IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v5y2014i1d10.1038_ncomms4657.html
   My bibliography  Save this article

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

Author

Listed:
  • Camille Berthelot

    (Ecole Normale Supérieure, Institut de Biologie de l’Ecole Normale Supérieur, IBENS
    Inserm, U1024
    CNRS, UMR 8197
    CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux)

  • 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
    INRA, UMR 1313 Génétique Animale et Biologie Intégrative)

  • 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
    Inserm, U1024
    CNRS, UMR 8197)

  • 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
    INRA, Plateforme Bioinformatique, 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
    Université d’Evry, UMR 8030
    Centre National de la Recherche Scientifique (CNRS), UMR 8030)

  • Olivier Jaillon

    (CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux
    Université d’Evry, UMR 8030
    Centre National de la Recherche Scientifique (CNRS), UMR 8030)

  • Hugues Roest Crollius

    (Ecole Normale Supérieure, Institut de Biologie de l’Ecole Normale Supérieur, IBENS
    Inserm, U1024
    CNRS, UMR 8197)

  • Yann Guiguen

    (INRA, UR1037 Fish Physiology and Genomics)

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.

Suggested Citation

  • Camille Berthelot & Frédéric Brunet & Domitille Chalopin & Amélie Juanchich & Maria Bernard & Benjamin Noël & Pascal Bento & Corinne Da Silva & Karine Labadie & Adriana Alberti & Jean-Marc Aury & Alex, 2014. "The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates," Nature Communications, Nature, vol. 5(1), pages 1-10, May.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms4657
    DOI: 10.1038/ncomms4657
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms4657
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/ncomms4657?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Min-Rui-Xuan Xu & Zhen-Yang Liao & Jordan R. Brock & Kang Du & Guo-Yin Li & Zhi-Qiang Chen & Ying-Hao Wang & Zhong-Nan Gao & Gaurav Agarwal & Kevin H-C Wei & Feng Shao & Shuai Pang & Adrian E. Platts , 2023. "Maternal dominance contributes to subgenome differentiation in allopolyploid fishes," Nature Communications, Nature, vol. 14(1), pages 1-19, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms4657. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.