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

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, David Jaffe, Sheila Fisher, Georges Lutfalla, Carole Dossat, Béatrice Segurens, Corinne Dasilva, Marcel Salanoubat, Michael Levy, Nathalie Boudet, Sergi Castellano, Véronique Anthouard, Claire Jubin, Vanina Castelli, Michael Katinka, Benoît Vacherie, Christian Biémont, Zineb Skalli, Laurence Cattolico, Julie Poulain, Véronique de Berardinis, Corinne Cruaud, Simone Duprat, Philippe Brottier, Jean-Pierre Coutanceau, Jérôme Gouzy, Genis Parra, Guillaume Lardier, Charles Chapple, Kevin J. McKernan, Paul McEwan, Stephanie Bosak, Manolis Kellis, Jean-Nicolas Volff, Roderic Guigó, Michael C. Zody, Jill Mesirov, Kerstin Lindblad-Toh, Bruce Birren, Chad Nusbaum, Daniel Kahn, Marc Robinson-Rechavi, Vincent Laudet, Vincent Schachter, Francis Quétier, William Saurin, Claude Scarpelli, Patrick Wincker, Eric S. Lander, Jean Weissenbach () and Hugues Roest Crollius
Additional contact information
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
Jean Weissenbach: UMR 8030 Genoscope, CNRS and Université d'Evry
Hugues Roest Crollius: UMR 8030 Genoscope, CNRS and Université d'Evry

Nature, 2004, vol. 431, issue 7011, 946-957

Abstract: 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.

Date: 2004
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DOI: 10.1038/nature03025

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