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

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.

Origin, Regulation, and Fitness Effect of Chromosomal Rearrangements in the Yeast Saccharomyces cerevisiae

“…Most information about the rates of these events was based on the genetic assay system involving single genes or partial chromosomes [ 51 , 52 ]. More recently, subculturing of yeast strains over many generations for mutation accumulation (MA) followed by whole-genome sequencing has allowed a more global analysis of chromosomal rearrangements [ 53 , 54 , 55 , 56 ]. Sui et al [ 53 ] performed MA experiments in a diploid S. cerevisiae strain ( spo11/spo11 ; unable to enter meiosis), identifying chromosomal rearrangements throughout the genome by deep-coverage genome sequencing.…”

“…More recently, subculturing of yeast strains over many generations for mutation accumulation (MA) followed by whole-genome sequencing has allowed a more global analysis of chromosomal rearrangements [ 53 , 54 , 55 , 56 ]. Sui et al [ 53 ] performed MA experiments in a diploid S. cerevisiae strain ( spo11/spo11 ; unable to enter meiosis), identifying chromosomal rearrangements throughout the genome by deep-coverage genome sequencing. This study detected 47 chromosomal rearrangements including 35 deletions, 12 duplications, and 1 translocation.…”

“…It was calculated that spontaneous chromosomal rearrangements occur at a rate of 1.8 × 10 −4 per cell division. This rate is one magnitude lower than that of LOH events (4.6 × 10 −3 per cell division; gene conversion and crossover) resulted from SDSA and DSBR pathways ( Figure 1 ) [ 53 ]. They also showed certain regions are more susceptible to rearrangements than other regions.…”

“…They also showed certain regions are more susceptible to rearrangements than other regions. For example, the region of 184–195 Kb (including three genes RRN11 , CAT2 , and VPS71 ) located between two flanking Ty elements (standing for transposons of yeast, which are dispersed repeat retrotransposons in the yeast genome) on chromosome XIII, and the region of the RDL1/2 locus on chromosome XV are two hotspots for interstitial deletion or duplication [ 53 ]. Non-allelic recombination between two sister chromatids by the DSBR pathway might be responsible for those frequent interstitial deletions and duplications ( Figure 1 ).…”

“…SSA to repair a DSB located between two direct repeats can be an alternative mechanism underlying spontaneous interstitial deletion ( Figure 1 ). In one subcultured isolate, they also found recombination between two directly oriented Ty transposons on chromosome III that resulted in a circular DNA molecule [ 53 ]. Most strikingly, this work demonstrated that spontaneous chromosomal rearrangements generally involve homologous recombination between non-allelic dispersed repeats in the yeast genome.…”