An Unbiased Genome-Wide View of the Mutation Rate and Spectrum of the Endosymbiotic Bacterium Teredinibacter turnerae

Abstract

Mutations contribute to genetic variation in all living systems. Thus, precise estimates of mutation rates and spectra across a diversity of organisms are required for a full comprehension of evolution. Here, a mutation-accumulation (MA) assay was carried out on the endosymbiotic bacterium Teredinibacter turnerae. After ∼3,025 generations, base-pair substitutions (BPSs) and insertion–deletion (indel) events were characterized by whole-genome sequencing analysis of 47 independent MA lines, yielding a BPS rate of 1.14 × 10−9 per site per generation and indel rate of 1.55 × 10−10 events per site per generation, which are among the highest within free-living and facultative intracellular bacteria. As in other endosymbionts, a significant bias of BPSs toward A/T and an excess of deletion mutations over insertion mutations are observed for these MA lines. However, even with a deletion bias, the genome remains relatively large (∼5.2 Mb) for an endosymbiotic bacterium. The estimate of the effective population size (Ne) in T. turnerae is quite high and comparable to free-living bacteria (∼4.5 × 107), suggesting that the heavy bottlenecking associated with many endosymbiotic relationships is not prevalent during the life of this endosymbiont. The efficiency of selection scales with increasing Ne and such strong selection may have been operating against the deletion bias, preventing genome erosion. The observed mutation rate in this endosymbiont is of the same order of magnitude of those with similar Ne, consistent with the idea that population size is a primary determinant of mutation-rate evolution within endosymbionts, and that not all endosymbionts have low Ne.

Low Base-Substitution Mutation Rate but High Rate of Slippage Mutations in the Sequence Repeat-Rich Genome of Dictyostelium discoideum

“…Bootstrapped confidence intervals describing the variation in n and T was estimated using the boot package for R with the BCa adjustment for 1000 bootstrap replicates. The expected probability of occurrence of multinucleotide mutations (MNM) within the window size 50 nucleotides in the genome of D. discoideum MA lines was calculated as in Senra et al (2018) .…”

Significant Strain Variation in the Mutation Spectra of Inbred Laboratory Mice

“…2015; Smeds et al. 2016; Senra et al. 2018), presumably reflecting species differences in DNA repair mechanisms (Hart and Setlow 1974; MacRae et al.…”

Patterns of Nucleotide Deletion and Insertion Inferred from Bacterial Pseudogenes

“…Possibly because insertion–deletion mutations (indels) have the highest potential to disrupt the production of proteins by introducing frameshift mutations in protein-coding genes, observed rates of indels per generation are generally an order of magnitude lower than base-substitution rates ( Sung et al. 2016 ; Senra et al. 2018 ), hindering statistically robust inference of indel mutation spectra.…”