Comparative genomics of protoploid Saccharomycetaceae
- The Génolevures Consortium1,
- Jean-Luc Souciet2,18,
- Bernard Dujon3,
- Claude Gaillardin4,
- Mark Johnston5,17,
- Philippe V. Baret6,
- Paul Cliften7,
- David J. Sherman8,
- Jean Weissenbach9,
- Eric Westhof10,
- Patrick Wincker9,
- Claire Jubin9,
- Julie Poulain9,
- Valérie Barbe9,
- Béatrice Ségurens9,
- François Artiguenave9,
- Véronique Anthouard9,
- Benoit Vacherie9,
- Marie-Eve Val9,
- Robert S. Fulton11,
- Patrick Minx11,
- Richard Wilson11,
- Pascal Durrens8,
- Géraldine Jean8,
- Christian Marck12,
- Tiphaine Martin8,
- Macha Nikolski8,
- Thomas Rolland3,
- Marie-Line Seret6,
- Serge Casarégola4,
- Laurence Despons2,
- Cécile Fairhead3,
- Gilles Fischer3,
- Ingrid Lafontaine3,
- Véronique Leh2,
- Marc Lemaire13,
- Jacky de Montigny2,
- Cécile Neuvéglise4,
- Agnès Thierry3,
- Isabelle Blanc-Lenfle4,
- Claudine Bleykasten2,
- Julie Diffels6,
- Emilie Fritsch2,
- Lionel Frangeul14,
- Adrien Goëffon8,
- Nicolas Jauniaux2,
- Rym Kachouri-Lafond10,
- Célia Payen3,
- Serge Potier2,
- Lenka Pribylova2,15,
- Christophe Ozanne4,
- Guy-Franck Richard3,
- Christine Sacerdot3,
- Marie-Laure Straub2 and
- Emmanuel Talla16
- 2 Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France;
- 3 Institut Pasteur, CNRS URA2171, University Pierre et Marie Curie, Paris 6 UFR927, F-75724, Paris-CEDEX15, France;
- 4 AgroParisTech, CNRS UMR2585, INRA UMR1238, Microbiologie et Génétique Moléculaire, F-78850 Thiverval-Grignon, France;
- 5 Washington University School of Medicine, Department of Genetics, St. Louis, Missouri 63110, USA;
- 6 Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium;
- 7 Department of Biology, Utah State University, Logan, Utah 84322, USA;
- 8 University of Bordeaux 1, CNRS UMR5800, LaBRI INRIA Bordeaux Sud-Ouest (MAGNOME) F-33405 Talence, France;
- 9 CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d'Evry Val d' Essonne, F-91057 Evry, France;
- 10 Université Louis Pasteur, Architecture et Réactivité de l'ARN, Institut de Biologie moléculaire et cellulaire du CNRS, F-67084 Strasbourg, France;
- 11 Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, St. Louis, Missouri 63108, USA;
- 12 Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, F-91191 Gif-sur-Yvette CEDEX, France;
- 13 Université de Lyon 1, CNRS, UMR5240 Microbiologie, Adaptation et Pathogénie, INSA de Lyon, Villeurbanne, F-69621 Villeurbanne, France;
- 14 Institut Pasteur, Platform Intégration et Analyse génomique, F-75015, Paris, France;
- 15 Institut of Physiology AS CR, Dept. of Membrane Transport, Videnska 1083, 14220 Prague 4, Czech Republic;
- 16 Université de la Méditerranée, Laboratoire de Chimie Bactérienne, CNRS-UPR9043, F-13402 Marseille CEDEX 20, France;
- 17 Present address: Department of Biochemistry and Molecular Genetics, University of Colorado—Denver, Anschutz Medical Campus, Mail Stop 8101, P.O. Box 6511, Aurora, Colorado 80045, USA
Abstract
Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call “protoploid” because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified.
Footnotes
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↵1 A complete list of authors and affiliations appears at the end of the paper, before the Acknowledgments section.
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↵18 Corresponding author.
E-mail jean-luc.souciet{at}gem.u-strasbg.fr; fax 33-3-90-24-20-28.
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[Supplemental material is available online at http://www.genome.org and at http://www.genolevures.org/. The sequence data for Zygosaccharomyces rouxii and Kluyveromyces thermotolerans have been submitted to EMBL-Bank (http://www.ebi.ac.uk/embl/) under accession nos. CU928173–CU928176, CU928178, CU928179, CU928181 and CU928165–CU928171, and CU928180, respectively. Saccharomyces kluyveri sequences were deposited to GenBank under accession no. AACE03000000.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.091546.109.
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- Received January 23, 2009.
- Accepted April 20, 2009.
- Copyright © 2009 by Cold Spring Harbor Laboratory Press
