Comparative genomics of protoploid Saccharomycetaceae
- Jean-Luc Souciet1,14,
- Bernard Dujon2,
- Claude Gaillardin3,
- Mark Johnston4,
- Philippe V Baret5,
- Paul Cliften6,
- David J Sherman7,
- Jean Weissenbach8,
- Eric Westhof9,
- Patrick Wincker8,
- Claire Jubin8,
- Julie Poulain8,
- Valerie Barbe8,
- BGeatrice Segurence8,
- Francois Artiguenave8,
- Veronique Anthouard8,
- Benoit Vacherie8,
- Marie-Eve Val8,
- Robert S Fulton10,
- Patrick Minx10,
- Richard Wilson10,
- Pascal Durrens7,
- Geraldine Jean7,
- Christian Marck11,
- Tiphaine Martin7,
- Macha Nikolski7,
- Thomas Rolland2,
- Marie-Line Seret5,
- Sege Casaregola3,
- Laurence Despons9,
- Cecile Fairhead2,
- Gilles Fischer2,
- Ingrid Lafontaine2,
- Veronique Leh9,
- Marc Lemaire12,
- Jacky de Montigny9,
- Cecile Neuveglise3,
- Agnes Thierry2,
- Isabelle Blanc-Lenfle3,
- Claudine Bleykasten9,
- Julie Diffels5,
- Emilie Fritsch9,
- Lionel Frangeul2,
- Adrien Goeffon7,
- Nicolas Jauniaux9,
- Rym Kachouri-Lafond9,
- Celia Payen2,
- Serge Potier9,
- Lenka Pribylova9,
- Christophe Ozanne3,
- Guy-Franck Richard2,
- Christine Sacerdot2,
- Marie-Laure Straub9 and
- Emmanuel Talla13
- 1 Unuiversite de Strasbourg;
- 2 Institut Pasteur;
- 3 AgroParisTech;
- 4 University of Colorado Denver;
- 5 Universite catholique de Louvain;
- 6 Utah State University;
- 7 Universite de Bordeaux 1;
- 8 Genoscope;
- 9 Universite de Strasbourg;
- 10 Washington University;
- 11 CEA;
- 12 Universite de Lyon 1;
- 13 Universite de la Mediterranee
- E-mail: jean-luc.souciet{at}gem.u-strasbg.fr
Abstract
Our knowledge on 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 Klyveromyces 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 ca. 3,300 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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- Received January 23, 2009.
- Accepted April 20, 2009.
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This manuscript is Open Access.
- Copyright © 2009, Cold Spring Harbor Laboratory Press
