014-01-01},
journal = {Biological Journal of the Linnean Society},
volume = {111},
pages = {334--349},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2013
Gkafas, Ga; Tsigenopoulos, C; Magoulas, A; Panagiotaki, P; Vafidis, D; Mamuris, Z; Exadactylos, A
Population subdivision of saddled seabream Oblada melanura in the Aegean Sea revealed by genetic and morphometric analyses Journal Article
In: Aquatic Biology, vol. 18, no. 1, pp. 69–80, 2013, ISSN: 1864-7782, 1864-7790.
@article{gkafas_population_2013,
title = {Population subdivision of saddled seabream Oblada melanura in the Aegean Sea revealed by genetic and morphometric analyses},
author = {Ga Gkafas and C Tsigenopoulos and A Magoulas and P Panagiotaki and D Vafidis and Z Mamuris and A Exadactylos},
url = {http://www.int-res.com/abstracts/ab/v18/n1/p69-80/},
doi = {10.3354/ab00490},
issn = {1864-7782, 1864-7790},
year = {2013},
date = {2013-02-01},
urldate = {2020-08-09},
journal = {Aquatic Biology},
volume = {18},
number = {1},
pages = {69--80},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Antoniou, A; Magoulas, A; Platis, P; Kotoulas, G
Assessing the genetic landscape of a contact zone: The case of European hare in northeastern Greece Journal Article
In: Genetica, vol. 141, no. 1-3, 2013, ISSN: 00166707.
@article{antoniou_assessing_2013,
title = {Assessing the genetic landscape of a contact zone: The case of European hare in northeastern Greece},
author = {A Antoniou and A Magoulas and P Platis and G Kotoulas},
doi = {10.1007/s10709-013-9703-z},
issn = {00166707},
year = {2013},
date = {2013-01-01},
journal = {Genetica},
volume = {141},
number = {1-3},
abstract = {The European hare populations of the Balkan Peninsula comprise two divergent phylogenetic lineages with discrete geographical distribution slightly overlapping in the area of northeastern Greece and Bulgaria. Here we elucidate their contact zone, by defining the spatial distributional pattern of the two highly divergent groups, detecting individuals of hybrid origin, and identifying genetic barriers present in the area of their co-existence. Specimens from northeastern Greece were assayed for lineage assignment and population genetic inference based on a 511 bp fragment of mitochondrial DNA control region and allelic data from 10 microsatellite loci. Bayesian analyses on original and simulated genotypes were performed allowing for the contact zone delineation. Our results indicate high genetic diversity in both nuclear and mitochondrial DNA, strong population structure and non random spatial distribution of the differentiated gene pools. The information provided by the two types of molecular markers yielded consistent results. This study comprises a fine scale analysis of the contact zone between the two evolutionary lineages of European brown hares in northeastern Greece. Specific questions on the spatial patterns where addressed for the first time. Furthermore, hypotheses regarding the presence of hybrids were also tested. As a result, interpretive power to the diversity patterns observed today in the Balkans was added and previously overlooked aspects of the species biology were highlighted. ? 2013 Springer Science+Business Media Dordrecht.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The European hare populations of the Balkan Peninsula comprise two divergent phylogenetic lineages with discrete geographical distribution slightly overlapping in the area of northeastern Greece and Bulgaria. Here we elucidate their contact zone, by defining the spatial distributional pattern of the two highly divergent groups, detecting individuals of hybrid origin, and identifying genetic barriers present in the area of their co-existence. Specimens from northeastern Greece were assayed for lineage assignment and population genetic inference based on a 511 bp fragment of mitochondrial DNA control region and allelic data from 10 microsatellite loci. Bayesian analyses on original and simulated genotypes were performed allowing for the contact zone delineation. Our results indicate high genetic diversity in both nuclear and mitochondrial DNA, strong population structure and non random spatial distribution of the differentiated gene pools. The information provided by the two types of molecular markers yielded consistent results. This study comprises a fine scale analysis of the contact zone between the two evolutionary lineages of European brown hares in northeastern Greece. Specific questions on the spatial patterns where addressed for the first time. Furthermore, hypotheses regarding the presence of hybrids were also tested. As a result, interpretive power to the diversity patterns observed today in the Balkans was added and previously overlooked aspects of the species biology were highlighted. ? 2013 Springer Science+Business Media Dordrecht.
Daskalakis, M I; Magoulas, A; Kotoulas, G; Catsikis, I; Bakolas, A; Karageorgis, A P; Mavridou, A; Doulia, D; Rigas, F
Pseudomonas, Pantoea and Cupriavidus isolates induce calcium carbonate precipitation for biorestoration of ornamental stone Journal Article
In: Journal of Applied Microbiology, vol. 115, no. 2, pp. 409–423, 2013, ISSN: 13645072.
@article{daskalakis_pseudomonas_2013,
title = {Pseudomonas, Pantoea and Cupriavidus isolates induce calcium carbonate precipitation for biorestoration of ornamental stone},
author = {M I Daskalakis and A Magoulas and G Kotoulas and I Catsikis and A Bakolas and A P Karageorgis and A Mavridou and D Doulia and F Rigas},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84880592623&doi=10.1111%2fjam.12234&partnerID=40&md5=ff0439bcd9c18b73d46fd4b0d361e34d},
doi = {10.1111/jam.12234},
issn = {13645072},
year = {2013},
date = {2013-01-01},
journal = {Journal of Applied Microbiology},
volume = {115},
number = {2},
pages = {409--423},
abstract = {Aims: Bacterially induced calcium carbonate precipitation from various isolates was investigated aiming at developing an environmentally friendly technique for ornamental stone protection and restoration. Methods and Results: Micro-organisms isolated from stone samples and identified using 16S rDNA and biochemical tests promoted calcium carbonate precipitation in solid and novel liquid growth media. Biomineral morphology was studied on marble samples with scanning electron microscopy. Most isolates demonstrated specimen weight increase, covering partially or even completely the marble surfaces mainly with vaterite. The conditions under which vaterite precipitated and its stability throughout the experimental runs are presented. Conclusions: A growth medium that facilitated bacterial growth of different species and promoted biomineralization was formulated. Most isolates induced biomineralization of CaCO3. Micro-organisms may actually be a milestone in the investigation of vaterite formation facilitating our understanding of geomicrobiological interactions. Pseudomonas, Pantoea and Cupriavidus strains could be candidates for bioconsolidation of ornamental stone protection. Significance and Impact of the Study: Characterization of biomineralization capacity of different bacterial species improves understanding of the bacterially induced mineralization processes and enriches the list of candidates for biorestoration applications. Knowledge of biomineral morphology assists in differentiating mineral from biologically induced precipitates. © 2013 The Society for Applied Microbiology.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Aims: Bacterially induced calcium carbonate precipitation from various isolates was investigated aiming at developing an environmentally friendly technique for ornamental stone protection and restoration. Methods and Results: Micro-organisms isolated from stone samples and identified using 16S rDNA and biochemical tests promoted calcium carbonate precipitation in solid and novel liquid growth media. Biomineral morphology was studied on marble samples with scanning electron microscopy. Most isolates demonstrated specimen weight increase, covering partially or even completely the marble surfaces mainly with vaterite. The conditions under which vaterite precipitated and its stability throughout the experimental runs are presented. Conclusions: A growth medium that facilitated bacterial growth of different species and promoted biomineralization was formulated. Most isolates induced biomineralization of CaCO3. Micro-organisms may actually be a milestone in the investigation of vaterite formation facilitating our understanding of geomicrobiological interactions. Pseudomonas, Pantoea and Cupriavidus strains could be candidates for bioconsolidation of ornamental stone protection. Significance and Impact of the Study: Characterization of biomineralization capacity of different bacterial species improves understanding of the bacterially induced mineralization processes and enriches the list of candidates for biorestoration applications. Knowledge of biomineral morphology assists in differentiating mineral from biologically induced precipitates. © 2013 The Society for Applied Microbiology.
Loukovitis, D; Batargias, C; Sarropoulou, E; Apostolidis, A P; Kotoulas, G; Magoulas, A; Tsigenopoulos, C S; Chatziplis, D
Quantitative trait loci affecting morphology traits in gilthead seabream (Sparus aurata L.) Journal Article
In: Animal Genetics, vol. 44, no. 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.
Polymenakou, P N; Nomikou, P; Mandalakis, M; Kilias, S P; Christakis, C; Kyrpides, N; Ivanova, N; Oulas, A; Dailianis, Thanos; Carey, S; Kotoulas, G; Magoulas, A; Papanikolaou, D
Microbiological exploration of a unique CO2-rich shallow submarine hydrothermal vent field (Kolumbo, Santorini island, Aegean Sea) Proceedings Article
In: Heraklion Crete, Greece, 2013, (Publication Title: Mediterranean Marine Biodiversity Conference Type: Oral Presentation).
@inproceedings{polymenakou_microbiological_2013,
title = {Microbiological exploration of a unique CO2-rich shallow submarine hydrothermal vent field (Kolumbo, Santorini island, Aegean Sea)},
author = {P N Polymenakou and P Nomikou and M Mandalakis and S P Kilias and C Christakis and N Kyrpides and N Ivanova and A Oulas and Thanos Dailianis and S Carey and G Kotoulas and A Magoulas and D Papanikolaou},
year = {2013},
date = {2013-01-01},
address = {Heraklion Crete, Greece},
note = {Publication Title: Mediterranean Marine Biodiversity Conference
Type: Oral Presentation},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Oulas, Anastasis; Polymenakou, Paraskevi N; Mandalakis, Manolis; Nomikou, Paraskevi; Carey, Steven; Christakis, Christos; Kotoulas, Georgios; Magoulas, Antonios; Tripp, James H; Espino, David Paez A; Ivanova, Natalia N; Kyrpides, Nikos C
Metagenomics of microbial communities inhabiting the Kolumbo volcano shallow-sea hydrothermal vent field and Santorini (caldera) Proceedings Article
In: 2013, (Publication Title: The 8th conference of the Hellenic Society for Computational Biology and Bioinformatics - HSCBB13).
@inproceedings{oulas_metagenomics_2013,
title = {Metagenomics of microbial communities inhabiting the Kolumbo volcano shallow-sea hydrothermal vent field and Santorini (caldera)},
author = {Anastasis Oulas and Paraskevi N Polymenakou and Manolis Mandalakis and Paraskevi Nomikou and Steven Carey and Christos Christakis and Georgios Kotoulas and Antonios Magoulas and James H Tripp and David Paez A Espino and Natalia N Ivanova and Nikos C Kyrpides},
year = {2013},
date = {2013-01-01},
note = {Publication Title: The 8th conference of the Hellenic Society for Computational Biology and Bioinformatics - HSCBB13},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Antoniou, Aglaia; Magoulas, Antonios
Application of Mitochondrial DNA in Stock Identification Book Section
In: Stock Identification Methods: Applications in Fishery Science: Second Edition, 2013, ISBN: 978-0-12-397003-9.
@incollection{antoniou_application_2013,
title = {Application of Mitochondrial DNA in Stock Identification},
author = {Aglaia Antoniou and Antonios Magoulas},
doi = {10.1016/B978-0-12-397003-9.00013-8},
isbn = {978-0-12-397003-9},
year = {2013},
date = {2013-01-01},
booktitle = {Stock Identification Methods: Applications in Fishery Science: Second Edition},
abstract = {Biological studies in the marine realm face some great challenges associated with the special attributes of the marine environment, in addition to the acceleration of environmental changes that increase the astounding rate of biodiversity loss. Molecular genetics has made some remarkable contributions to our understanding of populations, providing novel insights into previously inaccessible aspects of the natural history of marine organisms. Mitochondrial DNA (mtDNA) has proven to be an invaluable tool in species and stock identification as a population-genetic, phylogeographic, and phylogenetic marker. However, understanding the forces that drive the molecular evolution of mtDNA is necessary for the proper use of this molecule for stock and species identification by recognizing and avoiding potential pitfalls in data interpretation. mtDNA data are best interpreted under a more holistic framework, in which information from nuclear DNA as well as on the zoogeography, biology, and life history of the taxon under study are also taken into account. Information on the geological history, hydrographic characteristics, and present environmental conditions of the area under consideration is also of great importance. The main methods used for raw data acquisition, analysis, and interpretation are briefly illustrated in this chapter. mtDNA data, despite recent challenges, remain a mainstay of phylogenetic studies at different levels of divergence. The advantages outlined in this chapter depend not only on the biological attributes of mtDNA but also on the application of sophisticated statistical approaches to the data, the development of methods for extracting demographic information from gene genealogies, and the critical approach of the researcher. ?? 2014 Elsevier Inc. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
Biological studies in the marine realm face some great challenges associated with the special attributes of the marine environment, in addition to the acceleration of environmental changes that increase the astounding rate of biodiversity loss. Molecular genetics has made some remarkable contributions to our understanding of populations, providing novel insights into previously inaccessible aspects of the natural history of marine organisms. Mitochondrial DNA (mtDNA) has proven to be an invaluable tool in species and stock identification as a population-genetic, phylogeographic, and phylogenetic marker. However, understanding the forces that drive the molecular evolution of mtDNA is necessary for the proper use of this molecule for stock and species identification by recognizing and avoiding potential pitfalls in data interpretation. mtDNA data are best interpreted under a more holistic framework, in which information from nuclear DNA as well as on the zoogeography, biology, and life history of the taxon under study are also taken into account. Information on the geological history, hydrographic characteristics, and present environmental conditions of the area under consideration is also of great importance. The main methods used for raw data acquisition, analysis, and interpretation are briefly illustrated in this chapter. mtDNA data, despite recent challenges, remain a mainstay of phylogenetic studies at different levels of divergence. The advantages outlined in this chapter depend not only on the biological attributes of mtDNA but also on the application of sophisticated statistical approaches to the data, the development of methods for extracting demographic information from gene genealogies, and the critical approach of the researcher. ?? 2014 Elsevier Inc. All rights reserved.
2012
Vogiatzi, E; Hanel, R; Dailianis, Thanos; Lagnel, J; Hassan, M; Magoulas, A; Tsigenopoulos, C S
In: Biochemical Systematics and Ecology, vol. 44, pp. 279 – 285, 2012.
@article{vogiatzi_description_2012,
title = {Description of microsatellite markers in four mullids based on the development and cross-species amplification of 18 new markers in red mullet (Mullus barbatus)},
author = {E Vogiatzi and R Hanel and Thanos Dailianis and J Lagnel and M Hassan and A Magoulas and C S Tsigenopoulos},
url = {http://www.sciencedirect.com/science/article/pii/S0305197812001184},
doi = {10.1016/j.bse.2012.06.006},
year = {2012},
date = {2012-01-01},
journal = {Biochemical Systematics and Ecology},
volume = {44},
pages = {279 -- 285},
abstract = {We investigated the transferability and characterized the genetic diversity of 18 microsatellite markers newly developed for the red mullet (Mullus barbatus) in populations of four different species of the Mullidae family: the striped red mullet (Mullus surmuletus), the golden-banded goatfish (Upeneus moluccensis), the West African goatfish (Pseudupeneus prayensis) and the yellow goatfish (Mulloidichthys martinicus). Results indicate that the loci are polymorphic to different extent in M. surmuletus (94%), U. moluccensis (83%), P. prayensis (78%), and M. martinicus (67%). The high rates of successful cross-amplification of microsatellite loci among Mullidae species will offer excellent opportunities to investigate the genetic structure of wild populations, to explore their conservation genetics and fisheries management and to study any future interaction and introgression between them. © 2012 Elsevier Ltd.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We investigated the transferability and characterized the genetic diversity of 18 microsatellite markers newly developed for the red mullet (Mullus barbatus) in populations of four different species of the Mullidae family: the striped red mullet (Mullus surmuletus), the golden-banded goatfish (Upeneus moluccensis), the West African goatfish (Pseudupeneus prayensis) and the yellow goatfish (Mulloidichthys martinicus). Results indicate that the loci are polymorphic to different extent in M. surmuletus (94%), U. moluccensis (83%), P. prayensis (78%), and M. martinicus (67%). The high rates of successful cross-amplification of microsatellite loci among Mullidae species will offer excellent opportunities to investigate the genetic structure of wild populations, to explore their conservation genetics and fisheries management and to study any future interaction and introgression between them. © 2012 Elsevier Ltd.
Kasapidis, P; Silva, A; Zampicinini, G; Magoulas, A
In: Scientia Marina, vol. 76, no. 1, pp. 123–132, 2012, ISSN: 02148358.
@article{kasapidis_evidence_2012,
title = {Evidence for microsatellite hitchhiking selection in European sardine (Sardina pilchardus) and implications in inferring stock structure [Evidencia para selección hitchhiking de microsatélite en sardina europea (Sardina pilchardus) y las implicaciones para inferir la estructura del stock]},
author = {P Kasapidis and A Silva and G Zampicinini and A Magoulas},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84857560434&doi=10.3989%2fscimar.03366.29B&partnerID=40&md5=e9dfcaa4674c55f68be14a06ce7e34b1},
doi = {10.3989/scimar.03366.29B},
issn = {02148358},
year = {2012},
date = {2012-01-01},
journal = {Scientia Marina},
volume = {76},
number = {1},
pages = {123--132},
abstract = {The genetic structure of the European sardine (Sardina pilchardus) was assessed throughout its geographic range using five microsatellite loci. One of the loci seemed to be under hitchhiking selection and exhibited a latitudinal cline along the eastern Atlantic, with abrupt change in allele frequencies from the Alboran Sea to the western Mediterranean and from the east Atlantic coast to the Azores and Madeira. This pattern was very similar to that previously described for the allozymic locus SOD * and these 2 loci could be linked. A Bayesian analysis of environmental factors with the genetic data indicated temperature as a potential selection factor. Selection pressure may be stronger at the southern limit of sardine distribution, because heterozygosity of the non-neutral locus was much lower there. The abrupt change in allele frequencies of the non-neutral locus in certain regions seem to be related more to strong barriers to gene flow, which were not evident for neutral loci, than to abrupt changes in selection pressure. These areas of discontinuity provide a guideline to define and delineate genetic stocks and are generally consistent with areas of phenotypic change in sardine, but they are not in concordance with the currently recognized morphological subspecies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The genetic structure of the European sardine (Sardina pilchardus) was assessed throughout its geographic range using five microsatellite loci. One of the loci seemed to be under hitchhiking selection and exhibited a latitudinal cline along the eastern Atlantic, with abrupt change in allele frequencies from the Alboran Sea to the western Mediterranean and from the east Atlantic coast to the Azores and Madeira. This pattern was very similar to that previously described for the allozymic locus SOD * and these 2 loci could be linked. A Bayesian analysis of environmental factors with the genetic data indicated temperature as a potential selection factor. Selection pressure may be stronger at the southern limit of sardine distribution, because heterozygosity of the non-neutral locus was much lower there. The abrupt change in allele frequencies of the non-neutral locus in certain regions seem to be related more to strong barriers to gene flow, which were not evident for neutral loci, than to abrupt changes in selection pressure. These areas of discontinuity provide a guideline to define and delineate genetic stocks and are generally consistent with areas of phenotypic change in sardine, but they are not in concordance with the currently recognized morphological subspecies.
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
In: Aquaculture Research, vol. 43, no. 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.
Christodoulou, Magdalini; Antoniou, Aglaia; Magoulas, Antonios; Koukouras, Athanasios
Revision of the freshwater genus Atyaephyra (Crustacea, Decapoda, Atyidae) based on morphological and molecular data Journal Article
In: ZooKeys, 2012, ISSN: 13132989, (ISBN: 1313-2989).
@article{christodoulou_revision_2012,
title = {Revision of the freshwater genus Atyaephyra (Crustacea, Decapoda, Atyidae) based on morphological and molecular data},
author = {Magdalini Christodoulou and Aglaia Antoniou and Antonios Magoulas and Athanasios Koukouras},
doi = {10.3897/zookeys.229.3919},
issn = {13132989},
year = {2012},
date = {2012-01-01},
journal = {ZooKeys},
abstract = {Atyaephyra de Brito Capello, 1867 was described from the Mediterranean region almost 200 years ago. Since then, the genus has been recorded from various freshwater habitats in Europe, North Africa and the Middle East. Despite its long history, the taxonomic status of Atyaephyra species remains confusing and uncertain. Consequently numerous specimens from the known range of Atyaephyra were analysed using morphological characters and mitochondrial COI sequences in an attempt to clarify the taxonomy of this genus. The present study recognises seven Atyaephyra species, more than twice as many as previously recorded (three), four of which are considered as new. The new species are described, additional information to the original descriptions are provided for the remaining three taxa, while neotypes of Atyaephyra desmarestii Millet, 1831 and Atyaephyra stankoi Karaman, 1972 are designated to stabilize their taxonomy. Non-overlapping distinguishing morphological characters are used to discriminate the examined material into five species, e.g., Atyaephyra desmarestii, Atyaephyra stankoi, Atyaephyra orientalis Bouvier, 1913, Atyaephyra thyamisensissp. n., Atyaephyra strymonensissp. n. In addition, the genetic analysis supports the existence of multiple phylogenetic clades in the broader Mediterranean area and distinguishes two new cryptic species, namely Atyaephyra tuerkayisp. n. and Atyaephyra acheronensissp. n. The geographic distribution of these species is confirmed and their phylogenetic relationships are described.},
note = {ISBN: 1313-2989},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Atyaephyra de Brito Capello, 1867 was described from the Mediterranean region almost 200 years ago. Since then, the genus has been recorded from various freshwater habitats in Europe, North Africa and the Middle East. Despite its long history, the taxonomic status of Atyaephyra species remains confusing and uncertain. Consequently numerous specimens from the known range of Atyaephyra were analysed using morphological characters and mitochondrial COI sequences in an attempt to clarify the taxonomy of this genus. The present study recognises seven Atyaephyra species, more than twice as many as previously recorded (three), four of which are considered as new. The new species are described, additional information to the original descriptions are provided for the remaining three taxa, while neotypes of Atyaephyra desmarestii Millet, 1831 and Atyaephyra stankoi Karaman, 1972 are designated to stabilize their taxonomy. Non-overlapping distinguishing morphological characters are used to discriminate the examined material into five species, e.g., Atyaephyra desmarestii, Atyaephyra stankoi, Atyaephyra orientalis Bouvier, 1913, Atyaephyra thyamisensissp. n., Atyaephyra strymonensissp. n. In addition, the genetic analysis supports the existence of multiple phylogenetic clades in the broader Mediterranean area and distinguishes two new cryptic species, namely Atyaephyra tuerkayisp. n. and Atyaephyra acheronensissp. n. The geographic distribution of these species is confirmed and their phylogenetic relationships are described.
2011
Loukovitis, D; Sarropoulou, E; Tsigenopoulos, C S; Batargias, C; Magoulas, A; Apostolidis, A P; Chatziplis, D; Kotoulas, G
Quantitative Trait Loci involved in sex determination and body growth in the gilthead sea bream (Sparus aurata L.) through targeted genome scan Journal Article
In: PLoS ONE, vol. 6, no. 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.
Vogiatzi, E; Lagnel, J; Pakaki, V; Louro, B; Canario, A V. M.; Reinhardt, R; Kotoulas, G; Magoulas, A; Tsigenopoulos, C S
In: Marine Genomics, vol. 4, no. 2, pp. 83–91, 2011, ISSN: 18747787.
@article{vogiatzi_silico_2011,
title = {In silico mining and characterization of simple sequence repeats from gilthead sea bream (Sparus aurata) expressed sequence tags (EST-SSRs); PCR amplification, polymorphism evaluation and multiplexing and cross-species assays},
author = {E Vogiatzi and J Lagnel and V Pakaki and B Louro and A V.M. Canario and R Reinhardt and G Kotoulas and A Magoulas and C S Tsigenopoulos},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79956354483&doi=10.1016%2fj.margen.2011.01.003&partnerID=40&md5=3775ee5dbda814501d9fd8660740563b},
doi = {10.1016/j.margen.2011.01.003},
issn = {18747787},
year = {2011},
date = {2011-01-01},
journal = {Marine Genomics},
volume = {4},
number = {2},
pages = {83--91},
abstract = {We screened for simple sequence repeats (SSRs) found in ESTs derived from an EST-database development project ('Marine Genomics Europe' Network of Excellence). Different motifs of di-, tri-, tetra-, penta- and hexanucleotide SSRs were evaluated for variation in length and position in the expressed sequences, relative abundance and distribution in gilthead sea bream (Sparus aurata). We found 899 ESTs that harbor 997 SSRs (4.94%). On average, one SSR was found per 2.95. kb of EST sequence and the dinucleotide SSRs are the most abundant accounting for 47.6% of the total number.EST-SSRs were used as template for primer design. 664 primer pairs could be successfully identified and a subset of 206 pairs of primers was synthesized, PCR-tested and visualized on ethidium bromide stained agarose gels. The main objective was to further assess the potential of EST-SSRs as informative markers and investigate their cross-species amplification in sixteen teleost fish species: seven sparid species and nine other species from different families. Approximately 78% of the primer pairs gave PCR products of expected size in gilthead sea bream, and as expected, the rate of successful amplification of sea bream EST-SSRs was higher in sparids, lower in other perciforms and even lower in species of the Clupeiform and Gadiform orders. We finally determined the polymorphism and the heterozygosity of 63 markers in a wild gilthead sea bream population; fifty-eight loci were found to be polymorphic with the expected heterozygosity and the number of alleles ranging from 0.089 to 0.946 and from 2 to 27, respectively. These tools and markers are expected to enhance the available genetic linkage map in gilthead sea bream, to assist comparative mapping and genome analyses for this species and further with other model fish species and finally to help advance genetic analysis for cultivated and wild populations and accelerate breeding programs. © 2011 Elsevier B.V.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We screened for simple sequence repeats (SSRs) found in ESTs derived from an EST-database development project ('Marine Genomics Europe' Network of Excellence). Different motifs of di-, tri-, tetra-, penta- and hexanucleotide SSRs were evaluated for variation in length and position in the expressed sequences, relative abundance and distribution in gilthead sea bream (Sparus aurata). We found 899 ESTs that harbor 997 SSRs (4.94%). On average, one SSR was found per 2.95. kb of EST sequence and the dinucleotide SSRs are the most abundant accounting for 47.6% of the total number.EST-SSRs were used as template for primer design. 664 primer pairs could be successfully identified and a subset of 206 pairs of primers was synthesized, PCR-tested and visualized on ethidium bromide stained agarose gels. The main objective was to further assess the potential of EST-SSRs as informative markers and investigate their cross-species amplification in sixteen teleost fish species: seven sparid species and nine other species from different families. Approximately 78% of the primer pairs gave PCR products of expected size in gilthead sea bream, and as expected, the rate of successful amplification of sea bream EST-SSRs was higher in sparids, lower in other perciforms and even lower in species of the Clupeiform and Gadiform orders. We finally determined the polymorphism and the heterozygosity of 63 markers in a wild gilthead sea bream population; fifty-eight loci were found to be polymorphic with the expected heterozygosity and the number of alleles ranging from 0.089 to 0.946 and from 2 to 27, respectively. These tools and markers are expected to enhance the available genetic linkage map in gilthead sea bream, to assist comparative mapping and genome analyses for this species and further with other model fish species and finally to help advance genetic analysis for cultivated and wild populations and accelerate breeding programs. © 2011 Elsevier B.V.
Sarropoulou, E; Nousdili, D; Kotoulas, G; Magoulas, A
Functional Divergences of GAPDH Isoforms During Early Development in Two Perciform Fish Species Journal Article
In: Marine Biotechnology, vol. 13, no. 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.
Kasapidis, P; Kristoffersen, JB; Pakaki, V; Magoulas, A
The puzzling phylogeographic history of the European anchovy (Engraulis encrasicolus) Proceedings Article
In: Kasapidis, P (Ed.): 5th Biennial Conference of the International Biogeography Society, Heraklion, Greece, 2011.
@inproceedings{kasapidis_puzzling_2011,
title = {The puzzling phylogeographic history of the European anchovy (Engraulis encrasicolus)},
author = {P Kasapidis and JB Kristoffersen and V Pakaki and A Magoulas},
editor = {P Kasapidis},
year = {2011},
date = {2011-01-01},
booktitle = {5th Biennial Conference of the International Biogeography Society},
address = {Heraklion, Greece},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
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
In: Journal of Biomedicine and Biotechnology, vol. 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
Kochzius, Marc; Seidel, Christian; Antoniou, Aglaia; Botla, Sandeep Kumar; Campo, Daniel; Cariani, Alessia; Vazquez, Eva Garcia; Hauschild, Janet; Hervet, Caroline; Hjörleifsdottir, Sigridur; Hreggvidsson, Gudmundur; Kappel, Kristina; Landi, Monica; Magoulas, Antonios; Marteinsson, Viggo; Nölte, Manfred; Planes, Serge; Tinti, Fausto; Turan, Cemal; Venugopal, Moleyur N; Weber, Hannes; Blohm, Dietmar
Identifying Fishes through DNA Barcodes and Microarrays Journal Article
In: PLoS ONE, vol. 5, no. 9, pp. e12620, 2010, ISSN: 1932-6203.
@article{kochzius_identifying_2010,
title = {Identifying Fishes through DNA Barcodes and Microarrays},
author = {Marc Kochzius and Christian Seidel and Aglaia Antoniou and Sandeep Kumar Botla and Daniel Campo and Alessia Cariani and Eva Garcia Vazquez and Janet Hauschild and Caroline Hervet and Sigridur Hjörleifsdottir and Gudmundur Hreggvidsson and Kristina Kappel and Monica Landi and Antonios Magoulas and Viggo Marteinsson and Manfred Nölte and Serge Planes and Fausto Tinti and Cemal Turan and Moleyur N Venugopal and Hannes Weber and Dietmar Blohm},
editor = {Robert DeSalle},
url = {https://dx.plos.org/10.1371/journal.pone.0012620},
doi = {10.1371/journal.pone.0012620},
issn = {1932-6203},
year = {2010},
date = {2010-09-01},
urldate = {2020-08-09},
journal = {PLoS ONE},
volume = {5},
number = {9},
pages = {e12620},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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
In: Molecular Phylogenetics and Evolution, vol. 55, no. 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.
Louro, B; Passos, Ana Lúcia S; Souche, Erika L; Tsigenopoulos, C S; Beck, Alfred; Lagnel, J; Bonhomme, F; Cancela, Leonor; Cerdà, Joan; Clark, Melody S; Lubzens, Esther; A, Magoulas; Planas, Josep V; Volckaert, F A; Reinhardt, Richard; Canario, Adelino V M
In: Marine Genomics, vol. 3, no. 3-4, pp. 179–191, 2010, (ISBN: 1874-7787).
@article{louro_gilthead_2010,
title = {Gilthead sea bream (Sparus auratus) and European sea bass (Dicentrarchus labrax) expressed sequence tags: Characterization, tissue-specific expression and gene markers},
author = {B Louro and Ana Lúcia S Passos and Erika L Souche and C S Tsigenopoulos and Alfred Beck and J Lagnel and F Bonhomme and Leonor Cancela and Joan Cerdà and Melody S Clark and Esther Lubzens and Magoulas A and Josep V Planas and F A Volckaert and Richard Reinhardt and Adelino V M Canario},
url = {http://www.sciencedirect.com/science/article/B8JG7-5166W0F-1/2/a82e89b3bb9d10e05933287d876117af},
year = {2010},
date = {2010-01-01},
journal = {Marine Genomics},
volume = {3},
number = {3-4},
pages = {179--191},
abstract = {The gilthead sea bream, Sparus auratus, and the European sea bass, Dicentrarchus labrax, are two of the most important marine species cultivated in Southern Europe. This study aimed at increasing genomic resources for the two species and produced and annotated two sets of 30,000 expressed sequence tags (EST) each from 14 normalized tissue-specific cDNA libraries from sea bream and sea bass. Clustering and assembly of the ESTs formed 5268 contigs and 12,928 singletons for sea bream and 4573 contigs and 13,143 singletons for sea bass, representing 18,196 and 17,716 putative unigenes, respectively. Assuming a similar number of genes in sea bass, sea bream and in the model fish Gasterosteus aculeatus genomes, it was estimated that approximately two thirds of the sea bream and the sea bass transcriptomes were covered by the unigene collections. BLAST sequence similarity searches (using a cut off of e-value textless 10-5) against fully the curated SwissProt (and TrEMBL) databases produced matches of 28%(37%) and 43%(53%) of the sea bream and sea bass unigene datasets respectively, allowing some putative designation of function. A comparative approach is described using human Ensembl peptide ID homolog’s for functional annotation, which increased the number of unigenes with GO terms assigned and resulted in more GO terms assigned per unigene. This allowed the identification of tissue-specific genes using enrichment analysis for GO pathways and protein domains. The comparative annotation approach represents a good strategy for transferring more relevant biological information from highly studied species to genomic resource poorer species. It was possible to confirm by interspecies mRNA-to-genomic alignments 25 and 21 alternative splice events in sea bream and sea bass genes, respectively. Even using normalized cDNA from relatively few pooled individuals it was possible to identify 1145 SNPs and 1748 microsatellites loci for genetic marker development. The EST data are being applied to a range of projects, including the development microarrays, genetic and radiation hybrid maps and QTL genome scans. This highlights the important role of ESTs for generating genetic and genomic resources of aquaculture species.},
note = {ISBN: 1874-7787},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The gilthead sea bream, Sparus auratus, and the European sea bass, Dicentrarchus labrax, are two of the most important marine species cultivated in Southern Europe. This study aimed at increasing genomic resources for the two species and produced and annotated two sets of 30,000 expressed sequence tags (EST) each from 14 normalized tissue-specific cDNA libraries from sea bream and sea bass. Clustering and assembly of the ESTs formed 5268 contigs and 12,928 singletons for sea bream and 4573 contigs and 13,143 singletons for sea bass, representing 18,196 and 17,716 putative unigenes, respectively. Assuming a similar number of genes in sea bass, sea bream and in the model fish Gasterosteus aculeatus genomes, it was estimated that approximately two thirds of the sea bream and the sea bass transcriptomes were covered by the unigene collections. BLAST sequence similarity searches (using a cut off of e-value textless 10-5) against fully the curated SwissProt (and TrEMBL) databases produced matches of 28%(37%) and 43%(53%) of the sea bream and sea bass unigene datasets respectively, allowing some putative designation of function. A comparative approach is described using human Ensembl peptide ID homolog’s for functional annotation, which increased the number of unigenes with GO terms assigned and resulted in more GO terms assigned per unigene. This allowed the identification of tissue-specific genes using enrichment analysis for GO pathways and protein domains. The comparative annotation approach represents a good strategy for transferring more relevant biological information from highly studied species to genomic resource poorer species. It was possible to confirm by interspecies mRNA-to-genomic alignments 25 and 21 alternative splice events in sea bream and sea bass genes, respectively. Even using normalized cDNA from relatively few pooled individuals it was possible to identify 1145 SNPs and 1748 microsatellites loci for genetic marker development. The EST data are being applied to a range of projects, including the development microarrays, genetic and radiation hybrid maps and QTL genome scans. This highlights the important role of ESTs for generating genetic and genomic resources of aquaculture species.
2009
Cárdenas, Leyla; Silva, Andrea X; Magoulas, Antonios; Cabezas, Josefina; Poulin, Elie; Ojeda, Patricio F
Genetic population structure in the Chilean jack mackerel, Trachurus murphyi (Nichols) across the South-eastern Pacific Ocean Journal Article
In: Fisheries Research, vol. 100, no. 2, pp. 109–115, 2009, ISSN: 01657836.
@article{cardenas_genetic_2009,
title = {Genetic population structure in the Chilean jack mackerel, Trachurus murphyi (Nichols) across the South-eastern Pacific Ocean},
author = {Leyla Cárdenas and Andrea X Silva and Antonios Magoulas and Josefina Cabezas and Elie Poulin and Patricio F Ojeda},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0165783609001799},
doi = {10.1016/j.fishres.2009.06.013},
issn = {01657836},
year = {2009},
date = {2009-10-01},
urldate = {2020-08-09},
journal = {Fisheries Research},
volume = {100},
number = {2},
pages = {109--115},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sotiropoulos, K; Eleftherakos, K; Tsaparis, D; Kasapidis, P; Magoulas, A; Legakis, A
New polymorphic microsatellite loci for the Greek smooth newt, Lissotriton vulgaris graecus, and their utility in the nominotypical subspecies Journal Article
In: Molecular Ecology Resources, vol. 9, no. 1, pp. 292–295, 2009, ISSN: 1755098X.
@article{sotiropoulos_new_2009,
title = {New polymorphic microsatellite loci for the Greek smooth newt, Lissotriton vulgaris graecus, and their utility in the nominotypical subspecies},
author = {K Sotiropoulos and K Eleftherakos and D Tsaparis and P Kasapidis and A Magoulas and A Legakis},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-58949099095&doi=10.1111%2fj.1755-0998.2008.02245.x&partnerID=40&md5=541bd79e38722806c070c62462f9466a},
doi = {10.1111/j.1755-0998.2008.02245.x},
issn = {1755098X},
year = {2009},
date = {2009-01-01},
journal = {Molecular Ecology Resources},
volume = {9},
number = {1},
pages = {292--295},
abstract = {Eight polymorphic microsatellites were isolated from the Greek smooth newt (Lissotriton vulgaris graecus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)11 probe. The loci showed different variation patterns in a single breeding population (32 individuals) with mean number of alleles at 5.0 and mean observed heterozygosity at 0.520. The amplification success also in the nominotypical subspecies favours the use of these microsatellite loci in population genetic analyses as well as in the study of contact zones between smooth newt subspecies. © 2008 The Authors.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Eight polymorphic microsatellites were isolated from the Greek smooth newt (Lissotriton vulgaris graecus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)11 probe. The loci showed different variation patterns in a single breeding population (32 individuals) with mean number of alleles at 5.0 and mean observed heterozygosity at 0.520. The amplification success also in the nominotypical subspecies favours the use of these microsatellite loci in population genetic analyses as well as in the study of contact zones between smooth newt subspecies. © 2008 The Authors.
Kasapidis, P; Pakaki, V; Kotoulas, G; Magoulas, A
Isolation and characterization of 18 new polymorphic microsatellite loci for the swordfish, Xiphias gladius Journal Article
In: Molecular Ecology Resources, vol. 9, no. 5, pp. 1383–1386, 2009, ISSN: 1755098X.
@article{kasapidis_isolation_2009,
title = {Isolation and characterization of 18 new polymorphic microsatellite loci for the swordfish, Xiphias gladius},
author = {P Kasapidis and V Pakaki and G Kotoulas and A Magoulas},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-68949088416&doi=10.1111%2fj.1755-0998.2009.02665.x&partnerID=40&md5=1d9054fa754b8be29bee29ef86e5c592},
doi = {10.1111/j.1755-0998.2009.02665.x},
issn = {1755098X},
year = {2009},
date = {2009-01-01},
journal = {Molecular Ecology Resources},
volume = {9},
number = {5},
pages = {1383--1386},
abstract = {Eighteen microsatellite loci (13 di- and 5 tri-repeats) were isolated from swordfish and characterized in two populations from the Atlantic Ocean and Mediterranean Sea. The number of alleles per locus ranged from two to 29 and the observed heterozygosity from 0.302 to 0.953. All but one locus conformed to Hardy-Weinberg expectations and there was no evidence for linkage disequilibrium between loci. © 2009 Blackwell Publishing Ltd.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Eighteen microsatellite loci (13 di- and 5 tri-repeats) were isolated from swordfish and characterized in two populations from the Atlantic Ocean and Mediterranean Sea. The number of alleles per locus ranged from two to 29 and the observed heterozygosity from 0.302 to 0.953. All but one locus conformed to Hardy-Weinberg expectations and there was no evidence for linkage disequilibrium between loci. © 2009 Blackwell Publishing Ltd.
Pakaki, V; Magoulas, A; Kasapidis, P
New polymorphic microsatellite loci for population studies in the European anchovy, Engraulis encrasicolus (L.) Journal Article
In: Molecular Ecology Resources, vol. 9, no. 5, pp. 1406–1409, 2009, ISSN: 1755098X.
@article{pakaki_new_2009,
title = {New polymorphic microsatellite loci for population studies in the European anchovy, Engraulis encrasicolus (L.)},
author = {V Pakaki and A Magoulas and P Kasapidis},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-68949083365&doi=10.1111%2fj.1755-0998.2009.02681.x&partnerID=40&md5=0821f16843bcdc50f7b239e6b4e4aad9},
doi = {10.1111/j.1755-0998.2009.02681.x},
issn = {1755098X},
year = {2009},
date = {2009-01-01},
journal = {Molecular Ecology Resources},
volume = {9},
number = {5},
pages = {1406--1409},
abstract = {Eleven microsatellite loci were developed in the European anchovy, Engraulis encrasicolus, and tested in samples from two geographically distant populations (Atlantic and Mediterranean Sea). Number of alleles ranged from eight to 28 and observed heterozygosity from 0.440 to 0.920. There was no evidence of linkage disequilibrium, although two loci are indeed linked. All loci were in Hardy-Weinberg equilibrium, except for one locus in the Atlantic and two loci in the Mediterranean sample. These three loci plus two more showed evidence for null alleles. © 2009 Blackwell Publishing Ltd.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Eleven microsatellite loci were developed in the European anchovy, Engraulis encrasicolus, and tested in samples from two geographically distant populations (Atlantic and Mediterranean Sea). Number of alleles ranged from eight to 28 and observed heterozygosity from 0.440 to 0.920. There was no evidence of linkage disequilibrium, although two loci are indeed linked. All loci were in Hardy-Weinberg equilibrium, except for one locus in the Atlantic and two loci in the Mediterranean sample. These three loci plus two more showed evidence for null alleles. © 2009 Blackwell Publishing Ltd.
Kristoffersen, J B; Magoulas, A
Fluctuating asymmetry and fitness correlations in two Engraulis encrasicolus populations Journal Article
In: Journal of Fish Biology, vol. 75, no. 10, pp. 2723–2736, 2009, ISSN: 00221112.
@article{kristoffersen_fluctuating_2009,
title = {Fluctuating asymmetry and fitness correlations in two Engraulis encrasicolus populations},
author = {J B Kristoffersen and A Magoulas},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-75149159614&doi=10.1111%2Fj.1095-8649.2009.02473.x&partnerID=40&md5=e2390cc6c9f4ad9fc16c1101907979a6},
doi = {10.1111/j.1095-8649.2009.02473.x},
issn = {00221112},
year = {2009},
date = {2009-01-01},
journal = {Journal of Fish Biology},
volume = {75},
number = {10},
pages = {2723--2736},
abstract = {Correlations among several measures of fluctuating asymmetry (FA) and fitness-related variables were assessed in two populations of the European anchovy Engraulis encrasicolus with fast growth (Aegean Sea) and slow growth (Ionian Sea), respectively. FA levels were borderline significantly higher in the Ionian than in the Aegean for some variables. Variation in otolith shape (deviation from population norm) was lower in the Ionian than the Aegean, contrary to expectation. Within the Aegean, there was no relation between any of the FA indexes and fitness estimators, while in the Ionian a composite otolith FA index was significantly negatively correlated to standard length at age only in 2 year-old individuals. This difference between the Aegean and Ionian may have been related to the lower growth rate in the Ionian, as FA-fitness relations may be more apparent in less-beneficial environments. The absence of significant correlations in the Aegean and the low correlation in one age group in the Ionian suggests that FA is not a sensitive indicator of individual fitness in adult E. encrasicolus. © 2009 The Fisheries Society of the British Isles.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Correlations among several measures of fluctuating asymmetry (FA) and fitness-related variables were assessed in two populations of the European anchovy Engraulis encrasicolus with fast growth (Aegean Sea) and slow growth (Ionian Sea), respectively. FA levels were borderline significantly higher in the Ionian than in the Aegean for some variables. Variation in otolith shape (deviation from population norm) was lower in the Ionian than the Aegean, contrary to expectation. Within the Aegean, there was no relation between any of the FA indexes and fitness estimators, while in the Ionian a composite otolith FA index was significantly negatively correlated to standard length at age only in 2 year-old individuals. This difference between the Aegean and Ionian may have been related to the lower growth rate in the Ionian, as FA-fitness relations may be more apparent in less-beneficial environments. The absence of significant correlations in the Aegean and the low correlation in one age group in the Ionian suggests that FA is not a sensitive indicator of individual fitness in adult E. encrasicolus. © 2009 The Fisheries Society of the British Isles.
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
In: BMC Genomics, vol. 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
In: Comparative Biochemistry and Physiology - B Biochemistry and Molecular Biology, vol. 153, no. 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.
Vogiatzi, E; Kalogianni, E; Giakoumi, S; Magoulas, A; Tsigenopoulos, C S
In: Conservation Genetics Resources, vol. 1, no. 1, pp. 27–30, 2009, ISSN: 18777252.
@article{vogiatzi_characterization_2009,
title = {Characterization of polymorphic microsatellite markers in valencia letourneuxi (Valenciidae) and cross-amplification in two other cyprinodontiform species},
author = {E Vogiatzi and E Kalogianni and S Giakoumi and A Magoulas and C S Tsigenopoulos},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84859960931&doi=10.1007%2fs12686-009-9006-y&partnerID=40&md5=96676b3d404c991ab4b0a8a6952ba535},
doi = {10.1007/s12686-009-9006-y},
issn = {18777252},
year = {2009},
date = {2009-01-01},
journal = {Conservation Genetics Resources},
volume = {1},
number = {1},
pages = {27--30},
abstract = {Fourteen microsatellite loci were isolated from the critically endangered Corfu toothcarp Valencia letourneuxi using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC) probe. Nine of these loci were polymorphic in a V. letourneuxi population of 20 individuals (Vlychos stream) with mean number of alleles per locus = 2.55 and mean observed heterozygosity = 0.3447. Moreover, some of these 9 microsatellite markers and the remaining five loci, monomorphic in V. letourneuxi, were found to be polymorphic in the Spanish samaruc Valencia hispanica and the Mediterranean toothcarp Aphanius fasciatus. These microsatellite loci are expected to be used for population genetic analysis as well as studying the genetic diversity of this endangered species. © Springer Science+Business Media B.V. 2009.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fourteen microsatellite loci were isolated from the critically endangered Corfu toothcarp Valencia letourneuxi using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC) probe. Nine of these loci were polymorphic in a V. letourneuxi population of 20 individuals (Vlychos stream) with mean number of alleles per locus = 2.55 and mean observed heterozygosity = 0.3447. Moreover, some of these 9 microsatellite markers and the remaining five loci, monomorphic in V. letourneuxi, were found to be polymorphic in the Spanish samaruc Valencia hispanica and the Mediterranean toothcarp Aphanius fasciatus. These microsatellite loci are expected to be used for population genetic analysis as well as studying the genetic diversity of this endangered species. © Springer Science+Business Media B.V. 2009.
2008
Skaraki, K; Kotoulas, Giorgios; Nicolaidou, Artemis; A, Magoulas; Pantazidou, Adriani
Bacterial symbiosis in marine polychaete Hermodice carunculata Pallas 1766 Proceedings Article
In: Athens, Greece, 2008, (Publication Title: 1st National MikroBioKosmos Society Conference, Athens, Greece, 12-14 December).
@inproceedings{skaraki_bacterial_2008,
title = {Bacterial symbiosis in marine polychaete Hermodice carunculata Pallas 1766},
author = {K Skaraki and Giorgios Kotoulas and Artemis Nicolaidou and Magoulas A and Adriani Pantazidou},
year = {2008},
date = {2008-12-01},
address = {Athens, Greece},
note = {Publication Title: 1st National MikroBioKosmos Society Conference, Athens, Greece, 12-14 December},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Bouchenak-Khelladi, Yanis; Durand, Jean-Dominique; Magoulas, Antonios; Borsa, Philippe
Geographic structure of European anchovy: A nuclear-DNA study Journal Article
In: Journal of Sea Research, vol. 59, no. 4, pp. 269–278, 2008, ISSN: 13851101.
@article{bouchenak-khelladi_geographic_2008,
title = {Geographic structure of European anchovy: A nuclear-DNA study},
author = {Yanis Bouchenak-Khelladi and Jean-Dominique Durand and Antonios Magoulas and Philippe Borsa},
url = {https://linkinghub.elsevier.com/retrieve/pii/S1385110108000142},
doi = {10.1016/j.seares.2008.03.001},
issn = {13851101},
year = {2008},
date = {2008-08-01},
urldate = {2020-08-09},
journal = {Journal of Sea Research},
volume = {59},
number = {4},
pages = {269--278},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abaunza, P; Murta, A G; Campbell, N; Cimmaruta, R; Comesaña, A S; Dahle, G; Santamaría, M T García; Gordo, L S; Iversen, S A; MacKenzie, K; Magoulas, A; Mattiucci, S; Molloy, J; Nascetti, G; Pinto, A L; Quinta, R; Ramos, P; Sanjuan, A; Santos, A T; Stransky, C; Zimmermann, C
In: Fisheries Research, vol. 89, no. 2, pp. 196–209, 2008, ISSN: 01657836.
@article{abaunza_stock_2008,
title = {Stock identity of horse mackerel (Trachurus trachurus) in the Northeast Atlantic and Mediterranean Sea: Integrating the results from different stock identification approaches},
author = {P Abaunza and A G Murta and N Campbell and R Cimmaruta and A S Comesaña and G Dahle and M T García Santamaría and L S Gordo and S A Iversen and K MacKenzie and A Magoulas and S Mattiucci and J Molloy and G Nascetti and A L Pinto and R Quinta and P Ramos and A Sanjuan and A T Santos and C Stransky and C Zimmermann},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0165783607002470},
doi = {10.1016/j.fishres.2007.09.022},
issn = {01657836},
year = {2008},
date = {2008-02-01},
urldate = {2020-08-09},
journal = {Fisheries Research},
volume = {89},
number = {2},
pages = {196--209},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abaunza, P; Murta, A G; Campbell, N; Cimmaruta, R; Comesaña, A S; Dahle, G; Gallo, E; Santamaría, M T García; Gordo, L S; Iversen, S A; MacKenzie, K; Magoulas, A; Mattiucci, S; Molloy, J; Nascetti, G; Pinto, A L; Quinta, R; Ramos, P; Ruggi, A; Sanjuan, A; Santos, A T; Stransky, C; Zimmermann, C
Considerations on sampling strategies for an holistic approach to stock identification: The example of the HOMSIR project Journal Article
In: Fisheries Research, vol. 89, no. 2, pp. 104–113, 2008, ISSN: 01657836.
@article{abaunza_considerations_2008,
title = {Considerations on sampling strategies for an holistic approach to stock identification: The example of the HOMSIR project},
author = {P Abaunza and A G Murta and N Campbell and R Cimmaruta and A S Comesaña and G Dahle and E Gallo and M T García Santamaría and L S Gordo and S A Iversen and K MacKenzie and A Magoulas and S Mattiucci and J Molloy and G Nascetti and A L Pinto and R Quinta and P Ramos and A Ruggi and A Sanjuan and A T Santos and C Stransky and C Zimmermann},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0165783607002366},
doi = {10.1016/j.fishres.2007.09.020},
issn = {01657836},
year = {2008},
date = {2008-02-01},
urldate = {2020-08-09},
journal = {Fisheries Research},
volume = {89},
number = {2},
pages = {104--113},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kochzius, M; Nölte, M; Weber, H; Silkenbeumer, N; Hjörleifsdottir, S; Hreggvidsson, G O; Marteinsson, V; Kappel, K; Planes, S; Tinti, F; Magoulas, A; Vazquez, E Garcia; Turan, C; Hervet, C; Falgueras, D Campo; Antoniou, A; Landi, M; Blohm, D
DNA microarrays for identifying fishes Journal Article
In: Marine Biotechnology, 2008, ISSN: 14362228, (ISBN: 1436-2228).
@article{kochzius_dna_2008,
title = {DNA microarrays for identifying fishes},
author = {M Kochzius and M Nölte and H Weber and N Silkenbeumer and S Hjörleifsdottir and G O Hreggvidsson and V Marteinsson and K Kappel and S Planes and F Tinti and A Magoulas and E Garcia Vazquez and C Turan and C Hervet and D Campo Falgueras and A Antoniou and M Landi and D Blohm},
doi = {10.1007/s10126-007-9068-3},
issn = {14362228},
year = {2008},
date = {2008-01-01},
journal = {Marine Biotechnology},
abstract = {In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a “Fish Chip” for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products.},
note = {ISBN: 1436-2228},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a “Fish Chip” for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products.
Kasapidis, P; Magoulas, A
Development and application of microsatellite markers to address the population structure of the horse mackerel Trachurus trachurus Journal Article
In: Fisheries Research, vol. 89, no. 2, pp. 132–135, 2008, ISSN: 01657836.
@article{kasapidis_development_2008,
title = {Development and application of microsatellite markers to address the population structure of the horse mackerel Trachurus trachurus},
author = {P Kasapidis and A Magoulas},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-38749149338&doi=10.1016%2fj.fishres.2007.09.015&partnerID=40&md5=fbea467751d7c1a424f5a26938b8f88e},
doi = {10.1016/j.fishres.2007.09.015},
issn = {01657836},
year = {2008},
date = {2008-01-01},
journal = {Fisheries Research},
volume = {89},
number = {2},
pages = {132--135},
abstract = {The genetic structure of the horse mackerel Trachurus trachurus was studied over almost its entire distribution range by genotyping 16 samples for 4 microsatellite loci. No temporal or spatial genetic differentiation was detected. A few statistically significant pairwise differences were most probably of stochastic nature, since they do not reveal any specific pattern. The lack of genetic differentiation in horse mackerel probably reflects the large population size and lack of barriers to the gene flow. However, this result should be viewed with caution, given the relatively low number of loci used in this study. © 2007 Elsevier B.V. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The genetic structure of the horse mackerel Trachurus trachurus was studied over almost its entire distribution range by genotyping 16 samples for 4 microsatellite loci. No temporal or spatial genetic differentiation was detected. A few statistically significant pairwise differences were most probably of stochastic nature, since they do not reveal any specific pattern. The lack of genetic differentiation in horse mackerel probably reflects the large population size and lack of barriers to the gene flow. However, this result should be viewed with caution, given the relatively low number of loci used in this study. © 2007 Elsevier B.V. All rights reserved.
Sarropoulou, E; Nousdili, D; Magoulas, A; Kotoulas, G
Linking the genomes of nonmodel teleosts through comparative genomics Journal Article
In: Marine Biotechnology, vol. 10, no. 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.
Kyriazi, P; Poulakakis, N; Parmakelis, A; Crochet, P A; Moravec, J; Rastegar-Pouyani, N; Tsigenopoulos, C S; Magoulas, A; Mylonas, M; Lymberakis, P
Mitochondrial DNA reveals the genealogical history of the snake-eyed lizards (Ophisops elegans and O. occidentalis) (Sauria: Lacertidae) Journal Article
In: Molecular Phylogenetics and Evolution, vol. 49, pp. 795 – 805, 2008.
@article{kyriazi_mitochondrial_2008,
title = {Mitochondrial DNA reveals the genealogical history of the snake-eyed lizards (Ophisops elegans and O. occidentalis) (Sauria: Lacertidae)},
author = {P Kyriazi and N Poulakakis and A Parmakelis and P A Crochet and J Moravec and N Rastegar-Pouyani and C S Tsigenopoulos and A Magoulas and M Mylonas and P Lymberakis},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-56749105770&partnerID=40&md5=c1a7d994264c6871db3860528ab105bf},
year = {2008},
date = {2008-01-01},
journal = {Molecular Phylogenetics and Evolution},
volume = {49},
pages = {795 -- 805},
abstract = {The snake-eyed lizards of the genus Ophisops (Lacertidae) have been through a series of taxonomical revisions, but still their phylogenetic relationships remain uncertain. In the present study we estimate the phylogeographic structure of O. elegans across its distributional range and we evaluate the relationships between O. elegans and the sympatric, in North Africa, species O. occidentalis, using partial mtDNA sequences (16S rRNA, COI, and cyt b). All phylogenetic analyses produced topologically identical trees where extant populations of O. elegans and O. occidentalis were found polyphyletic. Taking into account all the potential causes of polyphyly (introgressive hybridization, incomplete lineage sorting, and imperfect taxonomy) we suggest the inaccurate taxonomy as the most likely explanation for the observed pattern. Our results stress the need for re-evaluation of the current taxonomical status of these species and their subspecies. Furthermore, our biogeographic analyses and the estimated time of divergences suggest a late Miocene diversification within these species, where the present distribution of O. elegans and O. occidentalis was the result of several dispersal and vicariant events, which are associated with climatic oscillations (the late Miocene aridification of Asia and northern Africa) and paleogeographic barriers of late Miocene and Pliocene period. © 2008.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The snake-eyed lizards of the genus Ophisops (Lacertidae) have been through a series of taxonomical revisions, but still their phylogenetic relationships remain uncertain. In the present study we estimate the phylogeographic structure of O. elegans across its distributional range and we evaluate the relationships between O. elegans and the sympatric, in North Africa, species O. occidentalis, using partial mtDNA sequences (16S rRNA, COI, and cyt b). All phylogenetic analyses produced topologically identical trees where extant populations of O. elegans and O. occidentalis were found polyphyletic. Taking into account all the potential causes of polyphyly (introgressive hybridization, incomplete lineage sorting, and imperfect taxonomy) we suggest the inaccurate taxonomy as the most likely explanation for the observed pattern. Our results stress the need for re-evaluation of the current taxonomical status of these species and their subspecies. Furthermore, our biogeographic analyses and the estimated time of divergences suggest a late Miocene diversification within these species, where the present distribution of O. elegans and O. occidentalis was the result of several dispersal and vicariant events, which are associated with climatic oscillations (the late Miocene aridification of Asia and northern Africa) and paleogeographic barriers of late Miocene and Pliocene period. © 2008.
Kristoffersen, J B; Magoulas, A
Population structure of anchovy Engraulis encrasicolus L. in the Mediterranean Sea inferred from multiple methods Journal Article
In: Fisheries Research, vol. 91, no. 2-3, pp. 187–195, 2008, ISSN: 01657836.
@article{kristoffersen_population_2008,
title = {Population structure of anchovy Engraulis encrasicolus L. in the Mediterranean Sea inferred from multiple methods},
author = {J B Kristoffersen and A Magoulas},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-43049181335&doi=10.1016%2Fj.fishres.2007.11.024&partnerID=40&md5=087aa04263c4eaca6aacfe6bc2fb92ae},
doi = {10.1016/j.fishres.2007.11.024},
issn = {01657836},
year = {2008},
date = {2008-01-01},
journal = {Fisheries Research},
volume = {91},
number = {2-3},
pages = {187--195},
abstract = {Population structure of anchovy, Engraulis encrasicolus L., in the northern Mediterranean was investigated using multiple methods. Variation in body shape, otolith shape and growth was investigated in samples from the central Aegean and Ionian Seas. Intron length polymorphism from nuclear DNA, and mitochondrial DNA variation was investigated for samples from these basins, as well as northern Adriatic (ADR) and Gulf of Lions (LION). Two lineages (clades) of mtDNA that co-occur in the populations of anchovy throughout the region were compared with respect to growth, body shape, otolith shape, and intron variation, to check for any reproductive isolation within areas between the clades. The two clades were not different in any of the investigated parameters and appear to be completely crossbreeding. There were significant differences among areas with regard to mtDNA clade proportions, nuclear allele frequencies, body shape and otolith shape, indicating that several reproductively isolated populations of anchovy exists in the northern Mediterranean. There was an overall fair to good agreement between population structures inferred from the different classes of markers. The mitotype variation indicated a larger population differentiation than the two nuclear DNA loci, which may be related to the uniparental transmission and the lack of recombination of mtDNA. © 2007 Elsevier B.V. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Population structure of anchovy, Engraulis encrasicolus L., in the northern Mediterranean was investigated using multiple methods. Variation in body shape, otolith shape and growth was investigated in samples from the central Aegean and Ionian Seas. Intron length polymorphism from nuclear DNA, and mitochondrial DNA variation was investigated for samples from these basins, as well as northern Adriatic (ADR) and Gulf of Lions (LION). Two lineages (clades) of mtDNA that co-occur in the populations of anchovy throughout the region were compared with respect to growth, body shape, otolith shape, and intron variation, to check for any reproductive isolation within areas between the clades. The two clades were not different in any of the investigated parameters and appear to be completely crossbreeding. There were significant differences among areas with regard to mtDNA clade proportions, nuclear allele frequencies, body shape and otolith shape, indicating that several reproductively isolated populations of anchovy exists in the northern Mediterranean. There was an overall fair to good agreement between population structures inferred from the different classes of markers. The mitotype variation indicated a larger population differentiation than the two nuclear DNA loci, which may be related to the uniparental transmission and the lack of recombination of mtDNA. © 2007 Elsevier B.V. All rights reserved.
Antoniou, Aglaia; Kotoulas, Georgios; Magoulas, Antonios; Alves, Paulo Célio
Evidence of autumn reproduction in female European hares (Lepus europaeus) from southern Europe Journal Article
In: European Journal of Wildlife Research, 2008, ISSN: 16124642, (ISBN: 1612-4642).
@article{antoniou_evidence_2008,
title = {Evidence of autumn reproduction in female European hares (Lepus europaeus) from southern Europe},
author = {Aglaia Antoniou and Georgios Kotoulas and Antonios Magoulas and Paulo Célio Alves},
doi = {10.1007/s10344-008-0182-y},
issn = {16124642},
year = {2008},
date = {2008-01-01},
journal = {European Journal of Wildlife Research},
abstract = {Information on reproductive biology of the European hare (Lepus europaeus) in different environmental and landscape conditions comprises part of fundamental knowledge regarding species' adaptive responses as well as many aspects of its biology. Most of the studies conducted on European hare reproduction are confined to midlatitude and northern populations, whereas no data exist on the indigenous southern populations. Here, we present information on reproductive characteristics of European hares inhabiting Mediterranean ecosystems on the island of Crete, Greece for two successive hunting seasons. Although the annual reproductive cycle of the species is well known, with an autumn sexual inactivity, the duration of this period is subjected to fluctuations in different years and for different areas. According to our data, hare populations of Crete present an autumn-early winter reproductive activity with high proportions of pregnant females observed in all the months of the study. Furthermore, the estimated mean litter size (1.54 SE +/- 0.07) while signed to the lowest values ever observed for European hares is similar to values obtained in continuous breeding species of the same genus, Lepus granatensis, Lepus corsicanus, Lepus (capensis) mediterraneus, and Lepus capensis also inhabiting warm climates. In conclusion, our results suggest that Cretan European hare populations exhibit a reproductively active period during autumn-early winter where proportions of pregnant females and litter size give a strong indication of a continuous reproduction throughout the year.},
note = {ISBN: 1612-4642},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Information on reproductive biology of the European hare (Lepus europaeus) in different environmental and landscape conditions comprises part of fundamental knowledge regarding species' adaptive responses as well as many aspects of its biology. Most of the studies conducted on European hare reproduction are confined to midlatitude and northern populations, whereas no data exist on the indigenous southern populations. Here, we present information on reproductive characteristics of European hares inhabiting Mediterranean ecosystems on the island of Crete, Greece for two successive hunting seasons. Although the annual reproductive cycle of the species is well known, with an autumn sexual inactivity, the duration of this period is subjected to fluctuations in different years and for different areas. According to our data, hare populations of Crete present an autumn-early winter reproductive activity with high proportions of pregnant females observed in all the months of the study. Furthermore, the estimated mean litter size (1.54 SE +/- 0.07) while signed to the lowest values ever observed for European hares is similar to values obtained in continuous breeding species of the same genus, Lepus granatensis, Lepus corsicanus, Lepus (capensis) mediterraneus, and Lepus capensis also inhabiting warm climates. In conclusion, our results suggest that Cretan European hare populations exhibit a reproductively active period during autumn-early winter where proportions of pregnant females and litter size give a strong indication of a continuous reproduction throughout the year.
Daskalakis, M; Rigas, F; A, Magoulas; Kotoulas, Giorgios; Katsikis, I; Bakolas, A; Karageorgis, A; Antoniou, A; Skaraki, K
Development of a biotechnological method for the restoration of stone monuments Proceedings Article
In: pp. 61–62, Athens, Greece, 2008, (Publication Title: 1st National MikroBioKosmos Society Conference, Athens, Greece, 12-14 December Type: Poster).
@inproceedings{daskalakis_development_2008,
title = {Development of a biotechnological method for the restoration of stone monuments},
author = {M Daskalakis and F Rigas and Magoulas A and Giorgios Kotoulas and I Katsikis and A Bakolas and A Karageorgis and A Antoniou and K Skaraki},
year = {2008},
date = {2008-01-01},
pages = {61--62},
address = {Athens, Greece},
note = {Publication Title: 1st National MikroBioKosmos Society Conference, Athens, Greece, 12-14 December
Type: Poster},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Dailianis, Thanos; Limborg, M; Hanel, R; Bekkevold, D; Lagnel, J; A, Magoulas; Tsigenopoulos, C S
Characterization of nine polymorphic microsatellite markers in sprat (Sprattus sprattus L.) Journal Article
In: Molecular Ecology Resources, vol. 8, no. 4, pp. 861–863, 2008, (ISBN: 1755-0998).
@article{dailianis_characterization_2008,
title = {Characterization of nine polymorphic microsatellite markers in sprat (Sprattus sprattus L.)},
author = {Thanos Dailianis and M Limborg and R Hanel and D Bekkevold and J Lagnel and Magoulas A and C S Tsigenopoulos},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1755-0998.2008.02091.x},
doi = {10.1111/j.1755-0998.2008.02091.x},
year = {2008},
date = {2008-01-01},
journal = {Molecular Ecology Resources},
volume = {8},
number = {4},
pages = {861--863},
abstract = {Nine polymorphic microsatellites were isolated from sprat (Sprattus sprattus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)12 probe. The loci showed different variation patterns in a Baltic Sea population (44 individuals) with mean number of alleles at 12.7 and mean observed heterozygosity at 0.78. These microsatellite loci are expected to be used for taxonomic considerations in sprat, stock differentiation and population genetic analysis.},
note = {ISBN: 1755-0998},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nine polymorphic microsatellites were isolated from sprat (Sprattus sprattus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)12 probe. The loci showed different variation patterns in a Baltic Sea population (44 individuals) with mean number of alleles at 12.7 and mean observed heterozygosity at 0.78. These microsatellite loci are expected to be used for taxonomic considerations in sprat, stock differentiation and population genetic analysis.
2007
Laurent, V; Caneco, B; Magoulas, A; Planes, S
Isolation by distance and selection effects on genetic structure of sardines Sardina pilchardus Walbaum Journal Article
In: Journal of Fish Biology, vol. 71, no. sa, pp. 1–17, 2007, ISSN: 0022-1112, 1095-8649.
@article{laurent_isolation_2007,
title = {Isolation by distance and selection effects on genetic structure of sardines Sardina pilchardus Walbaum},
author = {V Laurent and B Caneco and A Magoulas and S Planes},
url = {http://doi.wiley.com/10.1111/j.1095-8649.2007.01450.x},
doi = {10.1111/j.1095-8649.2007.01450.x},
issn = {0022-1112, 1095-8649},
year = {2007},
date = {2007-08-01},
urldate = {2020-08-09},
journal = {Journal of Fish Biology},
volume = {71},
number = {sa},
pages = {1--17},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kotoulas, G; Mejuto, J; Antoniou, A; Kasapidis, P; Tserpes, G; Piccineti, C; Peristeraki, P; Garcia-Cortes, B; Oikonomaki, K; la Serna, M J De; Magoulas, A
Global genetic structure of the swordfish Xiphias gladius, as revealed by microsatellite markers Journal Article
In: Collect. Vol. Sci. Pap. ICCAT, vol. 61, pp. 79–88, 2007.
@article{kotoulas_global_2007,
title = {Global genetic structure of the swordfish Xiphias gladius, as revealed by microsatellite markers},
author = {G Kotoulas and J Mejuto and A Antoniou and P Kasapidis and G Tserpes and C Piccineti and P Peristeraki and B Garcia-Cortes and K Oikonomaki and M J De la Serna and A Magoulas},
year = {2007},
date = {2007-01-01},
journal = {Collect. Vol. Sci. Pap. ICCAT},
volume = {61},
pages = {79--88},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kasapidis, P; Peristeraki, P; Tserpes, G; Magoulas, A
First record of the Lessepsian migrant Lagocephalus sceleratus (Gmelin 1789) (Osteichthyes: Tetraodontidae) in the Cretan Sea (Aegean, Greece) Journal Article
In: Aquatic Invasions, vol. 2, no. 1, pp. 71–73, 2007, ISSN: 17986540, (Publisher: Regional Euro-Asian Biological Invasions Centre).
@article{kasapidis_first_2007,
title = {First record of the Lessepsian migrant Lagocephalus sceleratus (Gmelin 1789) (Osteichthyes: Tetraodontidae) in the Cretan Sea (Aegean, Greece)},
author = {P Kasapidis and P Peristeraki and G Tserpes and A Magoulas},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-56949103595&doi=10.3391%2fai.2007.2.1.9&partnerID=40&md5=c4ba957c29ae825b2870dc9302e3daa6},
doi = {10.3391/ai.2007.2.1.9},
issn = {17986540},
year = {2007},
date = {2007-01-01},
journal = {Aquatic Invasions},
volume = {2},
number = {1},
pages = {71--73},
abstract = {The Lessepsian migrant fish Lagocephalus sceleratus was recorded for the first time in July and in December 2005 from the Cretan Sea (Aegean, Greece). The species identity was confirmed by both morphometric and genetic analyses. These records indicate that the species has established populations around the continental shelf of Crete. © 2007 The Author(s).},
note = {Publisher: Regional Euro-Asian Biological Invasions Centre},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The Lessepsian migrant fish Lagocephalus sceleratus was recorded for the first time in July and in December 2005 from the Cretan Sea (Aegean, Greece). The species identity was confirmed by both morphometric and genetic analyses. These records indicate that the species has established populations around the continental shelf of Crete. © 2007 The Author(s).
Chatziplis, D; Batargias, C; Tsigenopoulos, C S; Magoulas, A; Kollias, S; Kotoulas, G; Volckaert, F A M; Haley, C S
Mapping quantitative trait loci in European sea bass (Dicentrarchus labrax): The BASSMAP pilot study Journal Article
In: Aquaculture, vol. 272, no. SUPPL. 1, pp. S172–S182, 2007, ISSN: 00448486.
@article{chatziplis_mapping_2007,
title = {Mapping quantitative trait loci in European sea bass (Dicentrarchus labrax): The BASSMAP pilot study},
author = {D Chatziplis and C Batargias and C S Tsigenopoulos and A Magoulas and S Kollias and G Kotoulas and F A M Volckaert and C S Haley},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-36448952022&doi=10.1016%2fj.aquaculture.2007.08.022&partnerID=40&md5=f7a9a7535621e9b63de89635c3dcf961},
doi = {10.1016/j.aquaculture.2007.08.022},
issn = {00448486},
year = {2007},
date = {2007-01-01},
journal = {Aquaculture},
volume = {272},
number = {SUPPL. 1},
pages = {S172--S182},
abstract = {There are great opportunities for genetic improvement in recently domesticated aquaculture species. However, the lack of appropriate tools limits the application of advanced techniques including the mapping of quantitative trait loci (QTL) and marker-assisted selection (MAS). The recent development of a genetic linkage map for the European sea bass allows the application of such methods for the first time in this species. We report a pilot trial of QTL mapping in a commercial sea bass population as a precursor to the application of MAS. Fertilized eggs collected on a single spawning day produced a population composed of a few large families. Fish were grown under commercial conditions, slaughtered at approximately 470 g and measurements were taken for several traits. Parentage analysis showed that the population consisted of 26 full sib families, with a common dam and several sires. Seven microsatellite markers spanning the largest linkage group (LG1) were then genotyped in 27 parents and their 422 progeny, in order to perform a QTL scan using half-sib interval mapping approaches. Significant QTL affecting six morphometric traits including length and depth, are reported. The success of the procedure demonstrates that QTL analysis can be applied in this species and will contribute to the study and future improvement of traits associated with production, profitability and sustainability. © 2007 Elsevier B.V. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
There are great opportunities for genetic improvement in recently domesticated aquaculture species. However, the lack of appropriate tools limits the application of advanced techniques including the mapping of quantitative trait loci (QTL) and marker-assisted selection (MAS). The recent development of a genetic linkage map for the European sea bass allows the application of such methods for the first time in this species. We report a pilot trial of QTL mapping in a commercial sea bass population as a precursor to the application of MAS. Fertilized eggs collected on a single spawning day produced a population composed of a few large families. Fish were grown under commercial conditions, slaughtered at approximately 470 g and measurements were taken for several traits. Parentage analysis showed that the population consisted of 26 full sib families, with a common dam and several sires. Seven microsatellite markers spanning the largest linkage group (LG1) were then genotyped in 27 parents and their 422 progeny, in order to perform a QTL scan using half-sib interval mapping approaches. Significant QTL affecting six morphometric traits including length and depth, are reported. The success of the procedure demonstrates that QTL analysis can be applied in this species and will contribute to the study and future improvement of traits associated with production, profitability and sustainability. © 2007 Elsevier B.V. All rights reserved.
Kasapidis, P; Magoulas, A
Genetic structure of fish stocks in the Hellenic Seas and the Mediterranean Book Section
In: Papaconstantinou, C; Zenetos, A (Ed.): State of the Hellenic Fisheries, pp. 391–399, HCMR, Athens, 2007, (Backup Publisher: HCMR Section: VII.4).
@incollection{kasapidis_genetic_2007-2,
title = {Genetic structure of fish stocks in the Hellenic Seas and the Mediterranean},
author = {P Kasapidis and A Magoulas},
editor = {C Papaconstantinou and A Zenetos},
year = {2007},
date = {2007-01-01},
booktitle = {State of the Hellenic Fisheries},
pages = {391--399},
publisher = {HCMR},
address = {Athens},
note = {Backup Publisher: HCMR
Section: VII.4},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
Lymberakis, P; Poulakakis, N; Manthalou, G; Tsigenopoulos, C S; Magoulas, A; Mylonas, M
Mitochondrial phylogeography of Rana (Pelophylax) populations in the Eastern Mediterranean region Journal Article
In: Molecular Phylogenetics and Evolution, vol. 44, pp. 115 – 125, 2007.
@article{lymberakis_mitochondrial_2007,
title = {Mitochondrial phylogeography of Rana (Pelophylax) populations in the Eastern Mediterranean region},
author = {P Lymberakis and N Poulakakis and G Manthalou and C S Tsigenopoulos and A Magoulas and M Mylonas},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-34249792357&partnerID=40&md5=4e1dbe1f34604b4421ce71c49b66606e},
year = {2007},
date = {2007-01-01},
journal = {Molecular Phylogenetics and Evolution},
volume = {44},
pages = {115 -- 125},
abstract = {Phylogenetic relationships in the western fraction of Rana (Pelophylax) have not been resolved till now, even though several works have been devoted to the subject. Here, we infer phylogenetic relationships among the species distributed in the area of the Eastern Mediterranean, comparing partial mitochondrial DNA sequences for the cytochrome b and 16S rRNA genes. The obtained molecular data clearly indicate that Western Palearctic water frogs underwent a basal radiation into at least 3 major lineages (the perezi, the lessonae, and the rindibunda/bedriagae lineages) advocating an upper Miocene speciation. Moreover, we consider that within the rindibunda/bedriagae lineage, R. (P.) ridibunda, R. (P.) epeirotica, R. (P.) cretensis, R. (P.) bedriagae, R. (P.) cerigensis and R. (P.) kurtmuelleri were differentiated from a common ancestor through a series of vicariant and dispersal events, during the last ∼5 Mya, even though the specific rank of some taxa may be questionable, such as R. cerigensis in respect with R. bedriagae and R. kurtmuelleri in respect with R. ridibunda. © 2007 Elsevier Inc. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Phylogenetic relationships in the western fraction of Rana (Pelophylax) have not been resolved till now, even though several works have been devoted to the subject. Here, we infer phylogenetic relationships among the species distributed in the area of the Eastern Mediterranean, comparing partial mitochondrial DNA sequences for the cytochrome b and 16S rRNA genes. The obtained molecular data clearly indicate that Western Palearctic water frogs underwent a basal radiation into at least 3 major lineages (the perezi, the lessonae, and the rindibunda/bedriagae lineages) advocating an upper Miocene speciation. Moreover, we consider that within the rindibunda/bedriagae lineage, R. (P.) ridibunda, R. (P.) epeirotica, R. (P.) cretensis, R. (P.) bedriagae, R. (P.) cerigensis and R. (P.) kurtmuelleri were differentiated from a common ancestor through a series of vicariant and dispersal events, during the last ∼5 Mya, even though the specific rank of some taxa may be questionable, such as R. cerigensis in respect with R. bedriagae and R. kurtmuelleri in respect with R. ridibunda. © 2007 Elsevier Inc. All rights reserved.
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
In: BMC Genomics, vol. 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.
Kasapidis, P; Peristeraki, P; Tserpes, G; Magoulas, A
A new record of the Lessepsian invasive fish Etrumeus teres (Osteichthyes: Clupeidae) in the Mediterranean Sea (Aegean, Greece) Journal Article
In: Aquatic Invasions, vol. 2, no. 2, pp. 152–154, 2007, ISSN: 17986540, (Publisher: Regional Euro-Asian Biological Invasions Centre).
@article{kasapidis_new_2007,
title = {A new record of the Lessepsian invasive fish Etrumeus teres (Osteichthyes: Clupeidae) in the Mediterranean Sea (Aegean, Greece)},
author = {P Kasapidis and P Peristeraki and G Tserpes and A Magoulas},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84892849154&doi=10.3391%2fai.2007.2.2.12&partnerID=40&md5=74a91588f31c323b30d07687778d9ce9},
doi = {10.3391/ai.2007.2.2.12},
issn = {17986540},
year = {2007},
date = {2007-01-01},
journal = {Aquatic Invasions},
volume = {2},
number = {2},
pages = {152--154},
abstract = {The Lessepsian invasive fish Etrumeus teres was recorded for the first time off Crete, Greece in July 2005. Their abundance suggests that the species may become of commercial importance in the south Aegean Sea. © 2007 The Author(s).},
note = {Publisher: Regional Euro-Asian Biological Invasions Centre},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The Lessepsian invasive fish Etrumeus teres was recorded for the first time off Crete, Greece in July 2005. Their abundance suggests that the species may become of commercial importance in the south Aegean Sea. © 2007 The Author(s).
Volckaert, F A M J; Batargias, C; Bonhomme, F; Canario, A; Chistiakov, D; Choudhuri, J V; Galibert, F; Georgoudis, A; Haley, C S; Hellemans, B; Kuhl, H; Kotoulas, G; Law, A; Libertini, A; Magoulas, A; McAndrew, B J; Reinhardt, R; Senger, F; Souche, E; Tsigenopoulos, C; Whitaker, H A
Genomic resources for the aquaculture of European sea bass Journal Article
In: Aquaculture, vol. 272, pp. S316–S317, 2007, ISSN: 00448486.
@article{volckaert_genomic_2007,
title = {Genomic resources for the aquaculture of European sea bass},
author = {F A M J Volckaert and C Batargias and F Bonhomme and A Canario and D Chistiakov and J V Choudhuri and F Galibert and A Georgoudis and C S Haley and B Hellemans and H Kuhl and G Kotoulas and A Law and A Libertini and A Magoulas and B J McAndrew and R Reinhardt and F Senger and E Souche and C Tsigenopoulos and H A Whitaker},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848607007831},
doi = {10.1016/j.aquaculture.2007.07.199},
issn = {00448486},
year = {2007},
date = {2007-01-01},
urldate = {2020-08-09},
journal = {Aquaculture},
volume = {272},
pages = {S316--S317},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kasapidis, P; Mejuto, J; Tserpes, G; Antoniou, A; Garcia-Cortes, B; Peristeraki, P; Oikonomaki, K; Kotoulas, Giorgios; A., Magoulas
Genetic structure of the swordfish (Xiphias gladius) stocks in the Atlantic using microsatellite DNA analysis Journal Article
In: Col. Vol. Sci. Pap., ICCAT SCRS-06-035, vol. 61, pp. 89–98, 2007.
@article{kasapidis_genetic_2007-1,
title = {Genetic structure of the swordfish (Xiphias gladius) stocks in the Atlantic using microsatellite DNA analysis},
author = {P Kasapidis and J Mejuto and G Tserpes and A Antoniou and B Garcia-Cortes and P Peristeraki and K Oikonomaki and Giorgios Kotoulas and Magoulas A.},
year = {2007},
date = {2007-01-01},
journal = {Col. Vol. Sci. Pap., ICCAT SCRS-06-035},
volume = {61},
pages = {89--98},
abstract = {The genetic structure of the swordfish (Xiphias gladius) in the Atlantic Ocean was examined by genotyping 1179 individuals for 4 microsatellite loci. These individuals were collected during the years 1999-2002 from the following regions: south Atlantic (up to 5oN), mid-Atlantic (9oN to 20oN), northeast Atlantic (North of 30oN and East of 31oW), northwest Atlantic (North of 30oN and West of 31oW). Gene diversity was very high (textbackslashtextgreater0.96) for all four loci. Heterogeneity tests and pairwise Fsts showed that the South Atlantic group was significantly different from all the other groups (ptextbackslashtextless0.000).These results are in agreement with previous mitochondrial DNA data and do not support a need for changing the 5oN latitude as a boundary for fisheries. Some individuals were also genotyped for the Calmodulin intron 4 gene (CaM) to compare with an earlier dataset for this marker. Allele frequencies found for CaM were in agreement with previous observation and showed a different population structure pattern compared to that revealed by microsatellites. However, the pattern reflected in CaM should be treated with caution, since CaM is only a single diallelic locus, possibly under strong selection. The genotyping of the samples for more microsatellite loci, which is in progress, is expected to further elucidate the genetic structure of the swordfish in the Atlantic, by further increasing resolution.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The genetic structure of the swordfish (Xiphias gladius) in the Atlantic Ocean was examined by genotyping 1179 individuals for 4 microsatellite loci. These individuals were collected during the years 1999-2002 from the following regions: south Atlantic (up to 5oN), mid-Atlantic (9oN to 20oN), northeast Atlantic (North of 30oN and East of 31oW), northwest Atlantic (North of 30oN and West of 31oW). Gene diversity was very high (textbackslashtextgreater0.96) for all four loci. Heterogeneity tests and pairwise Fsts showed that the South Atlantic group was significantly different from all the other groups (ptextbackslashtextless0.000).These results are in agreement with previous mitochondrial DNA data and do not support a need for changing the 5oN latitude as a boundary for fisheries. Some individuals were also genotyped for the Calmodulin intron 4 gene (CaM) to compare with an earlier dataset for this marker. Allele frequencies found for CaM were in agreement with previous observation and showed a different population structure pattern compared to that revealed by microsatellites. However, the pattern reflected in CaM should be treated with caution, since CaM is only a single diallelic locus, possibly under strong selection. The genotyping of the samples for more microsatellite loci, which is in progress, is expected to further elucidate the genetic structure of the swordfish in the Atlantic, by further increasing resolution.
2006
Daskalakis, M; Rigas, F; Magoulas, A; Katsikis, I; Karageorgis, A; Mavridou, A
Bioconservation of deteriorated stone monuments via calcium carbonate preciapitation by Pseudomonas spp Journal Article
In: WSEAS Transactions on Environement and development, vol. 2, no. 5, pp. 591– 598, 2006, ISSN: 1790-5079.
@article{daskalakis_bioconservation_2006,
title = {Bioconservation of deteriorated stone monuments via calcium carbonate preciapitation by Pseudomonas spp},
author = {M Daskalakis and F Rigas and A Magoulas and I Katsikis and A Karageorgis and A Mavridou},
issn = {1790-5079},
year = {2006},
date = {2006-01-01},
journal = {WSEAS Transactions on Environement and development},
volume = {2},
number = {5},
pages = {591-- 598},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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
In: Genetics, vol. 174, no. 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.
Magoulas, Antonios; Castilho, R; Caetano, S; Marcato, S; Patarnello, T
In: Mol Phylogenet Evol, vol. 39, no. 3, pp. 734–46, 2006.
@article{magoulas_mitochondrial_2006,
title = {Mitochondrial DNA reveals a mosaic pattern of phylogeographical structure in Atlantic and Mediterranean populations of anchovy (Engraulis encrasicolus)},
author = {Antonios Magoulas and R Castilho and S Caetano and S Marcato and T Patarnello},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16515866},
year = {2006},
date = {2006-01-01},
journal = {Mol Phylogenet Evol},
volume = {39},
number = {3},
pages = {734--46},
abstract = {This study extends the geographic coverage of a previous study of mitochondrial DNA restriction fragment length polymorphism in European anchovy. Both studies together include 24 samples representing 17 localities extending from the Black Sea, through the Mediterranean Sea to the eastern Atlantic as far south as Dakar, Senegal. Eighty-eight haplotypes define two clades (A and B) separated by 3.2% sequence divergence. Clade A has a star-like genealogy indicative of a recent population expansion. Clade B has a more complex genealogy, consisting of several haplotypes at intermediate frequencies. The distributions of these clades consist of a mosaic with abrupt changes between some areas and gradients between other areas. Clade A predominates the Black and Aegean seas, but is present throughout the Mediterranean. Unexpectedly, new data show that clade A is also at a high frequency in the Atlantic, from Portugal to at least Senegal. Overall, the level of genetic differentiation among populations is high (F(ST)=0.148, ptextless0.0001), with the greatest differences between basins. AMOVA reveals four main geographical groups: Atlantic, central Mediterranean, Aegean Sea, and Black Sea. Mismatch distribution clearly indicates historical bottleneck and population expansion for clade A, while for clade B such evidence is equivocal. This difference may reflect a range expansion for both clades, but with higher gene flow (Nm values) between demes for clade A. Both contemporary and historical processes are important in shaping the complex genetic population structure of European anchovy.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
This study extends the geographic coverage of a previous study of mitochondrial DNA restriction fragment length polymorphism in European anchovy. Both studies together include 24 samples representing 17 localities extending from the Black Sea, through the Mediterranean Sea to the eastern Atlantic as far south as Dakar, Senegal. Eighty-eight haplotypes define two clades (A and B) separated by 3.2% sequence divergence. Clade A has a star-like genealogy indicative of a recent population expansion. Clade B has a more complex genealogy, consisting of several haplotypes at intermediate frequencies. The distributions of these clades consist of a mosaic with abrupt changes between some areas and gradients between other areas. Clade A predominates the Black and Aegean seas, but is present throughout the Mediterranean. Unexpectedly, new data show that clade A is also at a high frequency in the Atlantic, from Portugal to at least Senegal. Overall, the level of genetic differentiation among populations is high (F(ST)=0.148, ptextless0.0001), with the greatest differences between basins. AMOVA reveals four main geographical groups: Atlantic, central Mediterranean, Aegean Sea, and Black Sea. Mismatch distribution clearly indicates historical bottleneck and population expansion for clade A, while for clade B such evidence is equivocal. This difference may reflect a range expansion for both clades, but with higher gene flow (Nm values) between demes for clade A. Both contemporary and historical processes are important in shaping the complex genetic population structure of European anchovy.
2005
Bargelloni, L; Alarcon, J A; Alvarez, M C; Penzo, E; Magoulas, A; Palma, J; Patarnello, T
The Atlantic–Mediterranean transition: Discordant genetic patterns in two seabream species, Diplodus puntazzo (Cetti) and Diplodus sargus (L.) Journal Article
In: Molecular Phylogenetics and Evolution, vol. 36, no. 3, pp. 523–535, 2005, ISSN: 10557903.
@article{bargelloni_atlanticmediterranean_2005,
title = {The Atlantic–Mediterranean transition: Discordant genetic patterns in two seabream species, Diplodus puntazzo (Cetti) and Diplodus sargus (L.)},
author = {L Bargelloni and J A Alarcon and M C Alvarez and E Penzo and A Magoulas and J Palma and T Patarnello},
url = {https://linkinghub.elsevier.com/retrieve/pii/S1055790305001430},
doi = {10.1016/j.ympev.2005.04.017},
issn = {10557903},
year = {2005},
date = {2005-09-01},
urldate = {2020-08-09},
journal = {Molecular Phylogenetics and Evolution},
volume = {36},
number = {3},
pages = {523--535},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cárdenas, Leyla; Hernández, Cristián E; Poulin, Elie; Magoulas, Antonios; Kornfield, Irv; Ojeda, Patricio F
Origin, diversification, and historical biogeography of the genus Trachurus (Perciformes: Carangidae) Journal Article
In: Molecular Phylogenetics and Evolution, vol. 35, no. 2, pp. 496–507, 2005, ISSN: 10557903.
@article{cardenas_origin_2005,
title = {Origin, diversification, and historical biogeography of the genus Trachurus (Perciformes: Carangidae)},
author = {Leyla Cárdenas and Cristián E Hernández and Elie Poulin and Antonios Magoulas and Irv Kornfield and Patricio F Ojeda},
url = {https://linkinghub.elsevier.com/retrieve/pii/S1055790305000291},
doi = {10.1016/j.ympev.2005.01.011},
issn = {10557903},
year = {2005},
date = {2005-05-01},
urldate = {2020-08-09},
journal = {Molecular Phylogenetics and Evolution},
volume = {35},
number = {2},
pages = {496--507},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kasapidis, P; Suchentrunk, F; Magoulas, A; Kotoulas, G
In: Molecular Phylogenetics and Evolution, vol. 34, no. 1, pp. 55–66, 2005, ISSN: 10557903.
@article{kasapidis_shaping_2005,
title = {The shaping of mitochondrial DNA phylogeographic patterns of the brown hare (Lepus europaeus) under the combined influence of Late Pleistocene climatic fluctuations and anthropogenic translocations},
author = {P Kasapidis and F Suchentrunk and A Magoulas and G Kotoulas},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-9744258860&doi=10.1016%2fj.ympev.2004.09.007&partnerID=40&md5=a65c976ffbb7419b3edd624a3efbeb4d},
doi = {10.1016/j.ympev.2004.09.007},
issn = {10557903},
year = {2005},
date = {2005-01-01},
journal = {Molecular Phylogenetics and Evolution},
volume = {34},
number = {1},
pages = {55--66},
abstract = {The phylogeographic structure of the brown hare (Lepus europaeus) was studied by analysing mtDNA control region sequences of 98 individuals from continental and insular Greece, Bulgaria, Cyprus and northern Israel, together with 44 published sequences from Italy and central Europe. We found two distinct clades separated by an average nucleotide divergence of 6.6%, which may correspond to a Balkan and to an Asia Minor refugium. The estimated time of separation of the two clades was dated back to 105,000- 490,000 years ago. These two clades coexist in the area of northeastern Greece and Bulgaria, most likely as a result of a post-glacial northward expansion. Within the southern Balkan refugium, network analyses showed geographical structuring, which supports the hypothesis of several isolated Late Pleistocene populations. The central European and Italian populations appear to have originated from a non-detected northern Balkan population that was genetically closely related to some northern Greek populations, as a result of postglacial expansion, translocations or a combination of both. Moreover, several cases of ancient and recent translocations by humans were detected, especially for some island populations, while the eastern Aegean islands off the Asia Minor coast were most likely colonized naturally through Late Pleistocene land bridge connection. The genetic analysis presented here provides a framework for designing proper conservation and management guidelines for this species. © 2004 Elsevier Inc. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The phylogeographic structure of the brown hare (Lepus europaeus) was studied by analysing mtDNA control region sequences of 98 individuals from continental and insular Greece, Bulgaria, Cyprus and northern Israel, together with 44 published sequences from Italy and central Europe. We found two distinct clades separated by an average nucleotide divergence of 6.6%, which may correspond to a Balkan and to an Asia Minor refugium. The estimated time of separation of the two clades was dated back to 105,000- 490,000 years ago. These two clades coexist in the area of northeastern Greece and Bulgaria, most likely as a result of a post-glacial northward expansion. Within the southern Balkan refugium, network analyses showed geographical structuring, which supports the hypothesis of several isolated Late Pleistocene populations. The central European and Italian populations appear to have originated from a non-detected northern Balkan population that was genetically closely related to some northern Greek populations, as a result of postglacial expansion, translocations or a combination of both. Moreover, several cases of ancient and recent translocations by humans were detected, especially for some island populations, while the eastern Aegean islands off the Asia Minor coast were most likely colonized naturally through Late Pleistocene land bridge connection. The genetic analysis presented here provides a framework for designing proper conservation and management guidelines for this species. © 2004 Elsevier Inc. All rights reserved.
Kasapidis, P; Magoulas, A; Mylonas, M; Zouros, E
The phylogeography of the gecko Cyrtopodion kotschyi (Reptilia: Gekkonidae) in the Aegean archipelago Journal Article
In: Molecular Phylogenetics and Evolution, vol. 35, no. 3, pp. 612–623, 2005, ISSN: 10557903.
@article{kasapidis_phylogeography_2005,
title = {The phylogeography of the gecko Cyrtopodion kotschyi (Reptilia: Gekkonidae) in the Aegean archipelago},
author = {P Kasapidis and A Magoulas and M Mylonas and E Zouros},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-18144425199&doi=10.1016%2fj.ympev.2005.02.005&partnerID=40&md5=51a9fa8e77d60205ccf8124439085449},
doi = {10.1016/j.ympev.2005.02.005},
issn = {10557903},
year = {2005},
date = {2005-01-01},
journal = {Molecular Phylogenetics and Evolution},
volume = {35},
number = {3},
pages = {612--623},
abstract = {Cyrtopodion kotschyi is a small gecko, widely distributed on the islands of the Aegean archipelago and the adjacent mainland. We unveiled the phylogeography of the species by using a portion of the cytochrome oxidase I mitochondrial DNA gene from 35 insular and mainland populations. The distinct geographic distribution of the major clades of the phylogenetic tree and its topology suggest a spatial and temporal sequence of phylogenetic separations that coincide with some major paleogeographical separations during the geological history of the Aegean and support a mainly vicariant pattern of differentiation. The separation times and 95% confidence limits among the different clades were estimated according to two different paleogeographical scenarios. The very high interpopulation genetic divergence (up to 20% uncorrected pairwise distances) and the better concordance between paleogeographical and phylogenetic separations for one of the scenarios suggest that species differentiation started during Miocene (about 10 Mya) due to the fragmentation of the united landmass of "Ägäis" that was Aegean at that time. © 2005 Elsevier Inc. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cyrtopodion kotschyi is a small gecko, widely distributed on the islands of the Aegean archipelago and the adjacent mainland. We unveiled the phylogeography of the species by using a portion of the cytochrome oxidase I mitochondrial DNA gene from 35 insular and mainland populations. The distinct geographic distribution of the major clades of the phylogenetic tree and its topology suggest a spatial and temporal sequence of phylogenetic separations that coincide with some major paleogeographical separations during the geological history of the Aegean and support a mainly vicariant pattern of differentiation. The separation times and 95% confidence limits among the different clades were estimated according to two different paleogeographical scenarios. The very high interpopulation genetic divergence (up to 20% uncorrected pairwise distances) and the better concordance between paleogeographical and phylogenetic separations for one of the scenarios suggest that species differentiation started during Miocene (about 10 Mya) due to the fragmentation of the united landmass of "Ägäis" that was Aegean at that time. © 2005 Elsevier Inc. All rights reserved.
Brown, R C; Tsalavouta, M; Terzoglou, V; Magoulas, A; McAndrew, B J
Additional microsatellites for Sparus aurata and cross-species amplification within the Sparidae family Journal Article
In: Molecular Ecology Notes, vol. 5, pp. 605 – 607, 2005.
@article{brown_additional_2005,
title = {Additional microsatellites for Sparus aurata and cross-species amplification within the Sparidae family},
author = {R C Brown and M Tsalavouta and V Terzoglou and A Magoulas and B J McAndrew},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-28344455572&partnerID=40&md5=7f56611349fb1cbe98f6e3fbe1c0e1a7},
doi = {10.1111/j.1471-8286.2005.01007.x},
year = {2005},
date = {2005-01-01},
journal = {Molecular Ecology Notes},
volume = {5},
pages = {605 -- 607},
abstract = {Six new microsatellite loci were isolated and characterized in 32 individuals from a farm population of gilthead seabream (Sparus aurata). Expected heterozygosity at all loci was high, ranging from 0.835 to 0.958 with between 10 and 27 alleles per locus. A multiplex polymerase chain reaction protocol was developed using four of the loci. Cross-species amplification of the loci was tested in six species of the Sparidae family and four loci were successfully amplified in two or more related species. © 2005 Blackwell Publishing Ltd.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Six new microsatellite loci were isolated and characterized in 32 individuals from a farm population of gilthead seabream (Sparus aurata). Expected heterozygosity at all loci was high, ranging from 0.835 to 0.958 with between 10 and 27 alleles per locus. A multiplex polymerase chain reaction protocol was developed using four of the loci. Cross-species amplification of the loci was tested in six species of the Sparidae family and four loci were successfully amplified in two or more related species. © 2005 Blackwell Publishing Ltd.
Poulakakis, N; Lymberakis, P; Tsigenopoulos, C S; Magoulas, A; Mylonas, M
Phylogenetic relationships and evolutionary history of snake-eyed skink Ablepharus kitaibelii (Sauria: Scincidae) Journal Article
In: Molecular Phylogenetics and Evolution, vol. 34, pp. 245 – 256, 2005.
@article{poulakakis_phylogenetic_2005,
title = {Phylogenetic relationships and evolutionary history of snake-eyed skink Ablepharus kitaibelii (Sauria: Scincidae)},
author = {N Poulakakis and P Lymberakis and C S Tsigenopoulos and A Magoulas and M Mylonas},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-11144266691&partnerID=40&md5=9ec5b39f41ecfb4a0f8fdb0d7b315756},
year = {2005},
date = {2005-01-01},
journal = {Molecular Phylogenetics and Evolution},
volume = {34},
pages = {245 -- 256},
abstract = {Sequence data derived from two mitochondrial markers, 16S rRNA and cytochrome b genes, were used to infer the phylogenetic relationships of 38 populations of the snake-eyed skinks of the genus Ablepharus with emphasis on A. kitaibelii from Greece and Turkey. The partition-homogeneity tests indicated that the combined data set was homogeneous, and maximum-parsimony, maximum-likelihood, and Bayesian analyses produced topologically identical trees that revealed a well-resolved phylogeny. All species except A. kitaibelii form monophyletic units. The latter species appears paraphyletic with respect to A. budaki and A. chernovi with populations clustering into two distinct clades. A. chernovi and A. budaki, which have recently been raised to species status, were confirmed as genetically distinct forms. We used sequence divergence and paleogeographic history of the Aegean region to reconstruct a biogeographic evolutionary scenario for A. kitaibelii. © 2004 Elsevier Inc. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Sequence data derived from two mitochondrial markers, 16S rRNA and cytochrome b genes, were used to infer the phylogenetic relationships of 38 populations of the snake-eyed skinks of the genus Ablepharus with emphasis on A. kitaibelii from Greece and Turkey. The partition-homogeneity tests indicated that the combined data set was homogeneous, and maximum-parsimony, maximum-likelihood, and Bayesian analyses produced topologically identical trees that revealed a well-resolved phylogeny. All species except A. kitaibelii form monophyletic units. The latter species appears paraphyletic with respect to A. budaki and A. chernovi with populations clustering into two distinct clades. A. chernovi and A. budaki, which have recently been raised to species status, were confirmed as genetically distinct forms. We used sequence divergence and paleogeographic history of the Aegean region to reconstruct a biogeographic evolutionary scenario for A. kitaibelii. © 2004 Elsevier Inc. All rights reserved.
Makridis, P; Martins, S; Tsalavouta, M; Dionisio, L C; Kotoulas, G; Magoulas, A; Dinis, M T
Antimicrobial activity in bacteria isolated from Senegalese sole, Solea senegalensis, fed with natural prey Journal Article
In: Aquaculture Research, vol. 36, no. 16, pp. 1619–1627, 2005, ISSN: 1355557X.
@article{makridis_antimicrobial_2005,
title = {Antimicrobial activity in bacteria isolated from Senegalese sole, Solea senegalensis, fed with natural prey},
author = {P Makridis and S Martins and M Tsalavouta and L C Dionisio and G Kotoulas and A Magoulas and M T Dinis},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-29044440557&doi=10.1111%2fj.1365-2109.2005.01388.x&partnerID=40&md5=64efc6efd5ef382391232a269eb428d1},
doi = {10.1111/j.1365-2109.2005.01388.x},
issn = {1355557X},
year = {2005},
date = {2005-01-01},
journal = {Aquaculture Research},
volume = {36},
number = {16},
pages = {1619--1627},
abstract = {Intestinal bacteria in marine fish may produce antimicrobial substances which inhibit pathogenic bacteria. The aim of this study was to determine the influence of a change of fish diet on the antimicrobial activity of the culturable aerobic gut microflora of Senegalese sole, Solea senegalensis. Pre-adult 15-month-old fish previously fed on an artificial diet, were fed polychaetes (Hediste diversicolor), which form part of the natural diet of Senegalese sole. Samples were taken 0, 3 and 6 weeks after start of the experiment from the stomach, small and large intestine of the fish. The bacterial strains isolated from these samples were sub-cultured to pure cultures and stored at - 80°C. Several biochemical tests were run to obtain some basic phenotypic characteristics of the isolated strains. Amplification and sequencing of 16S rDNA fragments were used to identify the majority of the bacterial strains isolated. The identification by use of this molecular approach gave results in agreement to the phenotypic characterization. Feeding with polychaetes significantly increased (P textless 0.05) the numbers of presumptive Vibrio isolates in the gut. The number of bacterial strains with antimicrobial activity, as determined by two in vitro approaches, was significantly (P textless 0.05) increased by feeding with polychaetes. © 2005 Blackwell Publishing Ltd.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Intestinal bacteria in marine fish may produce antimicrobial substances which inhibit pathogenic bacteria. The aim of this study was to determine the influence of a change of fish diet on the antimicrobial activity of the culturable aerobic gut microflora of Senegalese sole, Solea senegalensis. Pre-adult 15-month-old fish previously fed on an artificial diet, were fed polychaetes (Hediste diversicolor), which form part of the natural diet of Senegalese sole. Samples were taken 0, 3 and 6 weeks after start of the experiment from the stomach, small and large intestine of the fish. The bacterial strains isolated from these samples were sub-cultured to pure cultures and stored at - 80°C. Several biochemical tests were run to obtain some basic phenotypic characteristics of the isolated strains. Amplification and sequencing of 16S rDNA fragments were used to identify the majority of the bacterial strains isolated. The identification by use of this molecular approach gave results in agreement to the phenotypic characterization. Feeding with polychaetes significantly increased (P textless 0.05) the numbers of presumptive Vibrio isolates in the gut. The number of bacterial strains with antimicrobial activity, as determined by two in vitro approaches, was significantly (P textless 0.05) increased by feeding with polychaetes. © 2005 Blackwell Publishing Ltd.
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
In: Aquaculture, vol. 243, no. 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}
}
2004
Kasapidis, P; Planes, S; Laurent, V; Quinta, R; Teia, A; Lenfant, R; Darivianakis, S; Terzoglou, V; Kotoulas, G; Magoulas, A
Stock discrimination and temporal and spatial genetic variation of sardine (Sardina pilchardus) in northeastern Atlantic, with a combined analysis of nuclear (microsatellites and allozymes) and mitochondrial DNA markers. Proceedings Article
In: Kasapidis, P (Ed.): 2004 ICES Annual Science Conference, 2004.
@inproceedings{kasapidis_stock_2004,
title = {Stock discrimination and temporal and spatial genetic variation of sardine (Sardina pilchardus) in northeastern Atlantic, with a combined analysis of nuclear (microsatellites and allozymes) and mitochondrial DNA markers.},
author = {P Kasapidis and S Planes and V Laurent and R Quinta and A Teia and R Lenfant and S Darivianakis and V Terzoglou and G Kotoulas and A Magoulas},
editor = {P Kasapidis},
year = {2004},
date = {2004-09-01},
booktitle = {2004 ICES Annual Science Conference},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Alarcón, J A; Magoulas, A; Georgakopoulos, T; Zouros, E; Alvarez, M C
Genetic comparison of wild and cultivated European populations of the gilthead sea bream (Sparus aurata) Journal Article
In: Aquaculture, vol. 230, no. 1-4, pp. 65–80, 2004, ISSN: 00448486.
@article{alarcon_genetic_2004,
title = {Genetic comparison of wild and cultivated European populations of the gilthead sea bream (Sparus aurata)},
author = {J A Alarcón and A Magoulas and T Georgakopoulos and E Zouros and M C Alvarez},
url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848603004344},
doi = {10.1016/S0044-8486(03)00434-4},
issn = {00448486},
year = {2004},
date = {2004-02-01},
urldate = {2020-08-09},
journal = {Aquaculture},
volume = {230},
number = {1-4},
pages = {65--80},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Magoulas, A
Mitochondrial DNA Book Section
In: Cadrin, S; Friedland, K; Waldman, J (Ed.): Stock Ιdentification Μethods, pp. 311–330, ELSEVIER Academic Press, 2004, (Backup Publisher: ELSEVIER Academic Press Section: 16).
@incollection{magoulas_mitochondrial_2004,
title = {Mitochondrial DNA},
author = {A Magoulas},
editor = {S Cadrin and K Friedland and J Waldman},
year = {2004},
date = {2004-01-01},
booktitle = {Stock Ιdentification Μethods},
pages = {311--330},
publisher = {ELSEVIER Academic Press},
note = {Backup Publisher: ELSEVIER Academic Press
Section: 16},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
2003
Bargelloni, L; Alarcon, J A; Alvarez, M C; Penzo, E; Magoulas, A; Reis, C; Patarnello, T
Discord in the family Sparidae (Teleostei): divergent phylogeographical patterns across the Atlantic-Mediterranean divide Journal Article
In: Journal of Evolutionary Biology, vol. 16, no. 6, pp. 1149–1158, 2003, ISSN: 1010-061X, 1420-9101.
@article{bargelloni_discord_2003,
title = {Discord in the family Sparidae (Teleostei): divergent phylogeographical patterns across the Atlantic-Mediterranean divide},
author = {L Bargelloni and J A Alarcon and M C Alvarez and E Penzo and A Magoulas and C Reis and T Patarnello},
url = {http://doi.wiley.com/10.1046/j.1420-9101.2003.00620.x},
doi = {10.1046/j.1420-9101.2003.00620.x},
issn = {1010-061X, 1420-9101},
year = {2003},
date = {2003-11-01},
urldate = {2020-08-09},
journal = {Journal of Evolutionary Biology},
volume = {16},
number = {6},
pages = {1149--1158},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kotoulas, G; Mejuto, J; Tserpes, G; Garcia-Cortes, B; Peristeraki, P; la Serna, J M De; Magoulas, A
DNA microsatellite markers in service of swordfish stock-structure analysis in the Atlantic and Mediterranean Journal Article
In: ICCAT Col. Vol. Sci. Papers, vol. 55, no. 4, pp. 1632–1639, 2003.
@article{kotoulas_dna_2003,
title = {DNA microsatellite markers in service of swordfish stock-structure analysis in the Atlantic and Mediterranean},
author = {G Kotoulas and J Mejuto and G Tserpes and B Garcia-Cortes and P Peristeraki and J M De la Serna and A Magoulas},
year = {2003},
date = {2003-01-01},
journal = {ICCAT Col. Vol. Sci. Papers},
volume = {55},
number = {4},
pages = {1632--1639},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2002
Ladoukakis, E D; Saavedra, C; Magoulas, A; Zouros, E
In: Molecular Ecology, vol. 11, no. 4, pp. 755–769, 2002, ISSN: 0962-1083, 1365-294X.
@article{ladoukakis_mitochondrial_2002,
title = {Mitochondrial DNA variation in a species with two mitochondrial genomes: the case of Mytilus galloprovincialis from the Atlantic, the Mediterranean and the Black Sea},
author = {E D Ladoukakis and C Saavedra and A Magoulas and E Zouros},
url = {http://doi.wiley.com/10.1046/j.1365-294X.2002.01473.x},
doi = {10.1046/j.1365-294X.2002.01473.x},
issn = {0962-1083, 1365-294X},
year = {2002},
date = {2002-04-01},
urldate = {2020-08-09},
journal = {Molecular Ecology},
volume = {11},
number = {4},
pages = {755--769},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Garnier-Géré, P H; Naciri-Graven, Y; Bougrier, S; Magoulas, A; Héral, M; Kotoulas, G; Hawkins, A; Gérard, A
In: Molecular Ecology, vol. 11, no. 8, pp. 1499–1514, 2002, ISSN: 09621083.
@article{garnier-gere_influences_2002,
title = {Influences of triploidy, parentage and genetic diversity on growth of the Pacific oyster Crassostrea gigas reared in contrasting natural environments},
author = {P H Garnier-Géré and Y Naciri-Graven and S Bougrier and A Magoulas and M Héral and G Kotoulas and A Hawkins and A Gérard},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035993750&doi=10.1046%2fj.1365-294X.2002.01531.x&partnerID=40&md5=fda8b0e20f8e19d34fe231f8cfaf81a2},
doi = {10.1046/j.1365-294X.2002.01531.x},
issn = {09621083},
year = {2002},
date = {2002-01-01},
journal = {Molecular Ecology},
volume = {11},
number = {8},
pages = {1499--1514},
abstract = {An increasing number of hypotheses are being proposed to explain the faster growth potential of triploids in molluscs, including their partial sterility or their higher heterozygosity compared to diploids. Triploid advantage however, remains controversial for poorer sites, because of a potential trade-off with survival. These questions were addressed in Crassostrea gigas by deploying meiosis II triploids and their diploid siblings from a single mass spawning of three males and seven females, in two contrasting locations for their trophic resources. One hundred and fifty individuals were sampled at each site after nine months, measured for weight and biochemical composition, and genotyped using three microsatellite and seven allozyme loci. Higher performance was observed at the fastgrowing site for all traits except shell weight, and triploids had greater weights and biochemical contents than diploids at harvest. Triploids also grew faster at the poorer site, and showed similar survival rates to diploids at both sites. Triploids had significantly higher average allozyme and microsatellite diversity. However, they performed better for a wide range of individual heterozygosity values, arguing for an advantage of the triploid state per se, that could be due to positive effects on growth of both sterility of triploids with subsequent resource re-allocation and possible faster transcription with three copies of each gene. Despite evidence of very low or no inbreeding in the diploid sample, positive associations between individual allozyme diversity and growth were detected, which explained little but significant amounts of phenotypic variation. These associations were interpreted as direct effects of allozymes, either alone or including epistatic interactions with other loci. In addition, measures of individual distance (mean-d2) specific to microsatellites, were negatively correlated with growth in diploids, indicating possible effects of outbreeding depression between more distant genomes of parents from distinct populations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
An increasing number of hypotheses are being proposed to explain the faster growth potential of triploids in molluscs, including their partial sterility or their higher heterozygosity compared to diploids. Triploid advantage however, remains controversial for poorer sites, because of a potential trade-off with survival. These questions were addressed in Crassostrea gigas by deploying meiosis II triploids and their diploid siblings from a single mass spawning of three males and seven females, in two contrasting locations for their trophic resources. One hundred and fifty individuals were sampled at each site after nine months, measured for weight and biochemical composition, and genotyped using three microsatellite and seven allozyme loci. Higher performance was observed at the fastgrowing site for all traits except shell weight, and triploids had greater weights and biochemical contents than diploids at harvest. Triploids also grew faster at the poorer site, and showed similar survival rates to diploids at both sites. Triploids had significantly higher average allozyme and microsatellite diversity. However, they performed better for a wide range of individual heterozygosity values, arguing for an advantage of the triploid state per se, that could be due to positive effects on growth of both sterility of triploids with subsequent resource re-allocation and possible faster transcription with three copies of each gene. Despite evidence of very low or no inbreeding in the diploid sample, positive associations between individual allozyme diversity and growth were detected, which explained little but significant amounts of phenotypic variation. These associations were interpreted as direct effects of allozymes, either alone or including epistatic interactions with other loci. In addition, measures of individual distance (mean-d2) specific to microsatellites, were negatively correlated with growth in diploids, indicating possible effects of outbreeding depression between more distant genomes of parents from distinct populations.
2001
Palma, J; Alarcon, J A; Alvarez, C; Zouros, E; Magoulas, A; Andrade, J P
Developmental stability and genetic heterozygosity in wild and cultured stocks of gilthead sea bream (Sparus aurata) Journal Article
In: Journal of the Marine Biological Association of the United Kingdom, vol. 81, no. 2, pp. 283–288, 2001, ISSN: 0025-3154, 1469-7769.
@article{palma_developmental_2001,
title = {Developmental stability and genetic heterozygosity in wild and cultured stocks of gilthead sea bream (Sparus aurata)},
author = {J Palma and J A Alarcon and C Alvarez and E Zouros and A Magoulas and J P Andrade},
url = {https://www.cambridge.org/core/product/identifier/S0025315401003757/type/journal_article},
doi = {10.1017/S0025315401003757},
issn = {0025-3154, 1469-7769},
year = {2001},
date = {2001-04-01},
urldate = {2020-08-09},
journal = {Journal of the Marine Biological Association of the United Kingdom},
volume = {81},
number = {2},
pages = {283--288},
abstract = {The present study checks on the validity of the hypothesis that heterozygosity and the fluctuating asymmetry (FA), common measure of the developmental stability, are linked in populations of wild and cultured stocks of
Sparus aurata
from five countries. Muscle and liver samples were analysed for variation in 26 allozymes and three microsatellite loci. Pectoral fin rays and upper and lower gill rakers of the first branchial arch were counted on the left and on the right sides of each fish. Fluctuating asymmetry existed in the majority of the samples although their values were consistently low, (0·305±0·147), but higher in the cultured samples. The allozyme heterozygosity values were always high, but lower in the cultured samples. The microsatellite DNA analysis produced similar results. Heterozygosity was higher in cultured individuals (except for the Greek samples). These findings seem to be early evidence that the reared samples are losing some genetic variation, especially due to the loss of the rarest alleles (which were present in the wild populations). Genetic drift, probably caused by propagation practices, is most likely responsible for the decrease of the genetic variation. No distinct pattern of geographic separation was identified.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The present study checks on the validity of the hypothesis that heterozygosity and the fluctuating asymmetry (FA), common measure of the developmental stability, are linked in populations of wild and cultured stocks of
Sparus aurata
from five countries. Muscle and liver samples were analysed for variation in 26 allozymes and three microsatellite loci. Pectoral fin rays and upper and lower gill rakers of the first branchial arch were counted on the left and on the right sides of each fish. Fluctuating asymmetry existed in the majority of the samples although their values were consistently low, (0·305±0·147), but higher in the cultured samples. The allozyme heterozygosity values were always high, but lower in the cultured samples. The microsatellite DNA analysis produced similar results. Heterozygosity was higher in cultured individuals (except for the Greek samples). These findings seem to be early evidence that the reared samples are losing some genetic variation, especially due to the loss of the rarest alleles (which were present in the wild populations). Genetic drift, probably caused by propagation practices, is most likely responsible for the decrease of the genetic variation. No distinct pattern of geographic separation was identified.
Sparus aurata
from five countries. Muscle and liver samples were analysed for variation in 26 allozymes and three microsatellite loci. Pectoral fin rays and upper and lower gill rakers of the first branchial arch were counted on the left and on the right sides of each fish. Fluctuating asymmetry existed in the majority of the samples although their values were consistently low, (0·305±0·147), but higher in the cultured samples. The allozyme heterozygosity values were always high, but lower in the cultured samples. The microsatellite DNA analysis produced similar results. Heterozygosity was higher in cultured individuals (except for the Greek samples). These findings seem to be early evidence that the reared samples are losing some genetic variation, especially due to the loss of the rarest alleles (which were present in the wild populations). Genetic drift, probably caused by propagation practices, is most likely responsible for the decrease of the genetic variation. No distinct pattern of geographic separation was identified.
2000
Hawkins, A J S; Magoulas, A; Héral, M; Bougrier, S; Naciri-Graven, Y; Day, A J; Kotoulas, G
In: Genetical Research, vol. 76, no. 3, pp. 273–284, 2000, ISSN: 00166723.
@article{hawkins_separate_2000,
title = {Separate effects of triploidy, parentage and genomic diversity upon feeding behaviour, metabolic efficiency and net energy balance in the pacific oyster Crassostrea gigas},
author = {A J S Hawkins and A Magoulas and M Héral and S Bougrier and Y Naciri-Graven and A J Day and G Kotoulas},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034521887&doi=10.1017%2fS0016672300004766&partnerID=40&md5=b1e5a6ea52adb13f396dcec5d01c96d9},
doi = {10.1017/S0016672300004766},
issn = {00166723},
year = {2000},
date = {2000-01-01},
journal = {Genetical Research},
volume = {76},
number = {3},
pages = {273--284},
abstract = {Triploid oysters were induced using cytochalasin B upon retention of either the first (meiosis I triploids) or the second (meiosis II triploids) polar body in embryos from a single cohort derived from mixed parentage. Allozyme and microsatellite assays enabled the confirmation of both parentage and triploidy status in each oyster. Comparison of meiosis I triploids, meiosis II triploids and diploid siblings established that improved physiological performance in triploids was associated with increased allelic variation, rather than with the quantitative dosage effects of ploidy status. An unidentified maternal influence also interacted with genotype. Among full sibs, allelic variation measured as multi-locus enzyme heterozygosity accounted for up to 42% of the variance in physiological performance; significant positive influences were identified upon feeding rate, absorption efficiency, net energy balance and growth efficiency (= net energy balance ÷ energy absorbed). Whilst allelic variation was greater in both meiosis I and meiosis II triploids than in diploid siblings, both allelic variation and net energy balance were highest in triploids induced at meiosis I. This suggests that it may be preferable to induce triploidy by blocking meiosis I, rather than meiosis II as has traditionally been undertaken during commercial breeding programmes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Triploid oysters were induced using cytochalasin B upon retention of either the first (meiosis I triploids) or the second (meiosis II triploids) polar body in embryos from a single cohort derived from mixed parentage. Allozyme and microsatellite assays enabled the confirmation of both parentage and triploidy status in each oyster. Comparison of meiosis I triploids, meiosis II triploids and diploid siblings established that improved physiological performance in triploids was associated with increased allelic variation, rather than with the quantitative dosage effects of ploidy status. An unidentified maternal influence also interacted with genotype. Among full sibs, allelic variation measured as multi-locus enzyme heterozygosity accounted for up to 42% of the variance in physiological performance; significant positive influences were identified upon feeding rate, absorption efficiency, net energy balance and growth efficiency (= net energy balance ÷ energy absorbed). Whilst allelic variation was greater in both meiosis I and meiosis II triploids than in diploid siblings, both allelic variation and net energy balance were highest in triploids induced at meiosis I. This suggests that it may be preferable to induce triploidy by blocking meiosis I, rather than meiosis II as has traditionally been undertaken during commercial breeding programmes.
Magoulas, A; Kotoulas, G; Gérard, A; Naciri-Graven, Y; Dermitzakis, E; Hawkins, A J S
Comparison of genetic variability and parentage in different ploidy classes of the Japanese oyster Crassostrea gigas Journal Article
In: Genetical Research, vol. 76, no. 3, pp. 261–272, 2000, ISSN: 00166723.
@article{magoulas_comparison_2000,
title = {Comparison of genetic variability and parentage in different ploidy classes of the Japanese oyster Crassostrea gigas},
author = {A Magoulas and G Kotoulas and A Gérard and Y Naciri-Graven and E Dermitzakis and A J S Hawkins},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034520835&doi=10.1017%2fS0016672300004778&partnerID=40&md5=6f9a177082cb2cf8620b0bf2ba31d383},
doi = {10.1017/S0016672300004778},
issn = {00166723},
year = {2000},
date = {2000-01-01},
journal = {Genetical Research},
volume = {76},
number = {3},
pages = {261--272},
abstract = {Chemical treatments with cytochalasin B were used to induce triploidy in the progeny of a mass fertilization of 3 male and 7 female Crassostrea gigas parents. Triploids were produced either by retention of the first (meiosis I (MI) triploids) or the second (meiosis II (MII) triploids) polar bodies. These animals, together with their diploid siblings, were divided for two experiments. One set was used to compare physiological performance, and the other set deployed to compare growth in two different natural environments. For both experiments, genetic variability in different ploidy classes was estimated using three microsatellite loci and eight allozyme loci. The microsatellite loci were highly polymorphic, allowing independent confirmation of ploidy status and the unambiguous identification of parentage for each oyster. Significant differences in parentage were found between ploidy classes, despite the fact they originated from the same mass fertilization. This indicates that the assumptions of a common genetic background among random samples of animals taken from the same mass fertilization may be generally valid. Knowledge of parentage also allowed the more accurate scoring of allozyme loci. As expected, triploids were found to be significantly more polymorphic than diploids. However, MI triploids were not significantly more polymorphic than MII triploids. MII triploid genotypes were used to estimate recombination rates between loci and their centromeres. These rates varied between 0.29 and 0.71, indicating only moderate chiasma interference.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Chemical treatments with cytochalasin B were used to induce triploidy in the progeny of a mass fertilization of 3 male and 7 female Crassostrea gigas parents. Triploids were produced either by retention of the first (meiosis I (MI) triploids) or the second (meiosis II (MII) triploids) polar bodies. These animals, together with their diploid siblings, were divided for two experiments. One set was used to compare physiological performance, and the other set deployed to compare growth in two different natural environments. For both experiments, genetic variability in different ploidy classes was estimated using three microsatellite loci and eight allozyme loci. The microsatellite loci were highly polymorphic, allowing independent confirmation of ploidy status and the unambiguous identification of parentage for each oyster. Significant differences in parentage were found between ploidy classes, despite the fact they originated from the same mass fertilization. This indicates that the assumptions of a common genetic background among random samples of animals taken from the same mass fertilization may be generally valid. Knowledge of parentage also allowed the more accurate scoring of allozyme loci. As expected, triploids were found to be significantly more polymorphic than diploids. However, MI triploids were not significantly more polymorphic than MII triploids. MII triploid genotypes were used to estimate recombination rates between loci and their centromeres. These rates varied between 0.29 and 0.71, indicating only moderate chiasma interference.
Huvet, Arnaud; Lapègue, S; Magoulas, A; Boudry, P
Mitochondrial and nuclear DNA phylogeography of Crassostrea angulata, the Portuguese oyster endangered in Europe Journal Article
In: Conservation Genetics, vol. 1, no. 3, pp. 251–262, 2000, ISSN: 15660621.
@article{huvet_mitochondrial_2000,
title = {Mitochondrial and nuclear DNA phylogeography of Crassostrea angulata, the Portuguese oyster endangered in Europe},
author = {Arnaud Huvet and S Lapègue and A Magoulas and P Boudry},
url = {http://link.springer.com/10.1023/A:1011505805923},
doi = {10.1023/A:1011505805923},
issn = {15660621},
year = {2000},
date = {2000-01-01},
urldate = {2020-08-09},
journal = {Conservation Genetics},
volume = {1},
number = {3},
pages = {251--262},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
1999
Batargias, C; Dermitzakis, E; Magoulas, A; Zouros, E
Characterization of six polymorphic microsatellite markers in gilthead sea bream, Sparus aurata (Linnaeus 1758) Journal Article
In: Molecular Ecology, vol. 8, pp. 897–898, 1999.
@article{batargias_characterization_1999,
title = {Characterization of six polymorphic microsatellite markers in gilthead sea bream, Sparus aurata (Linnaeus 1758)},
author = {C Batargias and E Dermitzakis and A Magoulas and E Zouros},
year = {1999},
date = {1999-01-01},
journal = {Molecular Ecology},
volume = {8},
pages = {897--898},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
1998
Magoulas, A; Gjetvaj, B; Terzoglou, V; Zouros, E
Three polymorphic microsatellites in the Japanese oyster, Crassostrea gigas (Thunberg) Journal Article
In: Animal Genetics, vol. 29, pp. 69 – 70, 1998.
@article{magoulas_three_1998,
title = {Three polymorphic microsatellites in the Japanese oyster, Crassostrea gigas (Thunberg)},
author = {A Magoulas and B Gjetvaj and V Terzoglou and E Zouros},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-0031869608&partnerID=40&md5=d61c90542e845be7feace22b67b93902},
year = {1998},
date = {1998-01-01},
journal = {Animal Genetics},
volume = {29},
pages = {69 -- 70},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Magoulas, A
Application of molecular markers to aquaculture and broodstock management with special emphasis on microsatellite DNA Journal Article
In: Cahiers Options Mediterrannes, vol. 34, pp. 153– 168, 1998.
@article{magoulas_application_1998,
title = {Application of molecular markers to aquaculture and broodstock management with special emphasis on microsatellite DNA},
author = {A Magoulas},
year = {1998},
date = {1998-01-01},
journal = {Cahiers Options Mediterrannes},
volume = {34},
pages = {153-- 168},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Magoulas, A; Kotoulas, G; Batargias, C; Zouros, E
Genetic markers in marine biology and aquaculture research: when to use what Book Section
In: Agnese, J F (Ed.): Genetics and Aquaculture in Africa, pp. 67–78, ORSTOM, Paris, 1998, (Backup Publisher: ORSTOM).
@incollection{magoulas_genetic_1998,
title = {Genetic markers in marine biology and aquaculture research: when to use what},
author = {A Magoulas and G Kotoulas and C Batargias and E Zouros},
editor = {J F Agnese},
year = {1998},
date = {1998-01-01},
booktitle = {Genetics and Aquaculture in Africa},
pages = {67--78},
publisher = {ORSTOM},
address = {Paris},
note = {Backup Publisher: ORSTOM},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
Dermitzakis, E; Clark, A; Batargias, C; Magoulas, A; Zouros, E
Negative covariance indicates mutation bias in a two-locus microsatellite system in the fish Sparus aurata Journal Article
In: Genetics, vol. 150, pp. 1567–1575, 1998.
@article{dermitzakis_negative_1998,
title = {Negative covariance indicates mutation bias in a two-locus microsatellite system in the fish Sparus aurata},
author = {E Dermitzakis and A Clark and C Batargias and A Magoulas and E Zouros},
year = {1998},
date = {1998-01-01},
journal = {Genetics},
volume = {150},
pages = {1567--1575},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
1997
Volckaert, F; Alvarez, M C; Argenton, F; Bonhomme, F; Chatain, B; Colombo, L; Castilho, R; Chevassus, B; Gorshkova, G; Kohler, M; Magoulas, A; Martinez, G; McAndrew, B; Piferrer, F; Vandeputte, M; Zanuy, S
Has time come for the genetic management of sea bass? Journal Article
In: Aquaculture Europe, vol. 22, no. 2, pp. 46–47, 1997.
@article{volckaert_has_1997,
title = {Has time come for the genetic management of sea bass?},
author = {F Volckaert and M C Alvarez and F Argenton and F Bonhomme and B Chatain and L Colombo and R Castilho and B Chevassus and G Gorshkova and M Kohler and A Magoulas and G Martinez and B McAndrew and F Piferrer and M Vandeputte and S Zanuy},
year = {1997},
date = {1997-01-01},
journal = {Aquaculture Europe},
volume = {22},
number = {2},
pages = {46--47},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
1996
Magoulas, A; Tsimenides, N; Zouros, E
In: Molecular Biology and Evolution, vol. 13, no. 1, pp. 178–190, 1996, ISSN: 0737-4038, 1537-1719.
@article{magoulas_mitochondrial_1996,
title = {Mitochondrial DNA phylogeny and the reconstruction of the population history of a species: the case of the European anchovy (Engraulis encrasicolus)},
author = {A Magoulas and N Tsimenides and E Zouros},
url = {https://academic.oup.com/mbe/article-lookup/doi/10.1093/oxfordjournals.molbev.a025554},
doi = {10.1093/oxfordjournals.molbev.a025554},
issn = {0737-4038, 1537-1719},
year = {1996},
date = {1996-01-01},
urldate = {2020-08-09},
journal = {Molecular Biology and Evolution},
volume = {13},
number = {1},
pages = {178--190},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
1995
Magoulas, A; Sophronides, K; Patarnello, T; Hatzilaris, E; Zouros, E
Mitochondrial DNA variation in an experimental stock of gilthead sea bream (Sparus aurata) Journal Article
In: Molecular Marine Biology and Biotechnology, vol. 4, pp. 110–116, 1995.
@article{magoulas_mitochondrial_1995,
title = {Mitochondrial DNA variation in an experimental stock of gilthead sea bream (Sparus aurata)},
author = {A Magoulas and K Sophronides and T Patarnello and E Hatzilaris and E Zouros},
year = {1995},
date = {1995-01-01},
journal = {Molecular Marine Biology and Biotechnology},
volume = {4},
pages = {110--116},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kotoulas, Georgios; Magoulas, Antonios; Tsimenides, N; Zouros, E
Marked mitochondrial DNA differences between Mediterranean and Atlantic populations of the swordfish, Xiphias gladius Journal Article
In: Molecular Ecology, vol. 4, no. 4, pp. 473–482, 1995, ISSN: 09621083.
@article{kotoulas_marked_1995,
title = {Marked mitochondrial DNA differences between Mediterranean and Atlantic populations of the swordfish, Xiphias gladius},
author = {Georgios Kotoulas and Antonios Magoulas and N Tsimenides and E Zouros},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0028874118&doi=10.1111%2fj.1365-294X.1995.tb00241.x&partnerID=40&md5=529a83d003e7708c8e88bcf66c58b29e},
doi = {10.1111/j.1365-294X.1995.tb00241.x},
issn = {09621083},
year = {1995},
date = {1995-01-01},
journal = {Molecular Ecology},
volume = {4},
number = {4},
pages = {473--482},
abstract = {Restriction analysis of mitochondrial DNA (mtDNA) from 204 individuals of swordfish (Xiphias gladius) revealed no differentiation among samples from three sites in the Mediterranean Sea (Greece, Italy, Spain), but a high degree of differentiation between Mediterranean samples and a sample from the Gulf of Guinea. A fifth sample from the Atlantic side of the Straits of Gibraltar (Tarifa) consisted mostly of mitotypes that are common in the Mediterranean, but contained several of mtDNA types of the Guinea sample not found in the Mediterranean. We conclude that, in spite of free migration of swordfish across the Straits of Gibraltar, little genetic exchange occurs between the populations inhabiting the Mediterranean Sea and the tropical Atlantic ocean. This is the first evidence of genetic differentiation among geographic populations of this highly mobile species that supports a world‐wide fishery. Copyright © 1995, Wiley Blackwell. All rights reserved},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Restriction analysis of mitochondrial DNA (mtDNA) from 204 individuals of swordfish (Xiphias gladius) revealed no differentiation among samples from three sites in the Mediterranean Sea (Greece, Italy, Spain), but a high degree of differentiation between Mediterranean samples and a sample from the Gulf of Guinea. A fifth sample from the Atlantic side of the Straits of Gibraltar (Tarifa) consisted mostly of mitotypes that are common in the Mediterranean, but contained several of mtDNA types of the Guinea sample not found in the Mediterranean. We conclude that, in spite of free migration of swordfish across the Straits of Gibraltar, little genetic exchange occurs between the populations inhabiting the Mediterranean Sea and the tropical Atlantic ocean. This is the first evidence of genetic differentiation among geographic populations of this highly mobile species that supports a world‐wide fishery. Copyright © 1995, Wiley Blackwell. All rights reserved
1993
Magoulas, A; Kotoulas, G; Tsimenides, N; Zouros, E; la Serna, J M De; Metrio, G De
Genetic structure of swordfish (Xiphias gladius) populations of the Mediterranean and the eastern side of the Atlantic: analysis by mitochondrial DNA markers Journal Article
In: ICCAT Collective Volume of Scientific Papers, vol. XL, pp. 126–136, 1993.
@article{magoulas_genetic_1993,
title = {Genetic structure of swordfish (Xiphias gladius) populations of the Mediterranean and the eastern side of the Atlantic: analysis by mitochondrial DNA markers},
author = {A Magoulas and G Kotoulas and N Tsimenides and E Zouros and J M De la Serna and G De Metrio},
year = {1993},
date = {1993-01-01},
journal = {ICCAT Collective Volume of Scientific Papers},
volume = {XL},
pages = {126--136},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
1984
Matsakis, Ι; Frentzos, A; Magoulas, A; Molfetas, S; Bournazos, D
Observations Bio-ecologiques sur certaines populations insulaires de Ligidium de Grece (Isopode, Oniscoidae) Journal Article
In: Biologia Gallo-Hellenica, vol. 11, pp. 137–147, 1984.
@article{matsakis_observations_1984,
title = {Observations Bio-ecologiques sur certaines populations insulaires de Ligidium de Grece (Isopode, Oniscoidae)},
author = {Ι Matsakis and A Frentzos and A Magoulas and S Molfetas and D Bournazos},
year = {1984},
date = {1984-01-01},
journal = {Biologia Gallo-Hellenica},
volume = {11},
pages = {137--147},
keywords = {},
pubstate = {published},
tppubtype = {article}
}