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Nat Commun. 2014 Apr 22;5:3657. doi: 10.1038/ncomms4657.

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.

Author information

  • 11] 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.
  • 21] 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].
  • 31] INRA, UR1037 Fish Physiology and Genomics, F-35000 Rennes, France [2].
  • 41] 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.
  • 5CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057 Evry Cedex, France.
  • 61] 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.
  • 7INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, F-31326 Castanet-Tolosan Cedex, France.
  • 8INRA, UR1037 Fish Physiology and Genomics, F-35000 Rennes, France.
  • 91] INRA, UBIA UR 875, F-31320 Castanet-Tolosan, France [2] INRA, Plateforme Bioinformatique, UR 875, F-31320 Castanet-Tolosan, France.
  • 10School of Biological Sciences, Washington State University, PO Box 644236, Pullman, Washington 99164-4236, USA.
  • 11INRA, UMR 1313 Génétique Animale et Biologie Intégrative, F-78350 Jouy-en-Josas, France.
  • 12Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieur de Lyon-CNRS UMR 5242-UCBL, 46, allée d'Italie, F-69364 Lyon Cedex 07, France.
  • 131] 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.

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.

PMID:
24755649
[PubMed - in process]
PMCID:
PMC4071752
Free PMC Article

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