Background: In this study we determine the rate and spectrum of spontaneous mutations for the social amoeba, Dictyostelium discoideum, a key model organism in molecular and cell biology. Like many other microbial eukaryotes, D. discoideum has unusual life history and genome features, for example its AT-rich genome (77.5%) and high percentage of simple sequence repeats, including in coding sequence. This work enables us to explore evolutionary forces and molecular mechanisms that may have shaped the mutation rate and spectrum of D. discoideum.
Results and Discussion: Whole-genome sequencing of 19 mutation accumulation lines of D. discoideum after an average of 3,000 cell divisions yielded a base substitution mutation rate estimate of 3.55 × 10−11 per site per generation, substantially lower than that observed for most eukaryotic and prokaryotic organisms. Transversions biased transitions and base-substitution changes yielded a mutation rate in the AT direction. The deletion rate is higher than the insertion rate, which is inconsistent with the previous studies showing an insertion bias in unicellular eukaryotes. The base-substitution mutation rate in D. discoideum is on the same order of magnitude of that of the ciliates Paramecium tetraurelia and Tetrahymena thermophila. Like ciliates, D. discoideum maintains a large effective population size, reducing the power of random genetic drift, such that selection is relatively unhindered to reduce mutation rates. This observation is consistent with the drift barrier hypothesis that mutation rates are inversely proportional to effective population sizes, and furthers our understanding of the evolutionary forces and molecular mechanisms shaping the evolution of mutation rate.