Precise estimates of mutation rate and spectrum in yeast

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.

Keywords: neighbor-dependent mutation rate; strongly deleterious mutation.

Fig. 1.

Histogram of SNM counts per line in 97 MA lines with >60% of the genome covered to >8× read depth. Only positions sequenced to >8× read depth in all 97 lines were considered. A total of 256 SNMs were called in such regions in the 97 lines. Histogram shape may be Poisson (P = 0.07, G test) or negative binomial (P = 0.1, G test), but not binomial (P < 0.001, G test).

Fig. 2.

(x axis) Number of mutations observed per chromosome. (y axis) Length of chromosome. Number of mutations observed on a chromosome is strongly correlated with chromosomal length (adjusted R² = 0.94, P < 0.001).

Fig. 3.

Relative mutation rates of each of six possible nucleotide changes.

Fig. 4.

Relative mutation rates at all bases, only G/C bases, and only A/T bases with respect to local (Left) 1-kb GC content, (Center) transcription rate, and (Right) replication time during cell cycle. Categories were defined by obtaining bins that contain roughly equal numbers of SNMs.

Fig. 5.

(y axis) Relative mutation rate. (x axis) Neighbor environment. Neighbor-dependent mutation rate is defined as the effects of immediate flanking nucleotides (e.g., bases a and t in an aCt environment) on mutation rate at base of interest (base C in an aCt environment). Environment classes represent mutation rates regardless of strand orientation (aCt class includes overall mutation rate at aCt and aGt positions). Average mutation rate of 1.24 (1.11 when excluding cCg and tCg contexts) at C/G bases shows clear overall elevation over a corresponding rate of 0.52 at A/T bases. In addition, two environments (cCg and tCg) show additional elevations in mutation rate.

Fig. 6.

Summary of all mutations identified. Numbers in parentheses represent numbers of events called in each mutation class.