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Comparative genomics of protoploid Saccharomycetaceae

Jean-Luc Souciet 1, * Bernard Dujon 2 Claude Gaillardin 3 Mark Johnston 4 Philippe V Baret 5 Paul Cliften 6 David James Sherman 7, 8 Jean Weissenbach 9, 10 Eric Westhof 11 Patrick Wincker 10, 12 Claire Jubin 10 Julie Poulain 10 Valerie Barbe 9, 10 Béatrice Ségurens 10 François Artiguenave 10 Véronique Anthouard 9, 10 Benoit Vacherie 10 Marie-Eve Val 10 Robert S Fulton 4 Patrick Minx 4 Richard Wilson 4 Pascal Durrens 7, 8 Geraldine Jean 8 Christian Marck 13 Tiphaine Martin 7, 14 Macha Nikolski 7, 8 Thomas Rolland 2 Marie-Line Seret 5 Serge Casaregola 3 Laurence Despons 15 Cecile Fairhead 2 Gilles Fischer 2 Ingrid Lafontaine 2 Veronique Leh 1 Marc Lemaire 16 Jacky de Montigny 1 Cécile Neuvéglise 3 Agnes Thierry 2 Isabelle Blanc-Lenfle 3 Claudine Bleykasten 1 Julie Diffels 5 Emilie Fritsch 1 Lionel Frangeul 17 Adrien Goeffon 7, 8 Nicolas Jauniaux 1 Rym Kachouri-Lafond 11 Celia Payen 2 Serge Potier 1 Lenka Pribylova 1, 18 Christophe Ozanne 3 Guy-Franck Richard 2 Christine Sacerdot 2 Marie-Laure Straub 1 Emmanuel Talla 19
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.
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Jean-Luc Souciet, Bernard Dujon, Claude Gaillardin, Mark Johnston, Philippe V Baret, et al.. Comparative genomics of protoploid Saccharomycetaceae. Genome Research, Cold Spring Harbor Laboratory Press, 2009, 19, pp.1696-1709. ⟨10.1101/gr.091546.109⟩. ⟨inria-00407511⟩



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