Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains

Abstract

Lager brewing strains of Saccharomyces pastorianus are natural interspecific hybrids originating from the spontaneous hybridization of Saccharomyces cerevisiae and Saccharomyces eubayanus. Over the past 500 years, S. pastorianus has been domesticated to become one of the most important industrial microorganisms. Production of lager-type beers requires a set of essential phenotypes, including the ability to ferment maltose and maltotriose at low temperature, the production of flavors and aromas, and the ability to flocculate. Understanding of the molecular basis of complex brewing-related phenotypic traits is a prerequisite for rational strain improvement. While genome sequences have been reported, the variability and dynamics of S. pastorianus genomes have not been investigated in detail. Here, using deep sequencing and chromosome copy number analysis, we showed that S. pastorianus strain CBS1483 exhibited extensive aneuploidy. This was confirmed by quantitative PCR and by flow cytometry. As a direct consequence of this aneuploidy, a massive number of sequence variants was identified, leading to at least 1,800 additional protein variants in S. pastorianus CBS1483. Analysis of eight additional S. pastorianus strains revealed that the previously defined group I strains showed comparable karyotypes, while group II strains showed large interstrain karyotypic variability. Comparison of three strains with nearly identical genome sequences revealed substantial chromosome copy number variation, which may contribute to strain-specific phenotypic traits. The observed variability of lager yeast genomes demonstrates that systematic linking of genotype to phenotype requires a three-dimensional genome analysis encompassing physical chromosomal structures, the copy number of individual chromosomes or chromosomal regions, and the allelic variation of copies of individual genes.

Industrial Relevance of Chromosomal Copy Number Variation in Saccharomyces Yeasts

“…cerevisiae strains. In general, these alloploid genomes tolerate aneuploidy well, with massive diversity in chromosome copy numbers across strains (23, 125, 126). Some aneuploid lager brewing yeasts even sporulate, albeit at low efficiency, by anomalous cell division (79).…”

“…cerevisiae chromosomes can even be absent (e.g., S. cerevisiae chromosome III is absent in all group I strains sequenced so far) (23, 32, 141–143); group II strains generally have a more balanced genome composition, with (multiple) chromosomes from both S. eubayanus and S.…”

“…eubayanus and S. cerevisiae (23, 32, 141–143). These differences have been proposed to reflect different hybridization histories of the two groups (144).…”

“…cerevisiae strain with a haploid S. eubayanus strain (23) or from two subsequent hybridization events (141). Different hybridization histories appear to be contradicted by conserved chromosome rearrangement breakpoints in group I and group II strains (32, 143).…”

Novel brewing yeast hybrids: creation and application

“…Extensive chromosome loss and intrachromosomal translocations, sequence divergence, and chromosome copy number variation in the genomes of lager yeast (van den Broek et al 2015) indicate that the S. pastorianus genome is inherently unstable. Such instability is not unexpected given the high level of regulatory incompatibilities (Landry et al 2007) and functional redundancy that are associated with polyploid hybrids (Kumaran et al 2013; Selmecki et al 2015).…”