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Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

Author

Listed:
  • Olivier Jaillon

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Jean-Marc Aury

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Frédéric Brunet

    (Ecole Normale Supérieure de Lyon)

  • Jean-Louis Petit

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Nicole Stange-Thomann

    (Broad Institute of MIT and Harvard)

  • Evan Mauceli

    (Broad Institute of MIT and Harvard)

  • Laurence Bouneau

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Cécile Fischer

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Catherine Ozouf-Costaz

    (Service de Systématique Moléculaire, CNRS IFR 101)

  • Alain Bernot

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Sophie Nicaud

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • David Jaffe

    (Broad Institute of MIT and Harvard)

  • Sheila Fisher

    (Broad Institute of MIT and Harvard)

  • Georges Lutfalla

    (Défenses Antivirales et Antitumorales, CNRS UMR 5124)

  • Carole Dossat

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Béatrice Segurens

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Corinne Dasilva

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Marcel Salanoubat

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Michael Levy

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Nathalie Boudet

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Sergi Castellano

    (IMIM-UPF and Programa de Bioinformàtica i Genòmica (CRG))

  • Véronique Anthouard

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Claire Jubin

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Vanina Castelli

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Michael Katinka

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Benoît Vacherie

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Christian Biémont

    (CNRS UMR 5558 Biométrie et Biologie Evolutive, Université Lyon 1)

  • Zineb Skalli

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Laurence Cattolico

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Julie Poulain

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Véronique de Berardinis

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Corinne Cruaud

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Simone Duprat

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Philippe Brottier

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Jean-Pierre Coutanceau

    (Service de Systématique Moléculaire, CNRS IFR 101)

  • Jérôme Gouzy

    (INRA-CNRS Laboratoire des Interactions Plantes Micro-organismes)

  • Genis Parra

    (IMIM-UPF and Programa de Bioinformàtica i Genòmica (CRG))

  • Guillaume Lardier

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Charles Chapple

    (IMIM-UPF and Programa de Bioinformàtica i Genòmica (CRG))

  • Kevin J. McKernan

    (Agencourt Bioscience Corporation)

  • Paul McEwan

    (Agencourt Bioscience Corporation)

  • Stephanie Bosak

    (Agencourt Bioscience Corporation)

  • Manolis Kellis

    (Broad Institute of MIT and Harvard)

  • Jean-Nicolas Volff

    (Evolutionary Fish Genomics, Physiologische Chemie I, Biozentrum, University of Wuerzburg, Am Hubland)

  • Roderic Guigó

    (IMIM-UPF and Programa de Bioinformàtica i Genòmica (CRG))

  • Michael C. Zody

    (Broad Institute of MIT and Harvard)

  • Jill Mesirov

    (Broad Institute of MIT and Harvard)

  • Kerstin Lindblad-Toh

    (Broad Institute of MIT and Harvard)

  • Bruce Birren

    (Broad Institute of MIT and Harvard)

  • Chad Nusbaum

    (Broad Institute of MIT and Harvard)

  • Daniel Kahn

    (INRA-CNRS Laboratoire des Interactions Plantes Micro-organismes)

  • Marc Robinson-Rechavi

    (Ecole Normale Supérieure de Lyon)

  • Vincent Laudet

    (Ecole Normale Supérieure de Lyon)

  • Vincent Schachter

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Francis Quétier

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • William Saurin

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Claude Scarpelli

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Patrick Wincker

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Eric S. Lander

    (Broad Institute of MIT and Harvard
    Whitehead Institute for Biomedical Research)

  • Jean Weissenbach

    (UMR 8030 Genoscope, CNRS and Université d'Evry)

  • Hugues Roest Crollius

    (UMR 8030 Genoscope, CNRS and Université d'Evry
    CNRS UMR8541, Ecole Normale Supérieure)

Abstract

Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests ∼900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.

Suggested Citation

  • Olivier Jaillon & Jean-Marc Aury & Frédéric Brunet & Jean-Louis Petit & Nicole Stange-Thomann & Evan Mauceli & Laurence Bouneau & Cécile Fischer & Catherine Ozouf-Costaz & Alain Bernot & Sophie Nicaud, 2004. "Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype," Nature, Nature, vol. 431(7011), pages 946-957, October.
    • Handle: RePEc:nat:nature:v:431:y:2004:i:7011:d:10.1038_nature03025
    DOI: 10.1038/nature03025
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    Cited by:

    1. Woranop Sukparangsi & Elena Morganti & Molly Lowndes & Hélène Mayeur & Melanie Weisser & Fella Hammachi & Hanna Peradziryi & Fabian Roske & Jurriaan Hölzenspies & Alessandra Livigni & Benoit Gilbert G, 2022. "Evolutionary origin of vertebrate OCT4/POU5 functions in supporting pluripotency," Nature Communications, Nature, vol. 13(1), pages 1-21, December.

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