Similar Mutation Rates but Highly Diverse Mutation Spectra in Ascomycete and Basidiomycete Yeasts

Behringer, Megan G; Williams, Emily; Te, Ronald; Lynch, Michael

doi:10.1093/gbe/evw286

Cited by 44 publications

(36 citation statements)

References 48 publications

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“…The GC content can be of interest for the study of the orphan proteins, 35 mutation rate, spectrum of mutations 36 . The GC content for the reference strain CBS 2479 was 59%, as previously reported and varied between 55% and 59% for the clinical isolates.…”

Section: Discussionsupporting

confidence: 58%

Epidemiological investigation for grouped cases of Trichosporon asahii using whole genome and IGS1 sequencing

Desnos‐Ollivier

Maufrais

Pihet

et al. 2020

Mycoses

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Summary Background Trichosporonosis is a rare invasive infection in humans mainly due to Trichosporon asahii, and especially recovered from patients having haematological malignancy. Since 2012, IGS1 region sequencing is used as a genotyping method to distinguish isolates, with high frequency of one haplotype worldwide and a geographic specificity for some haplotypes. Objectives We compared the IGS1 genotyping method and whole genome sequencing (WGS) to study the relationship between clinical isolates involved in two grouped cases in France. Methods IGS1 sequencing and antifungal susceptibility testing were performed for 54 clinical isolates. Clinical data for 28 isolates included in surveillance programs were analysed. Whole genome was sequenced for 32 clinical isolates and the type strain. Results All isolates were intrinsically resistant to flucytosine, while voriconazole had the most potent in vitro activity. The majority of the isolates was recovered from patients with haematological malignancies (42.86%), with a high proportion of children (<15 yrs‐old, 32.14%) and a high mortality rate at three months (46.15%). Based on the WGS analysis, isolates exhibiting IGS1 haplotype 1, 3 and 7 belonged to different clades. Five isolates recovered during the first grouped cases had the same IGS1 haplotype and shared 99% of SNPs similarity. For the second grouped cases, four isolates had 98.7% of SNPs similarity while the isolate recovered 4 years earlier was totally unlinked. Conclusions We confirmed the usefulness of IGS1 sequencing for grouped cases infection of T. asahii. We underlined its limitation for the study of population structure and the utility of WGS analysis for the study of epidemiologically unrelated isolates.

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Section: Discussionsupporting

confidence: 58%

Epidemiological investigation for grouped cases of Trichosporon asahii using whole genome and IGS1 sequencing

Desnos‐Ollivier

Maufrais

Pihet

et al. 2020

Mycoses

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“…The evolution of the mutation rate is of longstanding interest to evolutionary theorists (Fisher 1930; Sturtevant 1937; Lynch et al 2016), and there is abundant empirical evidence that the overall rate, molecular spectrum, and phenotypic consequences of mutation - collectively, the mutational process - vary at many biological levels, from within an individual genome to among species and higher taxa (Drake et al 1998; Conrad et al 2011; Schrider et al 2013; Long et al 2016; Ness et al 2016; Carlson et al 2018). The mechanistic, environmental, ecological, and evolutionary factors that potentially influence variation in the mutational process are legion.…”

Section: Introductionmentioning

confidence: 99%

Evolution of the mutational process under relaxed selection inCaenorhabditis elegans

Saxena

Salomon

Matsuba

et al. 2018

Preprint

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The mutational process varies at many levels, from within genomes to among taxa. Many mechanisms have been linked to variation in mutation, but understanding of the evolution of the mutational process is rudimentary. Physiological condition is often implicated as a source of variation in microbial mutation rate and may contribute to mutation rate variation in multicellular organisms.Deleterious mutations are a ubiquitous source of variation in condition. We test the hypothesis that the mutational process depends on the underlying mutation load in two groups of Caenorhabditis elegans mutation accumulation (MA) lines that differ in their starting mutation loads. “First-Order MA” (O1MA) lines maintained under minimal selection for ∼250 generations were divided into high-fitness and low-fitness groups and sets of “second-order MA” (O2MA) lines derived from each O1MA line were maintained for ∼150 additional generations. Genomes of 48 O2MA lines and their progenitors were sequenced. There is significant variation among O2MA lines in base-substitution rate (µbs), but no effect of initial fitness, whereas the indel rate is greater in high-fitness O2MA lines. Overall, µbs is positively correlated with recombination and proximity to short tandem repeats and negatively correlated with 10 bp and 1 Kb GC content. However, probability of mutation is well-predicted by the three-nucleotide motif. ∼90% of the variance in standing nucleotide variation is explained by mutability. Total mutation rate increased in the O2MA lines, as predicted by the “drift barrier” model of mutation rate evolution. These data, combined with experimental estimates of fitness, suggest that epistasis is synergistic.

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“…We estimated the SNVs - using all SNVs and separated for A/T and G/C pairs - and indel mutation rates with the following formula: m /( t × c ) where m is the total number of mutations across the 7 lines, t is equal to 10 generations, c is the total number of callable sites over each line. A 95% confidence interval was obtained by using an exact Poisson test with the poisson.test R function, as suggested in (53).…”

Section: Methodsmentioning

confidence: 99%

Reversed sex-biased mutation rates for indels and base substitutions inDrosophila melanogaster

Törmä¹,

Burny²,

Schlötterer³

2020

Preprint

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1Sex biases in mutation rates may affect the rate of adaptive evolution. In many species, males 2 have higher mutation rates than females when single nucleotide variants (SNVs) are considered. 3In contrast, indel mutations in humans and chimpanzees are female-biased. In Drosophila 4 melanogaster, direct estimates of mutation rates did not uncover sex differences, but a recent 5 analysis suggested the presence of male-biased SNVs mutations. Here we study the sex-specific 6 mutation processes using mutation accumulation data from mismatch-repair deficient D. 7 melanogaster. We find that sex differences in flies are similar to the ones observed in humans: a 8 higher mutation rate for SNVs in males and a higher indel rate in females. These results have 9 major implications for the study of neutral variation and adaptation in Drosophila. 10 192

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Similar Mutation Rates but Highly Diverse Mutation Spectra in Ascomycete and Basidiomycete Yeasts

Cited by 44 publications

References 48 publications

Epidemiological investigation for grouped cases of Trichosporon asahii using whole genome and IGS1 sequencing

Epidemiological investigation for grouped cases of Trichosporon asahii using whole genome and IGS1 sequencing

Evolution of the mutational process under relaxed selection inCaenorhabditis elegans

Reversed sex-biased mutation rates for indels and base substitutions inDrosophila melanogaster

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