Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118

Abstract

Saccharomyces cerevisiae has been used for millennia in winemaking, but little is known about the selective forces acting on the wine yeast genome. We sequenced the complete genome of the diploid commercial wine yeast EC1118, resulting in an assembly of 31 scaffolds covering 97% of the S288c reference genome. The wine yeast differed strikingly from the other S. cerevisiae isolates in possessing 3 unique large regions, 2 of which were subtelomeric, the other being inserted within an EC1118 chromosome. These regions encompass 34 genes involved in key wine fermentation functions. Phylogeny and synteny analyses showed that 1 of these regions originated from a species closely related to the Saccharomyces genus, whereas the 2 other regions were of non-Saccharomyces origin. We identified Zygosaccharomyces bailii, a major contaminant of wine fermentations, as the donor species for 1 of these 2 regions. Although natural hybridization between Saccharomyces strains has been described, this report provides evidence that gene transfer may occur between Saccharomyces and nonSaccharomyces species. We show that the regions identified are frequent and differentially distributed among S. cerevisiae clades, being found almost exclusively in wine strains, suggesting acquisition through recent transfer events. Overall, these data show that the wine yeast genome is subject to constant remodeling through the contribution of exogenous genes. Our results suggest that these processes are favored by ecologic proximity and are involved in the molecular adaptation of wine yeasts to conditions of high sugar, low nitrogen, and high ethanol concentrations. adaptive evolution ͉ comparative genomics ͉ horizontal gene transfer ͉ introgression ͉ Zygosaccharomyces bailii

A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes

“…nidulans). Finally, even at the species level, this gene can show an uneven distribution as illustrated by S. cerevisiae where the gene is absent from the S288c laboratory strain and also from the W303 one, but present in several other strains used in wine making as exemplified by the EC1118 wine strain that possesses two closely linked copies on its chromosome XV (Novo et al, 2009).…”

“…FOT transporters are important for peptide uptake by a yeast strain The completely sequenced S. cerevisiae EC1118 wine strain differs from the laboratory S288c strain by the presence of long blocks of genes in its genome that could have been acquired by lateral transfer from different yeast species (Novo et al, 2009). In block C on chromosome XV two linked genes are present, separated by 2819 bp, and code for FOT transporters (S. cerevisiae FOT1 and FOT2 in Figure 1).…”

A sulphite-inducible form of the sulphite efflux gene SSU1 in a Saccharomyces cerevisiae wine yeast

“…Thus, we used real-time quantitative PCR to further investigate the expression pattern of genes involved in sulphite metabolism during alcoholic fermentation in strain 71B and in the reference wine strain EC1118 (Novo et al, 2009;Rossignol et al, 2003). Active dried yeasts were used to inoculate a natural must.…”

Widespread horizontal transfer of the cerato-ulmin gene between Ophiostoma novo-ulmi and Geosmithia species

“…In other instances the transferred sequence was found in the subtelomeric regions of chromosomes, characterized by frequent rearrangements and rich in transposable elements (Coelho et al 2013). On the other hand, homologous recombination was involved in the transfer of genetic material between the yeast wine strain Saccharomyces cerevisiae EC1118 and Zygosaccharomyces bailii (Novo et al 2009) and of the penicillin biosynthetic gene cluster in Penicillium chrysogenum (Rosewich & Kistler 2000).…”