Abstract
Saccharomyces pastorianus lager-brewing yeasts are domesticated hybrids of S. cerevisiae x S. eubayanus that display extensive inter-strain chromosome copy number variation and chromosomal recombinations. It is unclear to what extent such genome rearrangements are intrinsic to the domestication of hybrid brewing yeasts and whether they contribute to their industrial performance. Here, an allodiploid laboratory hybrid of S. cerevisiae and S. eubayanus was evolved for up to 418 generations on wort under simulated lager-brewing conditions in six independent sequential batch bioreactors. Characterization of 55 single-cell isolates from the evolved cultures showed large phenotypic diversity and whole-genome sequencing revealed a large array of mutations. Frequent loss of heterozygosity involved diverse, strain-specific chromosomal translocations, which differed from those observed in domesticated, aneuploid S. pastorianus brewing strains. In contrast to the extensive aneuploidy of domesticated S. pastorianus strains, the evolved isolates only showed limited (segmental) aneuploidy. Specific mutations could be linked to calcium-dependent flocculation, loss of maltotriose utilization and loss of mitochondrial activity, three industrially relevant traits that also occur in domesticated S. pastorianus strains. This study indicates that fast acquisition of extensive aneuploidy is not required for genetic adaptation of S. cerevisiae × S. eubayanus hybrids to brewing environments. In addition, this work demonstrates that, consistent with the diversity of brewing strains for maltotriose utilization, domestication under brewing conditions can result in loss of this industrially relevant trait. These observations have important implications for the design of strategies to improve industrial performance of novel laboratory-made hybrids.
Highlights
Saccharomyces yeasts are popular eukaryotic models for studying genome hybridization, chromosomesegregation and aneuploidy (Botstein et al, 1997; Sheltzer et al, 2011)
To simulate domestication under industrial lagerbrewing conditions, a laboratory evolution regime was designed in which the laboratory-made S. cerevisiae x S. eubayanus hybrid IMS0408 was grown at 12◦C in sequential batch bioreactors on industrial wort
Evolution of the laboratory S. cerevisiae x S. eubayanus IMS0408 under simulated lager-brewing conditions yielded a wide array of mutations, including SNPs, INDELs, chromosomal recombinations, aneuploidy and loss of mitochondrial DNA (Table 2, Additional Data File 1)
Summary
Saccharomyces yeasts are popular eukaryotic models for studying genome hybridization, chromosome (mis)segregation and aneuploidy (Botstein et al, 1997; Sheltzer et al, 2011). Several interspecies Saccharomyces hybrids are tightly associated with domestication in industrial processes. S. pastorianus lager-brewing yeasts are domesticated S. cerevisiae × S. eubayanus hybrids (Libkind et al, 2011). Double and triple hybrids between S. cerevisiae, S. kudriavzevii and S. uvarum are closely associated with wine fermentation (González et al, 2006; Querol and Bond, 2009; Marsit and Dequin, 2015). S. bayanus cider fermentation yeasts are domesticated S. uvarum × S. eubayanus hybrids (Naumov et al, 2001). Hybrids of S. cerevisiae, S. kudriavzevii and S. uvarum combined traits of their parental species relevant to industrial wine fermentation, such as flocculence, sugar utilization kinetics, stress tolerance and aroma production (Coloretti et al, 2006; Lopandic et al, 2016)
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