Comparative genomics among Saccharomyces cerevisiae × Saccharomyces kudriavzevii natural hybrid strains isolated from wine and beer reveals different origins

Abstract

Background: Interspecific hybrids between S. cerevisiae × S. kudriavzevii have frequently been detected in wine and beer fermentations. Significant physiological differences among parental and hybrid strains under different stress conditions have been evidenced. In this study, we used comparative genome hybridization analysis to evaluate the genome composition of different S. cerevisiae × S. kudriavzevii natural hybrids isolated from wine and beer fermentations to infer their evolutionary origins and to figure out the potential role of common S. kudriavzevii gene fraction present in these hybrids.

Results: Comparative genomic hybridization (CGH) and ploidy analyses carried out in this study confirmed the presence of individual and differential chromosomal composition patterns for most S. cerevisiae × S. kudriavzevii hybrids from beer and wine. All hybrids share a common set of depleted S. cerevisiae genes, which also are depleted or absent in the wine strains studied so far, and the presence a common set of S. kudriavzevii genes, which may be associated with their capability to grow at low temperatures. Finally, a maximum parsimony analysis of chromosomal rearrangement events, occurred in the hybrid genomes, indicated the presence of two main groups of wine hybrids and different divergent lineages of brewing strains.

Conclusion: Our data suggest that wine and beer S. cerevisiae × S. kudriavzevii hybrids have been originated by different rare-mating events involving a diploid wine S. cerevisiae and a haploid or diploid European S. kudriavzevii strains. Hybrids maintain several S. kudriavzevii genes involved in cold adaptation as well as those related to S. kudriavzevii mitochondrial functions.

Figure 1

Genome composition of hybrids deduced from aCGH analysis, ploidy estimates and a previous analysis of absence/presence of parental genes by RFLP analysis [[2],[19]]. White and black bars are used to represent the S. cerevisiae and S. kudriavzevii genome fractions, respectively. Chromosomes showing black and white regions correspond to chimerical chromosomes. The percentages of S. kudriavzevii genes maintained in each chromosome are shown for each chormosome. Strains names are depicted on a black or a gray background corresponding to wine or brewing strains, respectively. Asterisks in AMH Chr. III and VII indicate regions where non-reciprocal translocations or segmental duplications can be present.

Figure 2

Maximum parsimony tree indicating the minimum number of chromosomal rearrangements and restriction site changes (presence/absence matrix is given in Additional file2: Table S1) necessary to connect the different genotypes exhibited by the S. cerevisiae × S. kudriavzevii hybrids to a putative hybrid ancestor. This putative ancestor is not necessarily the same for all lineages, it just corresponds to an ancestral state containing the complete S. cerevisiae and S. kudriavzevii genomes, but it could be generated several times from different parental strains, as discussed in the main text. Genotypes are represented by white and gray circles for wine and brewing hybrids, respectively. Rearrangements are indicated by arrows giving the direction of the irreversible change and were treated under the Camin-Sokal criterion. Rearrangements were assumed to be caused by nonreciprocal recombination (rec) among homoeologous chromosomes (roman numbers) and whole chromosome losses (loss) of one of the parental chromosomes (kud, S. kudriavzevii). Restriction site changes can be reversible (gains/losses represented by diamonds) and were treated under the Wagner criterion. The gene region and the restriction patterns involved are also indicated (for a description see references [2] and [19]).