First Estimation of the Spontaneous Mutation Rate in Diatoms

Abstract

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 μbs = 4.77 × 10−10 and the insertion–deletion mutation rate is μid = 1.58 × 10−11. 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 mitochondria. 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 Ne∼8.72 × 106.

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

“…Red data points highlight the observed base pair substitution (BPS) rate of Dictyostelium discoideum from this study with respect to effective population size ( N e ) and nucleotide diversity (θ) ( Flowers et al 2010 ). Black data points correspond to the following additional unicellular eukaryote species for reference: Chlamydomonas reinhardtii ( Smith and Lee 2008 ; Sung et al 2012a ; Ness et al 2015 ); Paramecium biaurelia , Paramecium sexaurelia ( Long et al 2018a ); Paramecium tetraurelia ( Sung et al 2012b ); Ostreococcus tauri ( Krasovec et al 2017 ); Plasmodium falciparum ( Lynch 2010 ; Hamilton et al 2017 ); Saccharomyces cerevisiae ( Schacherer et al 2009 ; Zhu et al 2014 ); Schizosaccharomyces pombe ( Fawcett et al 2014 ; Behringer and Hall 2016a ); Tetrahymena thermophila ( Long et al 2016 ); Phaeodactylum tricornutum ( Krasovec et al 2019 ).…”

Evolution of Codon Usage Bias in Diatoms

“…Similarly, the two T. rotula , two T. weissflogii and two S. marinoi (MMETSP1039 and MMETSP1040) have π ~0.01, giving N e ~5 million individuals. Furthermore, it was previously reported that several other marine plankton species have N e ~10 million: diatom P. tricornum [42], coccolithophore E. huxleyi [46] and coastal green algae O. tauri [47]. Thus, effective population sizes of plankton species analysed so far are of the order of a few million individuals, which indicates the generality of the finding that marine plankton typically have relatively modest N e , despite astronomically large census population sizes [46].…”

“…In P. tricornutum , the mutation spectrum is known [42], so k is readily available. In the case of GC-rich preferred codon, u = 2.21 and v = 1.0, so k = 2.21.…”

Estimation of the SNP Mutation Rate in Two Vegetatively Propagating Species of Duckweed

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