Loss of Heterozygosity and Base Mutation Rates Vary Among Saccharomyces cerevisiae Hybrid Strains

Abstract

A growing body of evidence suggests that mutation rates exhibit intra-species specific variation. We estimated genome-wide loss of heterozygosity (LOH), gross chromosomal changes, and single nucleotide mutation rates to determine intra-species specific differences in hybrid and homozygous strains of Saccharomyces cerevisiae The mutation accumulation lines of the S. cerevisiae hybrid backgrounds - S288c/YJM789 (S/Y) and S288c/RM11-1a (S/R) were analyzed along with the homozygous diploids RM11, S288c, and YJM145. LOH was extensive in both S/Y and S/R hybrid backgrounds. The S/Y background also showed longer LOH tracts, gross chromosomal changes, and aneuploidy. Short copy number aberrations were observed in the S/R background. LOH data from the S/Y and S/R hybrids were used to construct a LOH map for S288c to identify hotspots. Further, we observe up to a sixfold difference in single nucleotide mutation rates among the S. cerevisiae S/Y and S/R genetic backgrounds. Our results demonstrate LOH is common during mitotic divisions in S. cerevisiae hybrids and also highlight genome-wide differences in LOH patterns and rates of single nucleotide mutations between commonly used S. cerevisiae hybrid genetic backgrounds.

Keywords: LOH hotspot; hybrid yeast; loss of heterozygosity; mitotic recombination; single nucleotide mutation.

Figure 1

Experimental set up of the mutation accumulation lines. 10 lines each of the S. cerevisiae S/R, S/Y hybrids and five lines each of the diploid homozygous S. cerevisiae strains, SS, YY and RR were propagated for 100 bottlenecks. Whole-genome sequences of the 35 MA lines after 100 bottlenecks were compared to the respective parent genomes to detect single nucleotide mutations, LOH, aneuploidy, and other gross chromosomal changes.

Figure 2

Genome-wide LOH plots for the S. cerevisiae S/Y and S/R hybrids. A) LOH plot for S/Y lines, B) LOH plot for S/R lines. Regions with LOH are in orange (2:0 or 0:2), and heterozygous regions are in cyan (1:1). Centromeres are shown in black dots, and SNMs are shown in asterisk (*).

Figure 3

Analysis of LOH in S/Y and S/R hybrids. A) Box plot showing the number of LOH tracts (supported by two or more SNPs) among different classes of LOH tract sizes in S/Y and S/R hybrids. Outliers are removed. Non-significant differences are shown as n.s (t-test). B) Individual S/Y and S/R lines sorted based on the number of LOH counts (supported by two or more SNPs). C) Percentage of SNPs fixed relative to the number of heterozygous SNP positions in the S/R and S/Y hybrids. n.s indicates non-significant (t-test).

Figure 4

Chromosomal map of LOH for S. cerevisiae S288c strain. Total count of LOH tracts from 15 S/Y (includes data from 5 S/Y hybrids from Dutta et al. 2017) and 10 S/R hybrids with their positions on each chromosome. Centromeres are shown in black dots. Chromosome boundaries are shown in gray vertical dash lines. Dash red lines show LOH count of 5 (shared in 20% of the lines). LOH hotspots are shown in red rectangle brackets. Orange dots show LTR retrotransposon positions.

Figure 5

Analysis of gross chromosomal changes in S/Y and S/R hybrids. A) Segmental duplications (Chromosomes IV and VII) in S/Y_2. B) Chromosome X aneuploidy in S/Y_9. C) Segmental deletions in S/R_7, S/R_9, and S/R_10. Gray vertical lines show chromosomal boundaries. Horizontal blue and red lines show the median and 2x median read counts that map to the chromosomes respectively. Orange dots show LTR retrotransposon positions in all panels.

Figure 6

SNM rate in S. cerevisiae MA lines. The box plot shows the SNM rate in the two hybrids (S/Y, S/R) and the diploid homozygous lines (RR, YY, SS). “***” indicates p-value <0.001 (t-test). n.s indicates non-significant differences.