1
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Meadows JRS, Kidd JM, Wang GD, Parker HG, Schall PZ, Bianchi M, Christmas MJ, Bougiouri K, Buckley RM, Hitte C, Nguyen AK, Wang C, Jagannathan V, Niskanen JE, Frantz LAF, Arumilli M, Hundi S, Lindblad-Toh K, Ginja C, Agustina KK, André C, Boyko AR, Davis BW, Drögemüller M, Feng XY, Gkagkavouzis K, Iliopoulos G, Harris AC, Hytönen MK, Kalthof DC, Liu YH, Lymberakis P, Poulakakis N, Pires AE, Racimo F, Ramos-Almodovar F, Savolainen P, Venetsani S, Tammen I, Triantafyllidis A, vonHoldt B, Wayne RK, Larson G, Nicholas FW, Lohi H, Leeb T, Zhang YP, Ostrander EA. Author Correction: Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biol 2023; 24:255. [PMID: 37936157 PMCID: PMC10631033 DOI: 10.1186/s13059-023-03101-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Affiliation(s)
- Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden.
| | - Jefrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA.
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Katia Bougiouri
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Reuben M Buckley
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Christophe Hitte
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Julia E Niskanen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Laurent A F Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E14NS, UK and Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, D-80539, Munich, Germany
| | - Meharji Arumilli
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Sruthi Hundi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catarina Ginja
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | | | - Catherine André
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Xin-Yao Feng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Konstantinos Gkagkavouzis
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Giorgos Iliopoulos
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Alexander C Harris
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Daniela C Kalthof
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Petros Lymberakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Nikolaos Poulakakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Ana Elisabete Pires
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | - Fernando Racimo
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | | | - Peter Savolainen
- Department of Gene Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, 17121, Solna, Sweden
| | - Semina Venetsani
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Imke Tammen
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Alexandros Triantafyllidis
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-7246, USA
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3TG, UK
| | - Frank W Nicholas
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA.
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Moulistanos A, Nikolaou T, Sismanoglou S, Gkagkavouzis K, Karaiskou N, Antonopoulou E, Triantafyllidis A, Papakostas S. Investigating the role of genetic variation in vgll3 and six6 in the domestication of gilthead seabream ( Sparus aurata Linnaeus) and European seabass ( Dicentrarchus labrax Linnaeus). Ecol Evol 2023; 13:e10727. [PMID: 38020694 PMCID: PMC10654472 DOI: 10.1002/ece3.10727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Gene function conservation is crucial in molecular ecology, especially for key traits like growth and maturation in teleost fish. The vgll3 and six6 genes are known to influence age-at-maturity in Atlantic salmon, but their impact on other fish species is poorly understood. Here, we investigated the association of vgll3 and six6 in the domestication of gilthead seabream and European seabass, both undergoing selective breeding for growth-related traits in the Mediterranean. We analysed two different sets of samples using two different genotyping approaches. The first dataset comprised farmed and wild populations from Greece, genotyped for SNPs within the two genes ('gene-level genotyping'). The second dataset examined 300-600 k SNPs located in the chromosomes of the two genes, derived from a meta-analysis of a Pool-Seq experiment involving farmed and wild populations distributed widely across the Mediterranean ('chromosome-level genotyping'). The gene-level analysis revealed a statistically significant allele frequency differences between farmed and wild populations on both genes in each species. This finding was partially supported by the chromosome-level analysis, identifying highly differentiated regions may be involved in the domestication process at varying distances from the candidate genes. Noteworthy genomic features were found, such as a CpG island in gilthead seabream and novel candidate genes in European seabass, warranting further investigation. These findings support a putative role of vgll3 and six6 in the maturation and growth of gilthead seabream and European seabass, emphasizing the need for further research on their conserved function.
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Affiliation(s)
- Aristotelis Moulistanos
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Theopisti Nikolaou
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
| | - Smaragda Sismanoglou
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
| | - Konstantinos Gkagkavouzis
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Nikoleta Karaiskou
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Efthimia Antonopoulou
- Department of Zoology, School of BiologyAristotle University of ThessalonikiThessalonikiGreece
| | - Alexandros Triantafyllidis
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Spiros Papakostas
- Department of Science and TechnologyInternational Hellenic UniversityThessalonikiGreece
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3
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Meadows JRS, Kidd JM, Wang GD, Parker HG, Schall PZ, Bianchi M, Christmas MJ, Bougiouri K, Buckley RM, Hitte C, Nguyen AK, Wang C, Jagannathan V, Niskanen JE, Frantz LAF, Arumilli M, Hundi S, Lindblad-Toh K, Ginja C, Agustina KK, André C, Boyko AR, Davis BW, Drögemüller M, Feng XY, Gkagkavouzis K, Iliopoulos G, Harris AC, Hytönen MK, Kalthoff DC, Liu YH, Lymberakis P, Poulakakis N, Pires AE, Racimo F, Ramos-Almodovar F, Savolainen P, Venetsani S, Tammen I, Triantafyllidis A, vonHoldt B, Wayne RK, Larson G, Nicholas FW, Lohi H, Leeb T, Zhang YP, Ostrander EA. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biol 2023; 24:187. [PMID: 37582787 PMCID: PMC10426128 DOI: 10.1186/s13059-023-03023-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/25/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function. RESULTS We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection. CONCLUSIONS We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.
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Affiliation(s)
- Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden.
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA.
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Katia Bougiouri
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Reuben M Buckley
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Christophe Hitte
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA
| | - Chao Wang
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Julia E Niskanen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Laurent A F Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E14NS, UK and Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, D-80539, Munich, Germany
| | - Meharji Arumilli
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Sruthi Hundi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catarina Ginja
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | | | - Catherine André
- University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, 930 Campus Road, Ithaca, NY, 14853, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Xin-Yao Feng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Konstantinos Gkagkavouzis
- Department of Genetics, School of Biology, ), Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Giorgos Iliopoulos
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Alexander C Harris
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Daniela C Kalthoff
- NGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Petros Lymberakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Nikolaos Poulakakis
- Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece
- Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece
- Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Ana Elisabete Pires
- BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal
| | - Fernando Racimo
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | | | - Peter Savolainen
- Department of Gene Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, 17121, Solna, Sweden
| | - Semina Venetsani
- Department of Genetics, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Imke Tammen
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Alexandros Triantafyllidis
- Department of Genetics, School of Biology, ), Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece
| | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-7246, USA
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3TG, UK
| | - Frank W Nicholas
- Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA.
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Moulistanos A, Karaiskou N, Gkagkavouzis K, Minoudi S, Drosopoulou E, Ioannidou C, Panteli N, Zografou S, Karaouglanis D, Kotouzas D, Kontodimas D, Antonopoulou E, Triantafyllidis A. Genetic Identification and Traceability of Insect Meals. Insects 2023; 14:610. [PMID: 37504616 PMCID: PMC10380534 DOI: 10.3390/insects14070610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
Insects have been proposed as a rich alternative source of protein for the partial or total replacement of fishmeal in aquaculture. For maximum safety and effectiveness of insect meals, control of the quality composition of these products is considered mandatory. The aim of this study was the genetic analysis of the composition of commercially available insect meals at the species level. Commercially available Hermetia illucens, Tenebrio molitor and Musca domestica individuals, as well as nine insect meals produced from these species, were analyzed. The genetic identification of insects at the species level was based on a COI fragment, and analysis of the insect meals' composition was performed with the processes of cloning and colony PCR. Genetic analysis indicated that the commercially available larvae morphologically identified as Musca domestica belonged to the species Muscina stabulans. In the commercially available insect meals, no other animal species was identified beyond the expected one. However, in the insect meal produced for research purposes, fungal growth was detected. The used methodology, herein, allows for the qualitative genetic identification of insect meals and could be included in the methods of traceability of products containing insects and other animal species.
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Affiliation(s)
- Aristotelis Moulistanos
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, 57001 Thessaloniki, Greece
| | - Nikoleta Karaiskou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, 57001 Thessaloniki, Greece
| | - Konstantinos Gkagkavouzis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, 57001 Thessaloniki, Greece
| | - Styliani Minoudi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, 57001 Thessaloniki, Greece
| | - Elena Drosopoulou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Chrysanthi Ioannidou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Nikolas Panteli
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Stella Zografou
- Department of Humanities, Social Sciences and Economics, School of Humanities, Social Sciences and Economics, International Hellenic University, 57001 Thessaloniki, Greece
| | - Damianos Karaouglanis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, 57001 Thessaloniki, Greece
| | - Dimitrios Kotouzas
- Laboratory of Agricultural Entomology, Benaki Phytopathological Institute, Kifissia, 14561 Athens, Greece
| | - Dimitrios Kontodimas
- Laboratory of Agricultural Entomology, Benaki Phytopathological Institute, Kifissia, 14561 Athens, Greece
| | - Efthimia Antonopoulou
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, 57001 Thessaloniki, Greece
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5
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Panteli N, Demertzioglou M, Feidantsis K, Karapanagiotis S, Tsele N, Tsakoniti K, Gkagkavouzis K, Mylonas CC, Kormas KA, Mente E, Antonopoulou E. Advances in understanding the mitogenic, metabolic, and cell death signaling in teleost development: the case of greater amberjack (Seriola dumerili, Risso 1810). Fish Physiol Biochem 2022; 48:1665-1684. [PMID: 36459361 DOI: 10.1007/s10695-022-01146-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Cell growth and differentiation signals of insulin-like growth factor-1 (IGF-1), a key regulator in embryonic and postnatal development, are mediated through the IGF-1 receptor (IGF-1R), which activates several downstream pathways. The present study aims to address crucial organogenesis and development pathways including Akt, MAPKs, heat shock response, apoptotic and autophagic machinery, and energy metabolism in relation to IGF-1R activation during five developmental stages of reared Seriola dumerili: 1 day prior to hatching fertilized eggs (D-1), hatching day (D0), 3 days post-hatching larvae (D3), 33 (D33) and 46 (D46) days post-hatching juveniles. During both the fertilized eggs stage and larval-to-juvenile transition, IGF-1R/Akt pathway activation may mediate the hypertrophic signaling, while p44/42 MAPK phosphorylation was apparent at S. dumerili post-hatching processes and juvenile organs completion. On the contrary, apoptosis was induced during embryogenesis and autophagy at hatching day indicating a potential involvement in morphogenetic rearrangements and yolk-sac reserves depletion. Larvae morphogenesis was accompanied by a metabolic turnover with increased substantial energy consumption. The findings of the present study demonstrate the developmental stages-specific shift in critical signaling pathways during the ontogeny of reared S. dumerili.
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Affiliation(s)
- Nikolas Panteli
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Maria Demertzioglou
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Konstantinos Feidantsis
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | | | | | | | - Konstantinos Gkagkavouzis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
- Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Buildings A & B 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001, Thessaloniki, Greece
| | - Constantinos C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, P.O. Box 2214, 71003, Heraklion, Crete, Greece
| | - Konstantinos Ar Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446, Volos, Greece
| | - Eleni Mente
- School of Veterinary Medicine, Laboratory of Ichthyology-Culture and Pathology of Aquatic Animals, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Efthimia Antonopoulou
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
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6
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Tsoupas A, Papavasileiou S, Minoudi S, Gkagkavouzis K, Petriki O, Bobori D, Sapounidis A, Koutrakis E, Leonardos I, Karaiskou N, Triantafyllidis A. DNA barcoding identification of Greek freshwater fishes. PLoS One 2022; 17:e0263118. [PMID: 35081163 PMCID: PMC8791500 DOI: 10.1371/journal.pone.0263118] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 01/12/2022] [Indexed: 11/18/2022] Open
Abstract
Biodiversity is a key factor for the functioning and efficiency of an ecosystem. Greece, though covering a relatively small surface area, hosts a great deal of species diversity. This is especially true for freshwater fishes. In recent years, the traditional methods of species identification have been supplemented by the use of molecular markers. The present study therefore aims to extensively produce DNA barcodes for Greek freshwater fish species and investigate thoroughly if the presently accepted species classification is in agreement with molecular data. A 624-bases long fragment of the COI gene was sequenced, from 406 freshwater fish specimens belonging to 24 genera and originating from 18 lake and river sites. These sequences were used along with 596 sequences from the same genera, recovered from BOLD, for the construction of phylogenetic trees and the estimation of genetic distances between individuals. In total, 1002 sequences belonging to 72 species were analyzed. The method was found to be effective for 55 of 72 studied species. 17 closely related species with low interspecific genetic distances were observed, for which further study is proposed. It should also be noted that, in four cases, cryptic diversity was observed, where groups originally identified as one species exhibited genetic distance great enough to be separated into discrete species. Region specific haplotypes were also detected within populations of 14 species, giving the possibility to identify even the geographic origin of a species. Our findings are discussed in the light of the rich history of the Balkan peninsula and provide a significant steppingstone for the further study of Greek and European freshwater fish biodiversity.
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Affiliation(s)
- Alexandros Tsoupas
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Papavasileiou
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Styliani Minoudi
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Konstantinos Gkagkavouzis
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Olga Petriki
- Faculty of Sciences, Department of Zoology, Laboratory of Ichthyology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitra Bobori
- Faculty of Sciences, Department of Zoology, Laboratory of Ichthyology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail: (DB); (AT)
| | - Argyrios Sapounidis
- Department of Inland Waters and Lagoons, Fisheries Research Institute, Hellenic Agricultural Organization “DEMETER”, Nea Peramos, Kavala, Greece
| | - Emmanouil Koutrakis
- Department of Inland Waters and Lagoons, Fisheries Research Institute, Hellenic Agricultural Organization “DEMETER”, Nea Peramos, Kavala, Greece
| | - Ioannis Leonardos
- Department of Biological Applications and Technologies, Laboratory of Zoology, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Nikoleta Karaiskou
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
- * E-mail: (DB); (AT)
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7
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Theodoridis G, Pechlivanis A, Thomaidis NS, Spyros A, Georgiou CA, Albanis T, Skoufos I, Kalogiannis S, Tsangaris GT, Stasinakis AS, Konstantinou I, Triantafyllidis A, Gkagkavouzis K, Kritikou AS, Dasenaki ME, Gika H, Virgiliou C, Kodra D, Nenadis N, Sampsonidis I, Arsenos G, Halabalaki M, Mikros E. FoodOmicsGR_RI. A Consortium for Comprehensive Molecular Characterisation of Food Products. Metabolites 2021; 11:74. [PMID: 33513809 PMCID: PMC7911248 DOI: 10.3390/metabo11020074] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 12/12/2022] Open
Abstract
The national infrastructure FoodOmicsGR_RI coordinates research efforts from eight Greek Universities and Research Centers in a network aiming to support research and development (R&D) in the agri-food sector. The goals of FoodOmicsGR_RI are the comprehensive in-depth characterization of foods using cutting-edge omics technologies and the support of dietary/nutrition studies. The network combines strong omics expertise with expert field/application scientists (food/nutrition sciences, plant protection/plant growth, animal husbandry, apiculture and 10 other fields). Human resources involve more than 60 staff scientists and more than 30 recruits. State-of-the-art technologies and instrumentation is available for the comprehensive mapping of the food composition and available genetic resources, the assessment of the distinct value of foods, and the effect of nutritional intervention on the metabolic profile of biological samples of consumers and animal models. The consortium has the know-how and expertise that covers the breadth of the Greek agri-food sector. Metabolomics teams have developed and implemented a variety of methods for profiling and quantitative analysis. The implementation plan includes the following research axes: development of a detailed database of Greek food constituents; exploitation of "omics" technologies to assess domestic agricultural biodiversity aiding authenticity-traceability control/certification of geographical/genetic origin; highlighting unique characteristics of Greek products with an emphasis on quality, sustainability and food safety; assessment of diet's effect on health and well-being; creating added value from agri-food waste. FoodOmicsGR_RI develops new tools to evaluate the nutritional value of Greek foods, study the role of traditional foods and Greek functional foods in the prevention of chronic diseases and support health claims of Greek traditional products. FoodOmicsGR_RI provides access to state-of-the-art facilities, unique, well-characterised sample sets, obtained from precision/experimental farming/breeding (milk, honey, meat, olive oil and so forth) along with more than 20 complementary scientific disciplines. FoodOmicsGR_RI is open for collaboration with national and international stakeholders.
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Affiliation(s)
- Georgios Theodoridis
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.P.); (C.V.); (D.K.)
- Biomic_Auth, Bioanalysis and Omics Laboratory, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece; (A.T.); (K.G.)
| | - Alexandros Pechlivanis
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.P.); (C.V.); (D.K.)
- Biomic_Auth, Bioanalysis and Omics Laboratory, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece; (A.T.); (K.G.)
| | - Nikolaos S. Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis, Zografou, 15771 Athens, Greece; (N.S.T.); (A.S.K.); (M.E.D.)
| | - Apostolos Spyros
- Department of Chemistry, University of Crete, Voutes Campus, 71003 Heraklion, Greece;
| | - Constantinos A. Georgiou
- Chemistry Laboratory, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece;
| | - Triantafyllos Albanis
- Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (T.A.); (I.K.)
| | - Ioannis Skoufos
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, University of Ioannina, 47100 Arta, Greece;
| | - Stavros Kalogiannis
- Department of Nutritional Sciences & Dietetics, International Hellenic University, Sindos Campus, 57400 Thessaloniki, Greece; (S.K.); (I.S.)
| | - George Th. Tsangaris
- Proteomics Research Unit, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
| | | | - Ioannis Konstantinou
- Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (T.A.); (I.K.)
| | - Alexander Triantafyllidis
- Biomic_Auth, Bioanalysis and Omics Laboratory, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece; (A.T.); (K.G.)
- Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Konstantinos Gkagkavouzis
- Biomic_Auth, Bioanalysis and Omics Laboratory, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece; (A.T.); (K.G.)
- Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anastasia S. Kritikou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis, Zografou, 15771 Athens, Greece; (N.S.T.); (A.S.K.); (M.E.D.)
| | - Marilena E. Dasenaki
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis, Zografou, 15771 Athens, Greece; (N.S.T.); (A.S.K.); (M.E.D.)
| | - Helen Gika
- Department of Medicine, Laboratory of Forensic Medicine & Toxicology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Christina Virgiliou
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.P.); (C.V.); (D.K.)
- Biomic_Auth, Bioanalysis and Omics Laboratory, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece; (A.T.); (K.G.)
| | - Dritan Kodra
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.P.); (C.V.); (D.K.)
- Biomic_Auth, Bioanalysis and Omics Laboratory, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, B1.4, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece; (A.T.); (K.G.)
| | - Nikolaos Nenadis
- Laboratory of Food Chemistry and Technology, School of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Ioannis Sampsonidis
- Department of Nutritional Sciences & Dietetics, International Hellenic University, Sindos Campus, 57400 Thessaloniki, Greece; (S.K.); (I.S.)
| | - Georgios Arsenos
- Department of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Maria Halabalaki
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupoli Zografou, 15771 Athens, Greece; (M.H.); (E.M.)
| | - Emmanuel Mikros
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupoli Zografou, 15771 Athens, Greece; (M.H.); (E.M.)
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8
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Maroso F, Gkagkavouzis K, De Innocentiis S, Hillen J, do Prado F, Karaiskou N, Taggart JB, Carr A, Nielsen E, Triantafyllidis A, Bargelloni L. Genome-wide analysis clarifies the population genetic structure of wild gilthead sea bream (Sparus aurata). PLoS One 2021; 16:e0236230. [PMID: 33428622 PMCID: PMC7799848 DOI: 10.1371/journal.pone.0236230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/22/2020] [Indexed: 11/30/2022] Open
Abstract
Gilthead sea bream is an important target for both recreational and commercial fishing in Europe, where it is also one of the most important cultured fish. Its distribution ranges from the Mediterranean to the African and European coasts of the North-East Atlantic. Until now, the population genetic structure of this species in the wild has largely been studied using microsatellite DNA markers, with minimal genetic differentiation being detected. In this geographically widespread study, 958 wild gilthead sea bream from 23 locations within the Mediterranean Sea and Atlantic Ocean were genotyped at 1159 genome-wide SNP markers by RAD sequencing. Outlier analyses identified 18 loci potentially under selection. Neutral marker analyses identified weak subdivision into three genetic clusters: Atlantic, West, and East Mediterranean. The latter group could be further subdivided into an Ionian/Adriatic and an Aegean group using the outlier markers alone. Seascape analysis suggested that this differentiation was mainly due to difference in salinity, this being also supported by preliminary genomic functional analysis. These results are of fundamental importance for the development of proper management of this species in the wild and are a first step toward the study of the potential genetic impact of the sea bream aquaculture industry.
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Affiliation(s)
- Francesco Maroso
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro (PD), Italy
| | - Konstantinos Gkagkavouzis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | | | - Jasmien Hillen
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Leuven, Belgium
| | - Fernanda do Prado
- Department of Biological Sciences, São Paulo State University, Bauru, Brazil
| | - Nikoleta Karaiskou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | | | - Adrian Carr
- Fios Genomics Ltd, Edinburgh, United Kingdom
| | - Einar Nielsen
- Section for Population Ecology and Genetics, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Alexandros Triantafyllidis
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro (PD), Italy
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9
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Karaiskou N, Gkagkavouzis K, Minoudi S, Botskaris D, Markou K, Kalafatakis S, Antonopoulou E, Triantafyllidis A. Genetic structure and divergence of tench Tinca tinca European populations. J Fish Biol 2020; 97:930-934. [PMID: 32598030 DOI: 10.1111/jfb.14448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/12/2020] [Accepted: 06/27/2020] [Indexed: 06/11/2023]
Abstract
The tench Tinca tinca is a freshwater species with human-mediated translocations, aquaculture interest and limited information on its genetic structure. mtDNA sequencing analysis of control region and two genes in 50 individuals from five European populations identified two phylogroups, with greater variability than that reported until now, and a hybridization zone in the Danube River region. Restriction analyses of additional samples reveal the complicated genetic structure characteristics of tench's wild and translocated populations, supporting future breeding practices.
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Affiliation(s)
- Nikoleta Karaiskou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Konstantinos Gkagkavouzis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stella Minoudi
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitrios Botskaris
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kyriaki Markou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stavros Kalafatakis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Efthimia Antonopoulou
- Department of Zoology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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10
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Gkagkavouzis K, Karaiskou N, Katopodi T, Leonardos I, Abatzopoulos TJ, Triantafyllidis A. The genetic population structure and temporal genetic stability of gilthead sea bream Sparus aurata populations in the Aegean and Ionian Seas, using microsatellite DNA markers. J Fish Biol 2019; 94:606-613. [PMID: 30746701 DOI: 10.1111/jfb.13932] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
We examined 662 gilthead sea bream Sparus aurata from wild samples of the species in the Aegean and Ionian Seas, using 20 EST-linked microsatellite markers, in three multiplex panels, as well as seven anonymous loci. Most of the markers were revealed to be highly polymorphic. We found low genetic differentiation between the sampling stations/areas with total FST 0.002 (P < 0.05). Based on comparison of five temporal samples, our results indicate genetic data consistency over time for all tested samples, pointing to stable populations, despite reported repeated escape events. Our results confirm the genetic population structure previously observed in these specific areas, using by far more markers than in previous studies in both coding and non-coding DNA loci. The limited genetic structure and the temporal genetic stability indicate neither major genetic differentiation of local populations by geographic isolation nor influence from anthropogenic factors. These results provide a baseline for future reference in any management programme of both wild and farmed population of S. aurata as well as of other aquaculture species with a potential introgression among farmed and wild populations.
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Affiliation(s)
- Konstantinos Gkagkavouzis
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikoleta Karaiskou
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Theodora Katopodi
- Department of Biological Sciences and Preventive Medicine, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Leonardos
- Department of Biological Applications and Technologies, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Theodore J Abatzopoulos
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Alexander Triantafyllidis
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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11
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Maroso F, Hillen JEJ, Pardo BG, Gkagkavouzis K, Coscia I, Hermida M, Franch R, Hellemans B, Van Houdt J, Simionati B, Taggart JB, Nielsen EE, Maes G, Ciavaglia SA, Webster LMI, Volckaert FAM, Martinez P, Bargelloni L, Ogden R. Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species. Mar Genomics 2018; 39:64-72. [PMID: 29496460 DOI: 10.1016/j.margen.2018.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 01/29/2023]
Abstract
The development of Genotyping-By-Sequencing (GBS) technologies enables cost-effective analysis of large numbers of Single Nucleotide Polymorphisms (SNPs), especially in "non-model" species. Nevertheless, as such technologies enter a mature phase, biases and errors inherent to GBS are becoming evident. Here, we evaluated the performance of double digest Restriction enzyme Associated DNA (ddRAD) sequencing in SNP genotyping studies including high number of samples. Datasets of sequence data were generated from three marine teleost species (>5500 samples, >2.5 × 1012 bases in total), using a standardized protocol. A common bioinformatics pipeline based on STACKS was established, with and without the use of a reference genome. We performed analyses throughout the production and analysis of ddRAD data in order to explore (i) the loss of information due to heterogeneous raw read number across samples; (ii) the discrepancy between expected and observed tag length and coverage; (iii) the performances of reference based vs. de novo approaches; (iv) the sources of potential genotyping errors of the library preparation/bioinformatics protocol, by comparing technical replicates. Our results showed use of a reference genome and a posteriori genotype correction improved genotyping precision. Individual read coverage was a key variable for reproducibility; variance in sequencing depth between loci in the same individual was also identified as an important factor and found to correlate to tag length. A comparison of downstream analysis carried out with ddRAD vs single SNP allele specific assay genotypes provided information about the levels of genotyping imprecision that can have a significant impact on allele frequency estimations and population assignment. The results and insights presented here will help to select and improve approaches to the analysis of large datasets based on RAD-like methodologies.
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Affiliation(s)
- F Maroso
- Department of Compared Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy.
| | - J E J Hillen
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium
| | - B G Pardo
- Departmento de Zoología, Genética y Antropología Física, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - K Gkagkavouzis
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - I Coscia
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium; School of Environmental and Life Science, Rm 332, Peel Building, University of Salford, Salford M5 4WT, UK
| | - M Hermida
- Departmento de Zoología, Genética y Antropología Física, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - R Franch
- Department of Compared Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - B Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium
| | - J Van Houdt
- Department of Human Genetics, University of Leuven, O&N I Herestraat 49 - Box 602, B-3000 Leuven, Belgium
| | - B Simionati
- BMR Genomics, Via Redipuglia 21a, Padova, Italy
| | - J B Taggart
- Division of Environmental and Evolutionary Biology, School of Biology and Biochemistry, The Queen's University of Belfast, Belfast BT7 INN, UK
| | - E E Nielsen
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark
| | - G Maes
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium; Department of Human Genetics, University of Leuven, O&N I Herestraat 49 - Box 602, B-3000 Leuven, Belgium; Centre for Sustainable Tropical Fisheries and Aquaculture, Comparative Genomics Centre, College of Marine and Environmental Sciences, Faculty of Science and Engineering, James Cook University, Townsville, 4811, QLD, Australia
| | - S A Ciavaglia
- Science and Advice for Scottish Agriculture, Roddinglaw Road, Edinburgh EH12 9FJ, UK
| | - L M I Webster
- Science and Advice for Scottish Agriculture, Roddinglaw Road, Edinburgh EH12 9FJ, UK
| | - F A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32 Box 2439, B-3000 Leuven, Belgium
| | - P Martinez
- Departmento de Zoología, Genética y Antropología Física, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - L Bargelloni
- Department of Compared Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - R Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
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Karaiskou N, Tsakogiannis A, Gkagkavouzis K, Papika S, Latsoudis P, Kavakiotis I, Pantis J, Abatzopoulos TJ, Triantaphyllidis C, Triantafyllidis A. Greece: a Balkan subrefuge for a remnant red deer (cervus elaphus) population. J Hered 2014; 105:334-44. [PMID: 24558101 DOI: 10.1093/jhered/esu007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A number of phylogeographic studies have revealed the existence of multiple ice age refugia within the Balkan Peninsula, marking it as a biodiversity hotspot. Greece has been reported to harbor genetically differentiated lineages from the rest of Balkans for a number of mammal species. We therefore searched for distinct red deer lineages in Greece, by analyzing 78 samples originating from its last population in Parnitha Mountain (Central Greece). Additionally, we tested the impact of human-induced practices on this population. The presence of 2 discrete mtDNA lineages was inferred: 1) an abundant one not previously sampled in the Balkans and 2) a more restricted one shared with other Balkan populations, possibly the result of successful translocations of Eastern European individuals. Microsatellite-based analyses of 14 loci strongly support the existence of 2 subpopulations with relative frequencies similar to mitochondrial analyses. This study stresses the biogeographic importance of Central Greece as a separate Last Glacial Maximum period refugium within the Balkans. It also delineates the possible effects that recent translocations of red deer populations had on the genetic structuring within Parnitha. We suggest that the Greek red deer population of Parnitha is genetically distinct, and restocking programs should take this genetic evidence into consideration.
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Affiliation(s)
- Nikoleta Karaiskou
- the Department of Genetics, Developmental and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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