Genomic Exploration of the Hemiascomycetous Yeasts: 18. Comparative analysis of chromosome maps and synteny withSaccharomyces cerevisiae

Abstract

We have analyzed the evolution of chromosome maps of Hemiascomycetes by comparing gene order and orientation of the 13 yeast species partially sequenced in this program with the genome map of Saccharomyces cerevisiae. From the analysis of nearly 8000 situations in which two distinct genes having homologs in S. cerevisiae could be identified on the sequenced inserts of another yeast species, we have quantified the loss of synteny, the frequency of single gene deletion and the occurrence of gene inversion. Traces of ancestral duplications in the genome of S. cerevisiae could be identified from the comparison with the other species that do not entirely coincide with those identified from the comparison of S. cerevisiae with itself. From such duplications and from the correlation observed between gene inversion and loss of synteny, a model is proposed for the molecular evolution of Hemiascomycetes. This model, which can possibly be extended to other eukaryotes, is based on the reiteration of events of duplication of chromosome segments, creating transient merodiploids that are subsequently resolved by single gene deletion events. ß

Genomic Exploration of the Hemiascomycetous Yeasts: 10.Kluyveromyces thermotolerans

“…We found 636^701 ORFs of K. thermotolerans matching with genes from structural families of S. cerevisiae. In general, the distribution of matches shows few di¡erences between the two yeasts [18]. Nevertheless, four large families are without representatives in K. thermotolerans and it is striking that they are located in the subtelomeric regions in S. cerevisiae (P24.1f23.1, P9.4f8.1 and P26.1f13.1 [19]) or correspond to the DUP family.…”

“…In a few cases, we were not able to determine the orthologous gene due to matches with several indistinguishable or closely related ORFs. In this category, we obtained 131 RSTs matching with 253 di¡erent genes from S. cerevisiae gene families [18].…”

“…Genet redundancy is thought to permit accumulation of mutations and thus create new functions due to relaxation of selective constraints in one copy of the duplicated gene [20]. We used a classi¢cation of S. cerevisiae genes in structural families [19] to determine speci¢c functional characteristics of K. thermotolerans [18,21]. We found 636^701 ORFs of K. thermotolerans matching with genes from structural families of S. cerevisiae.…”

“…We suggest that those tandem repeats appeared after the divergence of the Kluyveromyces and Saccharomyces genera. Largely, subtelomeric families are of unknown function and underrepresentation of these families may be correlated to general underrepresentation of subtelomeric genes [18]. Since S. cerevisiae has been used by humans for about 7000 years [23], selection may have ampli¢ed some interesting genes such as the FLO genes involved in £occulation during fermentation.…”

Genomic Exploration of the Hemiascomycetous Yeasts: 3. Methods and strategies used for sequence analysis and annotation

“…Biased libraries not only would result in a signi¢cant loss of e¤ciency of our sequencing program, but are prone to incorrect interpretations in terms of yeast-speci¢c genes [3], gene family distributions [4], functional analysis [5], or map comparisons [2]. For each of the 13 yeast species, we have, therefore, compared the number of contigs obtained from the set of RSTs to the theoretical distribution predicted from the work of [55,56].…”