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3 results on '"évolution génomique des poissons"'

1. Evolution of gene expression after whole-genome duplication: New insights from the spotted gar genome

Author

Peter Batzel, Cédric Cabau, Yann Guiguen, Jérôme Montfort, John H. Postlethwait, Christophe Klopp, Elodie Jouanno, Thuy Thao Vi Nguyen, Laurent Journot, Ingo Braasch, Jeremy Pasquier, Camille Berthelot, Julien Bobe, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Michigan State University [East Lansing], Michigan State University System, Institute of Neuroscience, University of Oregon [Eugene], Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, École normale supérieure - Cachan (ENS Cachan), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), This work was supported by ANR under grant agreement #ANR-10-GENM-017 (PhyloFish) to JB, NIH grants R01 OD011116 (alias R01 RR020833) and R24 OD01119004 (J.H.P.), a Feodor Lynen Fellowship from the Alexander von Humboldt Foundation and the Volkswagen Foundation Initiative Evolutionary Biology, grant I/84 815 (I.B.), ANR-10-GENM-0017,PhyloFish,Analyse phylogénomique des duplications géniques chez les poissons téléostéens: une approche par RNA-Seq(2010), Institute of Neuroscience, University of Oregon, Eugene, Oregon, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Unité de Biométrie et Intelligence Artificielle (UBIA), R01 OD011116 (alias R01 RR020833) and R24 OD01119004, National Institutes of Health, Alexander von Humboldt-Stiftung, I/84 815, Volkswagen Foundation, Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), ProdInra, Migration, Génomique, Biotechnologies végétales - Analyse phylogénomique des duplications géniques chez les poissons téléostéens: une approche par RNA-Seq - - PhyloFish2010 - ANR-10-GENM-0017 - Génomique - VALID, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ANR-10-GENM-017 (PhyloFish), Agence Nationale de la Recherche, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], Lineage (evolution), poisson zèbre, [SDV.GEN] Life Sciences [q-bio]/Genetics, [MATH] Mathematics [math], Genome, 0302 clinical medicine, poisson, cyprinidae, Gene Duplication, Gene duplication, évolution génomique des poissons, [MATH]Mathematics [math], duplication des génomes, Zebrafish, ComputingMilieux_MISCELLANEOUS, Genetics, 0303 health sciences, teleost, biology, Fishes, Spotted gar, lepisosteus oculatus, oryzias latipes, [SDV] Life Sciences [q-bio], medaka, PhyloFish, transcriptome, zebrafish, danio rerio, Molecular Medicine, Neofunctionalization, teleosteen, expression des gènes, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, [INFO] Computer Science [cs], Article, reproduction, Evolution, Molecular, 03 medical and health sciences, Species Specificity, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, [INFO]Computer Science [cs], adrianichthyidae, 14. Life underwater, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Whole genome sequencing, [SDV.GEN]Life Sciences [q-bio]/Genetics, lepisosteidae, génome, biology.organism_classification, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Gene Expression Regulation, Evolutionary biology, lépisosté tacheté, fonction des gènes, Subfunctionalization, Animal Science and Zoology, 030217 neurology & neurosurgery, Developmental Biology
Abstract

Whole genome duplications (WGD) are important evolutionary events. Our understanding of underlying mechanisms, including the evolution of duplicated genes after WGD, however remains incomplete. Teleost fish experienced a common WGD (teleost-specific genome duplication, or TGD) followed by a dramatic adaptive radiation leading to more than half of all vertebrate species. The analysis of gene expression patterns following TGD at the genome level has been limited by the lack of suitable genomic resources. The recent concomitant release of the genome sequence of spotted gar (a representative of holosteans, the closest lineage of teleosts that lacks the TGD) and the tissue-specific gene expression repertoires of over 20 holostean and teleostean fish species, including spotted gar, zebrafish and medaka (the PhyloFish project), offered a unique opportunity to study the evolution of gene expression following TGD in teleosts. We show that most TGD duplicates gained their current status (loss of one duplicate gene or retention of both duplicates) relatively rapidly after TGD (i.e. prior to the divergence of medaka and zebrafish lineages). The loss of one duplicate is the most common fate after TGD with a probability of approximately 80%. In addition, the fate of duplicate genes after TGD, including subfunctionalization, neofunctionalization, or retention of two ‘similar’ copies occurred not only before, but also after the radiation of species tested, in consistency with a role of the TGD in speciation and/or evolution of gene function. Finally, we report novel cases of TGD ohnolog subfunctionalization and neofunctionalization that further illustrate the importance of these processes.

Published
2017
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2. Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

Author

James W. Kijas, William S. Davidson, Steinar Bergseth, Patricia Iturra, Jon Olav Vik, Rachael J. Ritchie, Louis Bernatchez, Yniv Palti, Anna Wargelius, José M. Yáñez, Ross D. Houston, Craig R. Primmer, Matthew L. Rise, Kerry A. Naish, Alejandro Maass, Kristinn Olafsson, Tom Goldammer, Alfredo Tello, Patricia M. Schulte, Philip McGinnity, Martin Montecino, Sigbjørn Lien, Barbara F. Nowak, Krista M. Nichols, Ben F. Koop, Caird E. Rexroad, Yann Guiguen, Samuel A.M. Martin, Cristian Gallardo-Escárate, Stig W. Omholt, Graham Plastow, Simen Rød Sandve, Rodrigo Vidal, Daniel J. Macqueen, Institute of Biological and Environmental Sciences, (SFIRC), Department of Biology, Northern Arizona University [Flagstaff], The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Institute for Marine and Antarctic Studies [Horbat] (IMAS), University of Tasmania [Hobart, Australia] (UTAS), Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval [Québec] (ULaval), The Research Council of Norway, Department of Molecular Biology and Biochemistry, University of California [Irvine] (UCI), University of California-University of California, Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research, Department of Oceanography, Universidad de Concepción [Chile], Institute for Genome Biology, Fish Genetics Unit, Leibniz Institute for Farm Animal Biology (FBN), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Human Genetics Program ICBM Faculty of Medicine, University of Chile, CSIRO, Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (NMBU), Center for Mathematical Modelling - Centro de Modelamiento Matematico [Santiago] (CMM), Universidad de Chile = University of Chile [Santiago] (UCHILE)-Centre National de la Recherche Scientifique (CNRS), Center for Genome Regulation, FONDAP 15090007, School of Biological, Earth and Environmental Sciences [Sydney] (BEES), University of New South Wales [Sydney] (UNSW), Center for Biomedical Research, Universidad Andrés Bello [Santiago] (UNAB), FONDAP Center for Genome Regulation, Faculty of Biological Sciences and Faculty of Medicine, School of Aquatic and Fishery Sciences, University of Washington [Seattle], Conservation Biology Division [Seattle], Northwest Fisheries Science Center (NWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), National Center for Cool and Cold Water Aquaculture, ARS-USDA, USDA-ARS : Agricultural Research Service, Department of Agricultural, Food, and Nutritional Science, University of Alberta, Office of National Programs, Department of Ocean Sciences, Memorial University of Newfoundland [St. John's], Genome British Columbia, Department of Zoology, Auburn University (AU), INTESAL de SalmonChile, Instituto Tecnológico del Salmón S.A., Laboratory of Molecular Ecology, Genomics, and Evolutionary Studies, Department of Biology, University of Santiago, Norwegian Institute of Marine Research, Faculty of Veterinary and Animal Sciences, Universidad de Chile = University of Chile [Santiago] (UCHILE), Aquainnovo, Supported by the International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG), funded by: The Research Council of Norway (RCN), The Norwegian Seafood Research Fund (FHF), Genome British Columbia (GBC, Canada), The Chilean Economic Development Agency (CORFO) and the Innova Chile Committee (InnovaChile). FAASG has also received support from the Biotechnology and Biological Sciences Research Council (UK) (ref: BB/P02582X/1). Initial FAASG pilot studies (currently in process) are being funded by the ICSASG and the U.S. Department of Agriculture (USDA), through NIFA National Research Support Project 8., University of Tasmania (UTAS), Université Laval, Universidad de Concepción, Leibniz Institute for Farm Animal Biology, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), University of Chile [Santiago]-Centre National de la Recherche Scientifique (CNRS), Matis Ltd, National Center for Cool and Cold Water Aquaculture, University of Chile [Santiago], and Supported by the International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG), funded by: The Research Council of Norway (RCN), The Norwegian Seafood Research Fund (FHF), Genome British Columbia (GBC, Canada)), The Chilean Economic Development Agency (CORFO) and the Innova Chile Committee (InnovaChile). FAASG has also received support from the Biotechnology and Biological Sciences Research Council (UK) (ref: BB/P02582X/1). Initial FAASG pilot studies (currently in process) are being funded by the ICSASG and the U.S. Department of Agriculture (USDA), through NIFA National Research Support Project 8.

Subjects
0106 biological sciences, 0301 basic medicine, biologie comparative, Internationality, [SDV]Life Sciences [q-bio], Resistance, génomique fonctionnelle, Aquaculture, 01 natural sciences, Genome, genomic selection, Whole genome duplication, poisson, salmonids, Applied research, évolution génomique des poissons, duplication des génomes, Phylogeny, Genetics, DNA methylation, Populations, Functional annotation, Genomics, Salar, ChIP-seq, phénotype, Rainbow trout, Molecular Sequence Annotation, séquençage du génome, Editorial, Phenotype, Phenotyping, aquaculture, comparative biology, data sharing, evolution, functional annotation, genome biology, phenotyping, standardized data and metadata, salmonid fish, whole genome duplication, Identification (biology), annotation fonctionnelle, Salmonidae, Biotechnology, expression des gènes, Atlantic salmon, Genome evolution, Conservation of Natural Resources, lcsh:QH426-470, Evolution, lcsh:Biotechnology, Comparative biology, Biology, Insights, 010603 evolutionary biology, production aquacole, reproduction, Evolution, Molecular, 03 medical and health sciences, analyse de génome, Standardized data and metadata, lcsh:TP248.13-248.65, Animals, 14. Life underwater, sélection génomique, conservation des espèces, fish, Oncorhynchus tshawytscha, lcsh:Genetics, 030104 developmental biology, Genome biology, Evolutionary biology, variation phénotypique, Genome Biology, Standardized data and, Data sharing, évolution génomique, Salmonid fish
Abstract

We describe an emerging initiative - the ‘Functional Annotation of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance. © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/)

Published
2017
Full Text
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3. Functional Analysis of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

Author

Macqueen, Daniel J., Primmer, Craig R., Houston, Ross D., Nowak, Barbara F., Bernatchez, Louis, Bergseth, Steinar, Davidson, William S., Gallardo-Escárate, Cristian, Goldammer, Tom, Guiguen, Yann, Iturra, Patricia, Kijas, James W., Koop, Ben F., Lien, Sigbjørn, Maass, Alejandro, Martin, Samuel A.M., McGinnity, Philip, Montecino, Martin, Naish, Kerry A., Nichols, Krista M., Ólafsson, Kristinn, Omholt, Stig W., Palti, Yniv, Plastow, Graham S., Rexroad, Caird E., Rise, Matthew L., Ritchie, Rachael J., Sandve, Simen R., Schulte, Patricia M., Tello, Alfredo, Vidal, Rodrigo, Vik, Jon O., Wargelius, Anna, and Yáñez, José Manuel

Subjects
salmonidae, biologie comparative, génomique fonctionnelle, production aquacole, reproduction, analyse de génome, phénotype, séquençage du génome, poisson, aquaculture, variation phénotypique, comparative biology, data sharing, evolution, functional annotation, genome biology, phenotyping, standardized data and metadata, salmonid fish, whole genome duplication, évolution génomique des poissons, sélection génomique, évolution génomique, annotation fonctionnelle, conservation des espèces, duplication des génomes, expression des gènes
Abstract

We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

Published
2016

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