Precise estimates of mutation rate and spectrum in yeast

Significance

Spontaneous mutations are rare and difficult to observe in large numbers experimentally. By sequencing the genomes of 145 diploid mutation accumulation (MA) lines of the budding yeast Saccharomyces cerevisiae , we identified nearly 1,000 mutations, a larger number than in any prior eukaryotic MA experiment as far as we are aware. For the first time, to our knowledge, in MA data, we were able to estimate rates of context-dependent single-nucleotide mutations. We were also able to observe mutational classes not seen in earlier yeast MA experiments and infer the rate of strongly deleterious mutations from patterns of missing mutations in each mutational class. Our findings both answer outstanding questions in the field, as well as highlight the need for more studies of spontaneous mutation.

Abstract

Mutation is the ultimate source of genetic variation. The most direct and unbiased method of studying spontaneous mutations is via mutation accumulation (MA) lines. Until recently, MA experiments were limited by the cost of sequencing and thus provided us with small numbers of mutational events and therefore imprecise estimates of rates and patterns of mutation. We used whole-genome sequencing to identify nearly 1,000 spontaneous mutation events accumulated over ∼311,000 generations in 145 diploid MA lines of the budding yeast Saccharomyces cerevisiae . MA experiments are usually assumed to have negligible levels of selection, but even mild selection will remove strongly deleterious events. We take advantage of such patterns of selection and show that mutation classes such as indels and aneuploidies (especially monosomies) are proportionately much more likely to contribute mutations of large effect. We also provide conservative estimates of indel, aneuploidy, environment-dependent dominant lethal, and recessive lethal mutation rates. To our knowledge, for the first time in yeast MA data, we identified a sufficiently large number of single-nucleotide mutations to measure context-dependent mutation rates and were able to ( i ) confirm strong AT bias of mutation in yeast driven by high rate of mutations from C/G to T/A and ( ii ) detect a higher rate of mutation at C/G nucleotides in two specific contexts consistent with cytosine methylation in S. cerevisiae .