Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum inC. elegans

Abstract

Important clues about natural selection can be gleaned from discrepancies between the properties of segregating genetic variants and of mutations accumulated experimentally under minimal selection, provided the mutational process is the same in the lab as in nature. The ratio of transitions to transversions (Ts/Tv) is consistently lower in C. elegans mutation accumulation (MA) experiments than in nature, which has been argued to be in part due to increased oxidative stress in the lab environment. Using whole-genome sequence data from a set of C. elegans MA lines carrying a mutation (mev-1) that increases the cellular titer of reactive oxygen species (ROS), leading to increased endogenous oxidative stress, we find that the base-substitution spectrum is similar between mev-1 lines, its wild-type progenitor (N2), and another set of MA lines derived from a different wild strain (PB306). By contrast, the rate of short insertions is greater in the mev-1 lines, consistent with studies in other organisms in which environmental stress led to an increase in the rate of insertion-deletion mutations. Further, the mutational properties of mononucleotide repeats in all strains are qualitatively different from those of non-mononucleotide sequence, both for indels and base-substitutions, and whereas the non-mononucleotide spectra are fairly similar between MA lines and wild isolates, the mononucleotide spectra are very different. The discrepancy in mutational spectra between lab MA experiments and natural variation is likely due to a consistent (but unknown) effect of the lab environment that manifests itself via different modes of mutability and/or repair at mononucleotide loci.

Natural variation in C. elegans short tandem repeats

“…O1MA lines in both MA line panels have undergone passage for about 250 generations with minimal selection (Joyner-Matos et al 2011; Matsuba et al 2012; Saxena et al 2019; Rajaei et al 2021). To investigate STR mutations in MA lines, we calculated mutation rates for total mutations and three different mutations (deletions, insertions, and substitutions) between the ancestor and each O1MA line (ANC-O1MA) (See Materials and Methods) (fig.…”

“…Then, we compared the two alleles of each STR in the O1MA line to the two alleles in the ancestor, respectively, to identify insertion, deletion, substitution, or no mutation. We also obtained the number of generations between the O1MA line and the ancestor from the original studies (Saxena et al 2019; Rajaei et al 2021). The mutation rate (per-allele, per-STR, per-generation) µ for each type of mutation was calculated as m/2nt where m is the number of the mutation, n is the total number of STR sites between the two lines, and t is the number of generations.…”

Mutation, selection, and the prevalence of the C. elegans heat-sensitive mortal germline phenotype

“…Here, k =1 mutation in nt (67 lines)(250 generations)=16750 meioses, so the 95% confidence interval around U Mrt is (1.53×10 −6 – 3.28×10 −4 /genome/generation). The per-nucleotide mutation rate in these lines is approximately 2.8×10 −9 /generation (Saxena et al 2019; Rajaei et al 2021) and the C. elegans genome is approximately 10 8 bp, resulting in a point estimate of the mutational target of the Mrt phenotype of about 0.02%, and possibly as much as 0.1% of the C. elegans genome.…”

“…Given that one, and only one, MA line has a clear Mrt phenotype, we scrutinized its genome for candidate mutations (Rajaei et al 2021; Supplemental Methods ). Line 578 carries 37 unique base-substitutions, 13 deletions, and four insertions relative to the genome of the progenitor of the N2 MA lines ( Supplemental Table S2 ).…”

“…We estimated the rate of mutation to the Mrt phenotype from two sets of C. elegans laboratory mutation accumulation (MA) lines, which evolved in the near-absence of natural selection for approximately 250 generations. On average, each MA line carries about 65 unique spontaneous base-substitution and small indel mutations (Rajaei et al 2021), and probably a few larger structural variants (A. S. Saxena and Baer, unpublished results). In addition, we estimated the frequency of the Mrt phenotype in a worldwide collection of ~100 wild isolates.…”