title: Comparative genomics of protoploid Saccharomycetaceae.
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.
authors.affiliation: Université de Strasbourg, CNRS UMR, France. jean-luc.souciet@gem.u-strasbg.fr
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Souciet
authors.forename: Bernard
authors.initials: B
authors.lastname: Dujon
authors.forename: Claude
authors.initials: C
authors.lastname: Gaillardin
authors.forename: Mark
authors.initials: M
authors.lastname: Johnston
authors.forename: Philippe V
authors.initials: PV
authors.lastname: Baret
authors.forename: Paul
authors.initials: P
authors.lastname: Cliften
authors.forename: David J
authors.initials: DJ
authors.lastname: Sherman
authors.forename: Jean
authors.initials: J
authors.lastname: Weissenbach
authors.forename: Eric
authors.initials: E
authors.lastname: Westhof
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.forename: Claire
authors.initials: C
authors.lastname: Jubin
authors.forename: Julie
authors.initials: J
authors.lastname: Poulain
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
authors.forename: Béatrice
authors.initials: B
authors.lastname: Ségurens
authors.forename: François
authors.initials: F
authors.lastname: Artiguenave
authors.forename: Véronique
authors.initials: V
authors.lastname: Anthouard
authors.forename: Benoit
authors.initials: B
authors.lastname: Vacherie
authors.forename: Marie-Eve
authors.initials: ME
authors.lastname: Val
authors.forename: Robert S
authors.initials: RS
authors.lastname: Fulton
authors.forename: Patrick
authors.initials: P
authors.lastname: Minx
authors.forename: Richard
authors.initials: R
authors.lastname: Wilson
authors.forename: Pascal
authors.initials: P
authors.lastname: Durrens
authors.forename: Géraldine
authors.initials: G
authors.lastname: Jean
authors.forename: Christian
authors.initials: C
authors.lastname: Marck
authors.forename: Tiphaine
authors.initials: T
authors.lastname: Martin
authors.forename: Macha
authors.initials: M
authors.lastname: Nikolski
authors.forename: Thomas
authors.initials: T
authors.lastname: Rolland
authors.forename: Marie-Line
authors.initials: ML
authors.lastname: Seret
authors.forename: Serge
authors.initials: S
authors.lastname: Casarégola
authors.forename: Laurence
authors.initials: L
authors.lastname: Despons
authors.forename: Cécile
authors.initials: C
authors.lastname: Fairhead
authors.forename: Gilles
authors.initials: G
authors.lastname: Fischer
authors.forename: Ingrid
authors.initials: I
authors.lastname: Lafontaine
authors.forename: Véronique
authors.initials: V
authors.lastname: Leh
authors.forename: Marc
authors.initials: M
authors.lastname: Lemaire
authors.forename: Jacky
authors.initials: J
authors.lastname: de Montigny
authors.forename: Cécile
authors.initials: C
authors.lastname: Neuvéglise
authors.forename: Agnès
authors.initials: A
authors.lastname: Thierry
authors.forename: Isabelle
authors.initials: I
authors.lastname: Blanc-Lenfle
authors.forename: Claudine
authors.initials: C
authors.lastname: Bleykasten
authors.forename: Julie
authors.initials: J
authors.lastname: Diffels
authors.forename: Emilie
authors.initials: E
authors.lastname: Fritsch
authors.forename: Lionel
authors.initials: L
authors.lastname: Frangeul
authors.forename: Adrien
authors.initials: A
authors.lastname: Goëffon
authors.forename: Nicolas
authors.initials: N
authors.lastname: Jauniaux
authors.forename: Rym
authors.initials: R
authors.lastname: Kachouri-Lafond
authors.forename: Célia
authors.initials: C
authors.lastname: Payen
authors.forename: Serge
authors.initials: S
authors.lastname: Potier
authors.forename: Lenka
authors.initials: L
authors.lastname: Pribylova
authors.forename: Christophe
authors.initials: C
authors.lastname: Ozanne
authors.forename: Guy-Franck
authors.initials: GF
authors.lastname: Richard
authors.forename: Christine
authors.initials: C
authors.lastname: Sacerdot
authors.forename: Marie-Laure
authors.initials: ML
authors.lastname: Straub
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Talla
mesh_terms: D004251:DNA Transposable Elements / Q000235:genetics / Q000502:physiology; D055169:Eremothecium / Q000235:genetics; D020440:Gene Duplication; D005800:Genes, Fungal / Q000235:genetics; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods*; D047668:Inteins / Q000235:genetics; D007716:Kluyveromyces / Q000235:genetics; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D022661:RNA, Untranslated / Q000235:genetics; D012440:Saccharomyces / Q000235:genetics; D004718:Saccharomycetales / Q000235:genetics*; D017381:Spliceosomes / Q000378:metabolism; D020068:Zygosaccharomyces / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D022661:RNA, Untranslated