Pure and Mixed Genetic Lines of Saccharomyces bayanus and Saccharomyces pastorianus and Their Contribution to the Lager Brewing Strain Genome

Abstract

The yeast species Saccharomyces bayanus and Saccharomyces pastorianus are of industrial importance since they are involved in the production process of common beverages such as wine and lager beer; however, they contain strains whose variability has been neither fully investigated nor exploited in genetic improvement programs. We evaluated this variability by using PCR-restriction fragment length polymorphism analysis of 48 genes and partial sequences of 16. Within these two species, we identified "pure" strains containing a single type of genome and "hybrid" strains that contained portions of the genomes from the "pure" lines, as well as alleles termed "Lager" that represent a third genome commonly associated with lager brewing strains. The two pure lines represent S. uvarum and S. bayanus, the latter a novel group of strains that may be of use in strain improvement programs. Hybrid lines identified include (i) S. cerevisiae/S. bayanus/Lager, (ii) S. bayanus/S. uvarum/Lager, and (iii) S. cerevisiae/S. bayanus/S. uvarum/Lager. The genome of the lager strains may have resulted from chromosomal loss, replacement, or rearrangement within the hybrid genetic lines. This study identifies brewing strains that could be used as novel genetic sources in strain improvement programs and provides data that can be used to generate a model of how naturally occurring and industrial hybrid strains may have evolved.

Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus

“…We chose 17 strains of S. pastorianus to study; these strains represent a variety of collection dates, ranging from 1883 to 1976, as well as a variety of geographical locations and beer types (Table 1); many of them correspond to the strains studied by Rainieri et al (2006) as described above. Using custom two-species 60-mer oligonucleotide microarrays, specifically designed to detect and distinguish between sequences from both the S. cerevisiae and S. bayanus var.…”

“…The chimeric nature of the genome of S. pastorianus has been known for quite some time (e.g., Nilsson- Tillgren et al 1981;Martini and Martini 1987; for reviews, see Kodama et al 2005;Smart 2007), as has the existence of rearrangements and aneuploidies within the hybrid genome. However, previous work on such rearrangements and aneuploidies was performed only for single genes or chromosomes (e.g., Nillson-Tillgren et al 1981;Holmberg 1982;Pederson 1985;Casey 1986;Petersen et al 1987;Kielland-Brandt et al 1995;Tamai et al 1998), for multiple small regions across the genome (Rainieri et al 2006), for only one of the two coexisting genomes (Bond et al 2004), or for just one strain (Kodama et al 2005). …”

“…Most of these previous studies used single-locus techniques such as Southern blots (Yamagishi and Ogata 1999), or PCR-RFLP and single-locus DNA sequencing (Casaregola et al 2001;Rainieri et al 2006); however, limited S. cerevisiae-only aCGH results have also been reported (with data shown for chromosome XVI only) for these same three strains (Kodama et al 2005). For strains CBS1503 and CBS1513, our results match almost perfectly with all of the above published results in terms of which chromosomal regions are represented within the genome by S. cerevisiae and/or S. bayanus sequences; that is, the whole-chromosome aneuploidies as well as the breakpoint locations (and associated regional copy number changes) for the segmental aneuploidies that we see are consistent with the data presented in the above papers.…”

“…The fact that this organism is an interspecific hybrid has been known for more than two decades (e.g., Nilsson-Tillgren et al 1981;Martini and Martini 1987; for reviews, see Kodama et al 2005;Smart 2007), and work since then has shown conclusively that different brewing yeast isolates can contain different combinations of the genomes (or partial genomes) of the following closely related Saccharomyces sensu stricto species: S. cerevisiae, Saccharomyces bayanus, Saccharomyces bayanus var. uvarum, and possibly a fourth, unknown "lagertype" species (Casaregola et al 2001;Naumova et al 2005;Rainieri et al 2006; for reviews, see Hornsey 2003;Kodama et al 2005). Pulsed-field gel/Southern blot analysis of several S. pastorianus strains has shown distinct differences in the distribution of transposable elements (Pederson 1985;Liti et al 2005), while array-CGH studies, using S. cerevisiae-only arrays, showed limited chromosomal changes among several strains (Bond et al 2004;Kodama et al 2005), also indicating complexity within this group.…”

“…Most of the yeasts collected from actual lager fermentations have hybrid genomes consisting of S. cerevisiae, S. bayanus, and the "lager-type" sequences, and seem to lack S. bayanus var. uvarum sequences (Rainieri et al 2006). Here, we report array-CGH and DNA sequence analysis of 17 S. pastorianus strains that are hybrids of S. cerevisiae and S. bayanus, and describe the detailed determination of their genomic structure, with the reconstruction of both the origin(s) and the subsequent evolutionary lineages of the strains.…”