title: The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.
abstract: Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions.
authors.affiliation: 1] Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieur, IBENS, 46 rue d'Ulm, Paris F-75005, France [2] Inserm, U1024, 46 rue d'Ulm, Paris F-75005, France [3] CNRS, UMR 8197, 46 rue d'Ulm, Paris F-75005, France [4] CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057 Evry Cedex, France [5] European Molecular Biology Laboratory-European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Camille
authors.initials: C
authors.lastname: Berthelot
authors.affiliation: 1] Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieur de Lyon-CNRS UMR 5242-UCBL, 46, allée d'Italie, F-69364 Lyon Cedex 07, France [2].
authors.forename: Frédéric
authors.initials: F
authors.lastname: Brunet
authors.affiliation: 1] Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieur de Lyon-CNRS UMR 5242-UCBL, 46, allée d'Italie, F-69364 Lyon Cedex 07, France [2].
authors.forename: Domitille
authors.initials: D
authors.lastname: Chalopin
authors.affiliation: 1] INRA, UR1037 Fish Physiology and Genomics, F-35000 Rennes, France [2].
authors.forename: Amélie
authors.initials: A
authors.lastname: Juanchich
authors.affiliation: 1] CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057 Evry Cedex, France [2] INRA, UMR 1313 Génétique Animale et Biologie Intégrative, F-78350 Jouy-en-Josas, France.
authors.forename: Maria
authors.initials: M
authors.lastname: Bernard
authors.affiliation: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057 Evry Cedex, France.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Noël
authors.affiliation: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057 Evry Cedex, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Bento
authors.affiliation: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057 Evry Cedex, France.
authors.forename: Corinne
authors.initials: C
authors.lastname: Da Silva
authors.affiliation: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057 Evry Cedex, France.
authors.forename: Karine
authors.initials: K
authors.lastname: Labadie
authors.affiliation: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057 Evry Cedex, France.
authors.forename: Adriana
authors.initials: A
authors.lastname: Alberti
authors.affiliation: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057 Evry Cedex, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Aury
authors.affiliation: 1] Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieur, IBENS, 46 rue d'Ulm, Paris F-75005, France [2] Inserm, U1024, 46 rue d'Ulm, Paris F-75005, France [3] CNRS, UMR 8197, 46 rue d'Ulm, Paris F-75005, France.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Louis
authors.affiliation: INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, F-31326 Castanet-Tolosan Cedex, France.
authors.forename: Patrice
authors.initials: P
authors.lastname: Dehais
authors.affiliation: INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, F-31326 Castanet-Tolosan Cedex, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Bardou
authors.affiliation: INRA, UR1037 Fish Physiology and Genomics, F-35000 Rennes, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Montfort
authors.affiliation: INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, F-31326 Castanet-Tolosan Cedex, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.affiliation: INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, F-31326 Castanet-Tolosan Cedex, France.
authors.forename: Cédric
authors.initials: C
authors.lastname: Cabau
authors.affiliation: 1] INRA, UBIA UR 875, F-31320 Castanet-Tolosan, France [2] INRA, Plateforme Bioinformatique, UR 875, F-31320 Castanet-Tolosan, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Gaspin
authors.affiliation: School of Biological Sciences, Washington State University, PO Box 644236, Pullman, Washington 99164-4236, USA.
authors.forename: Gary H
authors.initials: GH
authors.lastname: Thorgaard
authors.affiliation: INRA, UMR 1313 Génétique Animale et Biologie Intégrative, F-78350 Jouy-en-Josas, France.
authors.forename: Mekki
authors.initials: M
authors.lastname: Boussaha
authors.affiliation: INRA, UMR 1313 Génétique Animale et Biologie Intégrative, F-78350 Jouy-en-Josas, France.
authors.forename: Edwige
authors.initials: E
authors.lastname: Quillet
authors.affiliation: INRA, UMR 1313 Génétique Animale et Biologie Intégrative, F-78350 Jouy-en-Josas, France.
authors.forename: René
authors.initials: R
authors.lastname: Guyomard
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieur de Lyon-CNRS UMR 5242-UCBL, 46, allée d'Italie, F-69364 Lyon Cedex 07, France.
authors.forename: Delphine
authors.initials: D
authors.lastname: Galiana
authors.affiliation: INRA, UR1037 Fish Physiology and Genomics, F-35000 Rennes, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Bobe
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieur de Lyon-CNRS UMR 5242-UCBL, 46, allée d'Italie, F-69364 Lyon Cedex 07, France.
authors.forename: Jean-Nicolas
authors.initials: JN
authors.lastname: Volff
authors.affiliation: INRA, UMR 1313 Génétique Animale et Biologie Intégrative, F-78350 Jouy-en-Josas, France.
authors.forename: Carine
authors.initials: C
authors.lastname: Genêt
authors.affiliation: 1] CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057 Evry Cedex, France [2] Université d'Evry, UMR 8030, CP5706 Evry, France [3] Centre National de la Recherche Scientifique (CNRS), UMR 8030, CP5706 Evry, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.affiliation: 1] CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057 Evry Cedex, France [2] Université d'Evry, UMR 8030, CP5706 Evry, France [3] Centre National de la Recherche Scientifique (CNRS), UMR 8030, CP5706 Evry, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Jaillon
authors.affiliation: 1] Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieur, IBENS, 46 rue d'Ulm, Paris F-75005, France [2] Inserm, U1024, 46 rue d'Ulm, Paris F-75005, France [3] CNRS, UMR 8197, 46 rue d'Ulm, Paris F-75005, France.
authors.forename: Hugues
authors.initials: H
authors.lastname: Roest Crollius
authors.affiliation: INRA, UR1037 Fish Physiology and Genomics, F-35000 Rennes, France.
authors.forename: Yann
authors.initials: Y
authors.lastname: Guiguen
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics; D017686:Oncorhynchus mykiss / Q000235:genetics*; D014714:Vertebrates / Q000235:genetics*
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