Genome-wide mapping of spontaneous genetic alterations in diploid yeast cells

Significance

Although geneticists often emphasize diversity generated during sexual reproduction, genomic alterations that occur during vegetative growth are an important source of genetic diversity. In the current study, we have measured the rate and location of single-base mutations, large deletions/duplications, ploidy alterations, and mitotic recombination events in extensively subcultured diploid isolates of the yeast Saccharomyces cerevisiae. We were able to determine the relative frequency of these events and to predict the frequency of loss of heterozygosity of allelic markers resulting from mitotic recombination. This analysis is relevant to understanding of genomic evolution, as well as the mitotic recombination events in humans that predispose cells to form tumors.

Abstract

Genomic alterations including single-base mutations, deletions and duplications, translocations, mitotic recombination events, and chromosome aneuploidy generate genetic diversity. We examined the rates of all of these genetic changes in a diploid strain of Saccharomyces cerevisiae by whole-genome sequencing of many independent isolates ( n = 93) subcloned about 100 times in unstressed growth conditions. The most common alterations were point mutations and small (<100 bp) insertion/deletions ( n = 1,337) and mitotic recombination events ( n = 1,215). The diploid cells of most eukaryotes are heterozygous for many single-nucleotide polymorphisms (SNPs). During mitotic cell divisions, recombination can produce derivatives of these cells that have become homozygous for the polymorphisms, termed loss-of-heterozygosity (LOH) events. LOH events can change the phenotype of the cells and contribute to tumor formation in humans. We observed two types of LOH events: interstitial events (conversions) resulting in a short LOH tract (usually less than 15 kb) and terminal events (mostly cross-overs) in which the LOH tract extends to the end of the chromosome. These two types of LOH events had different distributions, suggesting that they may have initiated by different mechanisms. Based on our results, we present a method of calculating the probability of an LOH event for individual SNPs located throughout the genome. We also identified several hotspots for chromosomal rearrangements (large deletions and duplications). Our results provide insights into the relative importance of different types of genetic alterations produced during vegetative growth.