Comparative genomics of protoploid Saccharomycetaceae.
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.
Université de Strasbourg, CNRS UMR, France. jean-luc.souciet@gem.u-strasbg.fr
Souciet
Jean-Luc
JL
Dujon
Bernard
B
Gaillardin
Claude
C
Johnston
Mark
M
Baret
Philippe V
PV
Cliften
Paul
P
Sherman
David J
DJ
Weissenbach
Jean
J
Westhof
Eric
E
Wincker
Patrick
P
Jubin
Claire
C
Poulain
Julie
J
Barbe
Valérie
V
Ségurens
Béatrice
B
Artiguenave
François
F
Anthouard
Véronique
V
Vacherie
Benoit
B
Val
Marie-Eve
ME
Fulton
Robert S
RS
Minx
Patrick
P
Wilson
Richard
R
Durrens
Pascal
P
Jean
Géraldine
G
Marck
Christian
C
Martin
Tiphaine
T
Nikolski
Macha
M
Rolland
Thomas
T
Seret
Marie-Line
ML
Casarégola
Serge
S
Despons
Laurence
L
Fairhead
Cécile
C
Fischer
Gilles
G
Lafontaine
Ingrid
I
Leh
Véronique
V
Lemaire
Marc
M
de Montigny
Jacky
J
Neuvéglise
Cécile
C
Thierry
Agnès
A
Blanc-Lenfle
Isabelle
I
Bleykasten
Claudine
C
Diffels
Julie
J
Fritsch
Emilie
E
Frangeul
Lionel
L
Goëffon
Adrien
A
Jauniaux
Nicolas
N
Kachouri-Lafond
Rym
R
Payen
Célia
C
Potier
Serge
S
Pribylova
Lenka
L
Ozanne
Christophe
C
Richard
Guy-Franck
GF
Sacerdot
Christine
C
Straub
Marie-Laure
ML
Talla
Emmanuel
E
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
D004251:DNA Transposable Elements; D022661:RNA, Untranslated