Genome Dynamics of Hybrid Saccharomyces cerevisiae During Vegetative and Meiotic Divisions

Abstract

Mutation and recombination are the major sources of genetic diversity in all organisms. In the baker's yeast, all mutation rate estimates are in homozygous background. We determined the extent of genetic change through mutation and loss of heterozygosity (LOH) in a heterozygous Saccharomyces cerevisiae genome during successive vegetative and meiotic divisions. We measured genome-wide LOH and base mutation rates during vegetative and meiotic divisions in a hybrid (S288c/YJM789) S. cerevisiae strain. The S288c/YJM789 hybrid showed nearly complete reduction in heterozygosity within 31 generations of meioses and improved spore viability. LOH in the meiotic lines was driven primarily by the mating of spores within the tetrad. The S288c/YJM789 hybrid lines propagated vegetatively for the same duration as the meiotic lines, showed variable LOH (from 2 to 3% and up to 35%). Two of the vegetative lines with extensive LOH showed frequent and large internal LOH tracts that suggest a high frequency of recombination repair. These results suggest significant LOH can occur in the S288c/YJM789 hybrid during vegetative propagation presumably due to return to growth events. The average base substitution rates for the vegetative lines (1.82 × 10^-10 per base per division) and the meiotic lines (1.22 × 10^-10 per base per division) are the first genome-wide mutation rate estimates for a hybrid yeast. This study therefore provides a novel context for the analysis of mutation rates (especially in the context of detecting LOH during vegetative divisions), compared to previous mutation accumulation studies in yeast that used homozygous backgrounds.

Keywords: hybrid yeast; loss of heterozygosity; meiosis; mitotic recombination; mutation rate.

Figure 1

(A) Experimental set up of the vegetative (V) and meiotic (M) lines from the parent diploid. The numbers in brackets indicate the number of V and M lines available at the vegetative bottleneck (V_19, V_57) or meiotic generations (M_3, M_5, M_7, M_10, M_15, M_31). LOH events are observed in both V and M lines. (B) LOH in the M lines following each generation of meiosis and intratetrad mating. Continuous lines (red and green) show the observed number of heterozygous SNPs in two M lines (Line 1 and 2). Black dashes show the number of heterozygous SNPs expected assuming wild-type S. cerevisiae recombination rates.

Figure 2

Genome-wide distribution of SNPs in the two M lines (1 and 2) after 3rd, 7th, 15th, and 31st generation of meiosis. Homozygous SNPs are shown in orange while heterozygous SNPs are shown in cyan. More than 99% of the heterozygous sites are fixed by M_31.

Figure 3

Genome-wide plots of LOH and new base mutations in the five V_57 lines. Regions showing loss of heterozygosity are in orange (2:0 or 0:2). Regions in cyan are heterozygous (1:1). Asterisk (*) symbols show the position of the new base mutations in the V_57 lines.

Figure 4

Heterozygosity is negatively correlated with spore viability. The number of heterozygous SNPs and spore viability are plotted against each other for the S288c × YJM789 diploid M lines and for hybrid crosses involving other S. cerevisiae strains. Data for the M lines are from Table 1. Data for other hybrid crosses are shown in the text.

Figure 5

Representative in silico genomes generated by crossing spores from M_3 and M_10 lines. White regions on the chromosome are homozygous for S288c or YJM789. Red and Blue indicate S288c and YJM789 SNPs respectively. The diploids generated from the cross have good viability (>90%) and are heterozygous at specific chromosomal regions. The green and gray regions indicate centromere positions and chromosome boundaries, respectively.