Spontaneous Mutation Rate in the Smallest Photosynthetic Eukaryotes

Abstract

Mutation is the ultimate source of genetic variation, and knowledge of mutation rates is fundamental for our understanding of all evolutionary processes. High throughput sequencing of mutation accumulation lines has provided genome wide spontaneous mutation rates in a dozen model species, but estimates from nonmodel organisms from much of the diversity of life are very limited. Here, we report mutation rates in four haploid marine bacterial-sized photosynthetic eukaryotic algae; Bathycoccus prasinos, Ostreococcus tauri, Ostreococcus mediterraneus, and Micromonas pusilla. The spontaneous mutation rate between species varies from μ = 4.4 × 10−10 to 9.8 × 10−10 mutations per nucleotide per generation. Within genomes, there is a two-fold increase of the mutation rate in intergenic regions, consistent with an optimization of mismatch and transcription-coupled DNA repair in coding sequences. Additionally, we show that deviation from the equilibrium GC content increases the mutation rate by ∼2% to ∼12% because of a GC bias in coding sequences. More generally, the difference between the observed and equilibrium GC content of genomes explains some of the inter-specific variation in mutation rates.

Mutational Landscape of Spontaneous Base Substitutions and Small Indels in Experimental Caenorhabditis elegans Populations of Differing Size

“…Higher G+C-content than expected by mutation pressure alone seems to be the 543 rule in genome evolution, and it is usually presumed that natural selection for higher G+C-544 content and/or biased gene conversion are responsible. However, this departure from equilibrium 545 G+C-content also has the effect of increasing the mutation rate (Krasovec et al 2017). substitution patterns in our MA lines.…”

“…Because natural variation is the result of an interplay between mutations, genetic drift and natural 59 selection, having a realistic hypothesis for genetic variation in the absence of selection is 60 essential. Furthermore, features of the genome can be shaped by prevailing mutational biases 61 such as base composition, and in turn, the base composition itself can influence mutation rates 62 (Smith et al 2002;Krasovec et al 2017). Moreover, mutation rates themselves are not uniformly 63 distributed across genes in the genome.…”

“…However, lower mutation rates in coding sequences relative to non-coding ones have been 557 observed in other MA experiments and were ascribed to transcription-coupled repair (TCR) and 558 differential efficiency of mismatch repair (MMR) between coding and non-coding DNA 559 (Krasovec et al 2017). Additionally, a recent study of somatic mutation rates in humans 560 concluded that introns have higher mutation rates than exons due in part to greater efficiency of 561 mismatch repair in exons (Frigola et al 2017).…”

Somatic mutations substantially increase the per-generation mutation rate in the coniferPicea sitchensis

“…By comparison, the mutation rates per cell division in other taxa tend to be at the higher end of this range, varying from 4.4 × 10 –10 to 9.8 × 10 –10 in four single‐celled piko‐phytoplankton (Krasovec et al. ) and estimated as 2 × 10 –10 in Arabidopsis (Ossowski et al. ).…”

Peer Review #1 of "The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns (v0.1)"

“…Therefore, mutation rate will increase until selection is strong enough to prevent the genome evolving a higher mutation rate (Lynch et al, 2016). Krasovec et al (2017) combined a review of literature with mutation rate estimates for four prasinophytes and found PeerJ reviewing PDF | (2019:09:41517:1:1:NEW 15 Nov 2019)…”