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

Camille Berthelot, Frédéric Brunet, Domitille Chalopin, Amélie Juanchich, Maria Bernard, Benjamin Noël, Pascal Bento, Corinne Da Silva, Karine Labadie, Adriana Alberti, Jean-Marc Aury, Alexandra Louis, Patrice Dehais, Philippe Bardou, Jérôme Montfort, Christophe Klopp, Cédric Cabau, Christine Gaspin, Gary H. Thorgaard, Mekki Boussaha, Edwige Quillet, René Guyomard, Delphine Galiana, Julien Bobe, Jean-Nicolas Volff, Carine Genêt, Patrick Wincker, Olivier Jaillon, Hugues Roest Crollius and Yann Guiguen ()
Additional contact information
Camille Berthelot: Ecole Normale Supérieure, Institut de Biologie de l’Ecole Normale Supérieur, IBENS
Frédéric Brunet: Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieur de Lyon-CNRS UMR 5242–UCBL, 46, allée d'Italie
Domitille Chalopin: Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieur de Lyon-CNRS UMR 5242–UCBL, 46, allée d'Italie
Amélie Juanchich: INRA, UR1037 Fish Physiology and Genomics
Maria Bernard: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux
Benjamin Noël: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux
Pascal Bento: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux
Corinne Da Silva: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux
Karine Labadie: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux
Adriana Alberti: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux
Jean-Marc Aury: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux
Alexandra Louis: Ecole Normale Supérieure, Institut de Biologie de l’Ecole Normale Supérieur, IBENS
Patrice Dehais: INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627
Philippe Bardou: INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627
Jérôme Montfort: INRA, UR1037 Fish Physiology and Genomics
Christophe Klopp: INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627
Cédric Cabau: INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627
Christine Gaspin: INRA, UBIA UR 875
Gary H. Thorgaard: School of Biological Sciences, Washington State University
Mekki Boussaha: INRA, UMR 1313 Génétique Animale et Biologie Intégrative
Edwige Quillet: INRA, UMR 1313 Génétique Animale et Biologie Intégrative
René Guyomard: INRA, UMR 1313 Génétique Animale et Biologie Intégrative
Delphine Galiana: Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieur de Lyon-CNRS UMR 5242–UCBL, 46, allée d'Italie
Julien Bobe: INRA, UR1037 Fish Physiology and Genomics
Jean-Nicolas Volff: Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieur de Lyon-CNRS UMR 5242–UCBL, 46, allée d'Italie
Carine Genêt: INRA, UMR 1313 Génétique Animale et Biologie Intégrative
Patrick Wincker: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux
Olivier Jaillon: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux
Hugues Roest Crollius: Ecole Normale Supérieure, Institut de Biologie de l’Ecole Normale Supérieur, IBENS
Yann Guiguen: INRA, UR1037 Fish Physiology and Genomics

Nature Communications, 2014, vol. 5, issue 1, 1-10

Abstract: 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.

Date: 2014
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DOI: 10.1038/ncomms4657

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