Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments

Abstract

Although the budding yeast Saccharomyces cerevisiae is arguably one of the most well-studied organisms on earth, the genome-wide variation within this species—i.e., its “pan-genome”—has been less explored. We created a multispecies microarray platform containing probes covering the genomes of several Saccharomyces species: S. cerevisiae, including regions not found in the standard laboratory S288c strain, as well as the mitochondrial and 2-μm circle genomes–plus S. paradoxus, S. mikatae, S. kudriavzevii, S. uvarum, S. kluyveri, and S. castellii. We performed array-Comparative Genomic Hybridization (aCGH) on 83 different S. cerevisiae strains collected across a wide range of habitats; of these, 69 were commercial wine strains, while the remaining 14 were from a diverse set of other industrial and natural environments. We observed interspecific hybridization events, introgression events, and pervasive copy number variation (CNV) in all but a few of the strains. These CNVs were distributed throughout the strains such that they did not produce any clear phylogeny, suggesting extensive mating in both industrial and wild strains. To validate our results and to determine whether apparently similar introgressions and CNVs were identical by descent or recurrent, we also performed whole-genome sequencing on nine of these strains. These data may help pinpoint genomic regions involved in adaptation to different industrial milieus, as well as shed light on the course of domestication of S. cerevisiae.

Molecular and Phenotypic Characterization of Metschnikowia pulcherrima Strains from Douro Wine Region

“…As seen previously for the genotypic profiles of these strains, no correlation was found between the source of isolation and the phenotypic patterns (chi-test, p > 0.05). This observation was already described for S. cerevisiae strains [47,56], C. zemplinina [21] and other non-Saccharomyces strains of the same species from different origins [48].…”

Review of Aroma Formation through Metabolic Pathways of Saccharomyces cerevisiae in Beverage Fermentations

“…The genetic dissimilarities between laboratory and industrial strains are due to hybridization, introgression, and variation in gene copy numbers (Dunn et al 2012). Differences in secondary metabolite composition are observed when industrial strains are used in fermentation, suggesting that genetic differences between lab and industrial strains account for the differences in secondary metabolite production (Howell et al 2005, Rossouw et al 2008, Richter et al 2013.…”

Genomic Insights into the Saccharomyces sensu stricto Complex

“…In addition to naturally occurring interspecific hybrids, hybrids of S. cerevisiae and either S. paradoxus, S. kudriavzevii, or S. mikatae have been artificially induced for commercialization purposes (Bellon et al 2011(Bellon et al , 2013. Like the situation observed for S. pastorianus, these hybrid strains are often not complete and contain varying amounts of each parental genome (Dunn et al 2012;Erny et al 2012).…”