Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection

Abstract

The Peterhof genetic collection of Saccharomyces cerevisiae strains (PGC) is a large laboratory stock that has accumulated several thousands of strains for over than half a century. It originated independently of other common laboratory stocks from a distillery lineage (race XII). Several PGC strains have been extensively used in certain fields of yeast research but their genomes have not been thoroughly explored yet. Here we employed whole genome sequencing to characterize five selected PGC strains including one of the closest to the progenitor, 15V-P4, and several strains that have been used to study translation termination and prions in yeast (25-25-2V-P3982, 1B-D1606, 74-D694, and 6P-33G-D373). The genetic distance between the PGC progenitor and S288C is comparable to that between two geographically isolated populations. The PGC seems to be closer to two bakery strains than to S288C-related laboratory stocks or European wine strains. In genomes of the PGC strains, we found several loci which are absent from the S288C genome; 15V-P4 harbors a rare combination of the gene cluster characteristic for wine strains and the RTM1 cluster. We closely examined known and previously uncharacterized gene variants of particular strains and were able to establish the molecular basis for known phenotypes including phenylalanine auxotrophy, clumping behavior and galactose utilization. Finally, we made sequencing data and results of the analysis available for the yeast community. Our data widen the knowledge about genetic variation between Saccharomyces cerevisiae strains and can form the basis for planning future work in PGC-related strains and with PGC-derived alleles.

Haploid yeast cells undergo a reversible phenotypic switch associated with chromosome II copy number

“…These genes have been linked to chromosome stability [32], but as we also found additional chromosome I in a SUP35 SUP45 strain ([ psi − ]), we consider sup35-25 or sup45-400 an unlikely cause of the genome instability. In an attempt to find other genes which could be connected to genome instability in 25-25-2V-P3982, we compared the list of 46 genes with premature stop codons found in the genome of this strain [33] to the curated list of 692 chromosome instability genes [32]. Intersection of these lists returned three genes, ADE1 , MNL1 and CNN1 .…”

“…The third gene, CNN1 , encodes a kinetochore component; deletion of this gene had been associated with chromosome segregation defects in several works [35, 36]. CNN1 contains a premature stop codon in 25-25-2V-P3982 but not in other related strains of the Peterhof genetic collection [33] and might contribute to the observed chromosome instability.…”

“…2-P-2V-P3982 (clone [ psi − ]) is derived from P-2V-P3982 with passaging on YEPD medium with 5mM guanidine hydrochloride three times. 25-25-2V-P3982 ( MATa ade1-14 his7-1 lys2-87 ura3Δ0 thr4-B15 leu2-B2 sup35-25 sup45-400 ) was described earlier [11, 13, 33]; generation of isolates is summarized in Fig. 2.…”

“…DNA extraction for whole genome sequencing, library preparation and data analysis methods was described earlier [33]. DNA extraction for PCR was performed as described in [38].…”

“…aCGH data were analysed with CGH-Miner Excel add-in [52]. Details of next generation sequencing data analysis and expression microarray data analysis are provided in [24, 33], respectively.…”