First Estimation of the Spontaneous Mutation Rate in Diatoms

Marc Krasovec (1) , Sophie Sanchez-Brosseau , Gwenael Piganeau

1 BIOM - Biologie intégrative des organismes marins

Mutations are the origin of genetic diversity, and the mutation rate is a fundamental parameter to understand all aspects of molecular evolution. The combination of mutation-accumulation experiments and high-throughput sequencing enabled the estimation of mutation rates in most model organisms, but several major eukaryotic lineages remain unexplored. Here, we report the first estimation of the spontaneous mutation rate in a model unicellular eukaryote from the Stramenopile kingdom, the diatom Phaeodactylum tricornutum (strain RCC2967). We sequenced 36 mutation accumulation lines for an average of 181 generations per line and identified 156 de novo mutations. The base substitution mutation rate per site per generation is l bs ¼ 4.77 Â 10 À10 and the insertion-deletion mutation rate is l id ¼ 1.58 Â 10 À11. The mutation rate varies as a function of the nucleotide context and is biased toward an excess of mutations from GC to AT, consistent with previous observations in other species. Interestingly, the mutation rates between the genomes of organelles and the nucleus differ, with a significantly higher mutation rate in the mito-chondria. This confirms previous claims based on indirect estimations of the mutation rate in mitochondria of photosynthetic eukaryotes that acquired their plastid through a secondary endosymbiosis. This novel estimate enables us to infer the effective population size of P. tricornutum to be N e $8.72 Â 10 6 .

Mots clés: spontaneous mutation rate; mutation accumulation; mutation spectrum; Phaeodactylum tricornutum; diatoms; spontaneous mutation rate

Domaines: Sciences du Vivant [q-bio]

Marc Krasovec, Sophie Sanchez-Brosseau, Gwenael Piganeau. First Estimation of the Spontaneous Mutation Rate in Diatoms. Genome Biology and Evolution, 2019, ⟨10.1093/gbe/evz130⟩. ⟨hal-02978190v2⟩