Comparative genomics of commercial Saccharomyces cerevisiae isolates recovered from vineyard environments

Abstract

The use of commercial Saccharomyces cerevisiae wine yeast strains as fermentation starters has been extensively generalised over the past two decades. These strains are used by wineries every year at the harvest time in large quantities. Within our previous work we showed that such strains are disseminated from the winery and can be recovered from locations in close proximity (10-200m) (Valero et al., 2005). Their permanence in natural environments induced genetic changes such as loss of heterozygosity, microsatellite expansion and size variations of chromosomes III and/or VI. These changes were not found among a group of isolates that were used as a control and that derived from the commercial “mother” strain (Schuller et al., 2007). The objective of the present study was to evaluate genome variations among four isolates of the commercial strain S. cerevisiae Zymaflore VL1 that were re-isolated from vineyards surrounding the wineries where this strain was applied, in comparison to the commercial “mother” strain by the use of comparative genome hybridization on array (aCGH). These approaches were carried out as previously described (Carreto, et al., 2008). Hierarchical cluster analysis showed some genome variability between isolates recovered from the environment and the commercial VL1 reference strain. Using one-way ANOVA we identified more than 50 genes with significant differences between the environmental isolates and the original VL1 strain. Multi-class significance analysis (SAM) for two-class unpaired comparisons revealed a group of 130 genes with significantly reduced fold changes in the recovered strains. The most relevant genes (PAU2, PAU3 and PAU5) belonged to the seripauperin family. They are located in subtelomeric chromosomal regions, where gene families are maintained that serve for adaptive purposes. These genes are involved in the adaptation of yeast cells to stress during alcoholic fermentations and are highly upregulated during early stages of wine fermentation. Our studies showed that genetic changes occur among isogenic strains of the commercial yeast S. cerevisiae Zymaflore VL1 that were re-isolated from environments close to vineyards where this strain is used as starter yeast. The depletion of several genes may reflect adaptive mechanisms that strains undergo as response to the ecological conditions of vineyards that are very distinct from must fermentation environments.