Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

Jean-Marc Aury, Olivier Jaillon, Laurent Duret, Benjamin Noel, Claire Jubin, Betina M. Porcel, Béatrice Ségurens, Vincent Daubin, Véronique Anthouard, Nathalie Aiach, Olivier Arnaiz, Alain Billaut, Janine Beisson, Isabelle Blanc, Khaled Bouhouche, Francisco Câmara, Sandra Duharcourt, Roderic Guigo, Delphine Gogendeau, Michael Katinka, Anne-Marie Keller, Roland Kissmehl, Catherine Klotz, France Koll, Anne Le Mouël, Gersende Lepère, Sophie Malinsky, Mariusz Nowacki, Jacek K. Nowak, Helmut Plattner, Julie Poulain, Françoise Ruiz, Vincent Serrano, Marek Zagulski, Philippe Dessen, Mireille Bétermier, Jean Weissenbach, Claude Scarpelli, Vincent Schächter, Linda Sperling, Eric Meyer, Jean Cohen and Patrick Wincker ()
Additional contact information
Jean-Marc Aury: Genoscope and CNRS UMR 8030
Olivier Jaillon: Genoscope and CNRS UMR 8030
Laurent Duret: Laboratoire de Biométrie et Biologie Évolutive CNRS UMR 5558, Université Lyon 1
Benjamin Noel: Genoscope and CNRS UMR 8030
Claire Jubin: Genoscope and CNRS UMR 8030
Betina M. Porcel: Genoscope and CNRS UMR 8030
Béatrice Ségurens: Genoscope and CNRS UMR 8030
Vincent Daubin: Laboratoire de Biométrie et Biologie Évolutive CNRS UMR 5558, Université Lyon 1
Véronique Anthouard: Genoscope and CNRS UMR 8030
Nathalie Aiach: Genoscope and CNRS UMR 8030
Olivier Arnaiz: Centre de Génétique Moléculaire, CNRS
Alain Billaut: Genoscope and CNRS UMR 8030
Janine Beisson: Centre de Génétique Moléculaire, CNRS
Isabelle Blanc: Centre de Génétique Moléculaire, CNRS
Khaled Bouhouche: Laboratoire de Génétique Moléculaire, CNRS UMR 8541, École Normale Supérieure
Francisco Câmara: Universitat Pompeu Fabra
Sandra Duharcourt: Laboratoire de Génétique Moléculaire, CNRS UMR 8541, École Normale Supérieure
Roderic Guigo: Universitat Pompeu Fabra
Delphine Gogendeau: Centre de Génétique Moléculaire, CNRS
Michael Katinka: Genoscope and CNRS UMR 8030
Anne-Marie Keller: Centre de Génétique Moléculaire, CNRS
Roland Kissmehl: University of Konstanz
Catherine Klotz: Centre de Génétique Moléculaire, CNRS
France Koll: Centre de Génétique Moléculaire, CNRS
Anne Le Mouël: Laboratoire de Génétique Moléculaire, CNRS UMR 8541, École Normale Supérieure
Gersende Lepère: Laboratoire de Génétique Moléculaire, CNRS UMR 8541, École Normale Supérieure
Sophie Malinsky: Laboratoire de Génétique Moléculaire, CNRS UMR 8541, École Normale Supérieure
Mariusz Nowacki: Laboratoire de Génétique Moléculaire, CNRS UMR 8541, École Normale Supérieure
Jacek K. Nowak: Polish Academy of Sciences
Helmut Plattner: University of Konstanz
Julie Poulain: Genoscope and CNRS UMR 8030
Françoise Ruiz: Centre de Génétique Moléculaire, CNRS
Vincent Serrano: Laboratoire de Génétique Moléculaire, CNRS UMR 8541, École Normale Supérieure
Marek Zagulski: Polish Academy of Sciences
Philippe Dessen: Laboratoire Génomes et Cancers, FRE 2939 CNRS, Institut Gustave Roussy
Mireille Bétermier: Centre de Génétique Moléculaire, CNRS
Jean Weissenbach: Genoscope and CNRS UMR 8030
Claude Scarpelli: Genoscope and CNRS UMR 8030
Vincent Schächter: Genoscope and CNRS UMR 8030
Linda Sperling: Centre de Génétique Moléculaire, CNRS
Eric Meyer: Laboratoire de Génétique Moléculaire, CNRS UMR 8541, École Normale Supérieure
Jean Cohen: Centre de Génétique Moléculaire, CNRS
Patrick Wincker: Genoscope and CNRS UMR 8030

Nature, 2006, vol. 444, issue 7116, 171-178

Abstract: Abstract The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints.

Date: 2006
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DOI: 10.1038/nature05230

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