Genome-Wide Estimates of Mutation Rates and Spectrum inSchizosaccharomyces pombeIndicate CpG Sites are Highly Mutagenic Despite the Absence of DNA Methylation

Abstract

We accumulated mutations for 1952 generations in 79 initially identical, haploid lines of the fission yeast Schizosaccharomyces pombe, and then performed whole-genome sequencing to determine the mutation rates and spectrum. We captured 696 spontaneous mutations across the 79 mutation accumulation (MA) lines. We compared the mutation spectrum and rate to a recently published equivalent experiment on the same species, and to another model ascomycetous yeast, the budding yeast Saccharomyces cerevisiae. While the two species are approximately 600 million years diverged from each other, they share similar life histories, genome size and genomic G/C content. We found that Sc. pombe and S. cerevisiae have similar mutation rates, but Sc. pombe exhibits a stronger insertion bias. Intriguingly, we observed an increased mutation rate at cytosine nucleotides, specifically CpG nucleotides, which is also seen in S. cerevisiae. However, the absence of methylation in Sc. pombe and the pattern of mutation at these sites, primarily C → A as opposed to C → T, strongly suggest that the increased mutation rate is not caused by deamination of methylated cytosines. This result implies that the high mutability of CpG dinucleotides in other species may be caused in part by a methylation-independent mechanism. Many of our findings mirror those seen in the recent study, despite the use of different passaging conditions, indicating that MA is a reliable method for estimating mutation rates and spectra.

Similar Mutation Rates but Highly Diverse Mutation Spectra in Ascomycete and Basidiomycete Yeasts

“… Note .—The ts/tv ratio is calculated by $\frac{\underset{1}{\overset{n}{false\sum }}transitions}{\underset{1}{\overset{n}{false\sum }}transversions}$, where n is the number of MA lines.*Mutations from strains CC2344 and CC2931 are not included due to presence of MA lines with affected DNA repair.aAverage value of Behringer and Hall (2015) and Farlow et al (2015). …”

Intraspecific diversity of fission yeast mitochondrial genomes

“…To obtain an independent estimate of the divergence time, we also used BEAST to analyse the 29 K-region types ( Figure 6B). Based on the nuclear mutation rate of 2.00 × 10 −10 substitutions per site per generation (Behringer & Hall 2015;Farlow et al 2015), we obtained a divergence time of 39.7 million generations for the two ancient lineages. Taken together, our molecular dating results suggest that the two ancient lineages of S. pombe diverged about 40 million generations ago.…”

Nitrogen starvation reveals the mitotic potential of mutants in the S/MAPK pathways

“…The culture is then transferred to minimum medium without nitrogen at low cell density (10 6 cells per mL) and kept in non-proliferative conditions for 3 months without changing the medium (Methods). Based on previous work establishing somatic and quiescence mutation rates 23,24,27 and our experimental settings reducing somatic mutations, we anticipated 0.6 mutations per genome, generated mainly during the 3 months of starvation. The viability curve (Fig.…”

“…During growth, spontaneous mutations accumulate as a function of cell division 21 or DNA replication 22 . Under growth conditions, genome-wide sequencing approaches have shown that the mutation rate is in the range of 2 × 10 −10 mutation per nucleotide and per generation in fission yeast 23,24 . Extensive work in many species has shown a similar mutation spectrum where singlenucleotide variants (SNVs) are more frequent than insertions and deletions (indels) during growth 25 .…”