Low Mutation Rate and Atypical Mutation Spectrum in Prasinoderma coloniale: Insights From an Early Diverging Green Lineage

Mettrop, Lisa; Lipzen, Anna; Vandecasteele, Celine; Eché, Camille; Labécot, Anaïs; Barry, Kerrie; Grigoriev, Igor V.; Piganeau, Gwenaël; Krasovec, Marc

doi:10.1093/gbe/evaf026

Title: Low Mutation Rate and Atypical Mutation Spectrum in Prasinoderma coloniale: Insights From an Early Diverging Green Lineage

Journal Article · 05 March 2025 · Genome Biology and Evolution

DOI: https://doi.org/10.1093/gbe/evaf026 · OSTI ID:2557483

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Sorbonne Univ., Paris (France); Centre National de la Recherche Scientifique (CNRS) (France)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
French National Research Institute for Agriculture, Food and Environment (INRAE) (France); Univ. of Toulouse (France)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); University of California, Berkeley, CA (United States)

Mutations are the ultimate source of genetic diversity on which natural selection and genetic drift act, playing a crucial role in evolution and long-term adaptation. At the molecular level, the spontaneous mutation rate (µ), defined as the number of mutations per base per generation, thus determines the adaptive potential of a species. Through a mutation accumulation experiment, we estimate the mutation rate and spectrum in Prasinoderma coloniale, a phytoplankton species from an early-branching lineage within the Archaeplastida, characterized by an unusually high genomic guanine-cytosine (GC) content (69.8%). We find that P. coloniale has a very low total mutation rate of µ = 2.00 × 10^-10. The insertion–deletion mutation rate is almost 5 times lesser than the single nucleotide mutation rate with µ_ID = 3.40 × 10^-11 and µ_SNM = 1.62 × 10^-10. Prasinoderma coloniale also exhibits an atypical mutational spectrum: While essentially all other eukaryotes show a bias toward GC to AT mutations, no evidence of this AT-bias is observed in P. coloniale. Since cytosine methylation is known to be mutagenic, we hypothesized that this may result from an absence of C-methylation. Surprisingly, we found high levels of C-methylation (14% in 5mC, 25% in 5mCG contexts). Methylated cytosines did not show increased mutation rates compared with unmethylated ones, not supporting the prevailing notion that C-methylation universally leads to higher mutation rates. Overall, P. coloniale combines a GC-rich genome with a low mutation rate and original mutation spectrum, suggesting the almost universal AT-bias may not have been present in the ancestor of the green lineage.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2557483

Journal Information:: Genome Biology and Evolution, Journal Name: Genome Biology and Evolution Journal Issue: 3 Vol. 17; ISSN 1759-6653

Publisher:: Society for Molecular Biology and EvolutionCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
DNA methylation
green algae
mutation rate
mutation spectrum
spontaneous mutation

Title: Low Mutation Rate and Atypical Mutation Spectrum in Prasinoderma coloniale: Insights From an Early Diverging Green Lineage

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