Extraordinary Genetic Diversity in a Wood Decay Mushroom

Baranova, Maria A.; Logacheva, Maria D.; Penin, Aleksey A.; Seplyarskiy, Vladimir B.; Safonova, Yana; Naumenko, Sergey; Klepikova, Anna V.; Gerasimov, Evgeny S.; Bazykin, Georgii A.; James, Timothy Y.; Kondrashov, Alexey S.

doi:10.1093/molbev/msv153

Cited by 45 publications

(53 citation statements)

References 33 publications

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“…In the American population, where the bias was weaker than expected, one specimen (from Florida) was significantly differentiated from all others (from Michigan, Fig. 1 in [13]). However, excluding this specimen from the analysis only has a minor effect on the bias for this population (not shown), suggesting the discrepancy with our theoretical expectation is not necessarily explained by population structure.…”

Section: Discussionmentioning

confidence: 96%

“…To measure the RAD-seq bias in real data, we performed in silico RAD-seq experiments, using full genome sequences from natural populations of Drosophila melanogaster [12] and Schizophyllum commune [13]. For both species, the sequences that are available correspond to haploid genomes.…”

Section: Methodsmentioning

confidence: 99%

“…We then confronted theoretical predictions to ideal empirical data, that is, in silico digestions of full genomes from natural populations of the fruit fly Drosophila melanogaster (DPGP [12]), harbouring moderate polymorphism, and the fungus Schizophyllum commune [13], harbouring high polymorphism. These two case studies generally confirm the expected relation between the level of polymorphism and the intensity of the RAD-seq bias: the bias is much stronger in the highly polymorphic species.…”

Section: Introductionmentioning

confidence: 99%

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How and how much does RAD-seq bias genetic diversity estimates?

2016

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BackgroundRAD-seq is a powerful tool, increasingly used in population genomics. However, earlier studies have raised red flags regarding possible biases associated with this technique. In particular, polymorphism on restriction sites results in preferential sampling of closely related haplotypes, so that RAD data tends to underestimate genetic diversity.ResultsHere we (1) clarify the theoretical basis of this bias, highlighting the potential confounding effects of population structure and selection, (2) confront predictions to real data from in silico digestion of full genomes and (3) provide a proof of concept toward an ABC-based correction of the RAD-seq bias. Under a neutral and panmictic model, we confirm the previously established relationship between the true polymorphism and its RAD-based estimation, showing a more pronounced bias when polymorphism is high. Using more elaborate models, we show that selection, resulting in heterogeneous levels of polymorphism along the genome, exacerbates the bias and leads to a more pronounced underestimation. On the contrary, spatial genetic structure tends to reduce the bias. We confront the neutral and panmictic model to “ideal” empirical data (in silico RAD-sequencing) using full genomes from natural populations of the fruit fly Drosophila melanogaster and the fungus Shizophyllum commune, harbouring respectively moderate and high genetic diversity. In D. melanogaster, predictions fit the model, but the small difference between the true and RAD polymorphism makes this comparison insensitive to deviations from the model. In the highly polymorphic fungus, the model captures a large part of the bias but makes inaccurate predictions. Accordingly, ABC corrections based on this model improve the estimations, albeit with some imprecisions.ConclusionThe RAD-seq underestimation of genetic diversity associated with polymorphism in restriction sites becomes more pronounced when polymorphism is high. In practice, this means that in many systems where polymorphism does not exceed 2 %, the bias is of minor importance in the face of other sources of uncertainty, such as heterogeneous bases composition or technical artefacts. The neutral panmictic model provides a practical mean to correct the bias through ABC, albeit with some imprecisions. More elaborate ABC methods might integrate additional parameters, such as population structure and selection, but their opposite effects could hinder accurate corrections.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0791-0) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 96%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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How and how much does RAD-seq bias genetic diversity estimates?

2016

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“…To better understand the link between the somatic accumulation of mutations during growth and their contribution to the per generation mutation rate, we take advantage of a basidiomycete wood-decay fungus Schizophyllum commune . S. commune is characterized by the highest genetic diversity among all studied species, with nucleotide diversity reaching 20% within a single population (Baranova et al 2015) . The cause of this remains unclear.…”

Section: Introductionmentioning

confidence: 98%

Rapid accumulation of mutations in growing mycelia of a hypervariable fungus Schizophyllum commune

Bezmenova

Zvyagina

Федотова

et al. 2019

Preprint

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AbstractThe number of mutations that occur per nucleotide per generation varies between species by several orders of magnitude. In multicellular eukaryotes, the per generation mutation rate depends both on the per cell division mutation rate and on the number of germline cell divisions per generation. In a range of species, from fungi to humans, the number of germline cell divisions is lower than that of somatic cells, reducing the mutation burden on the offspring. The basidiomycete Schizophyllum commune has the highest level of genetic polymorphism known among eukaryotes. In a previous study, it was also found to have a high per generation mutation rate, probably contributing to its high polymorphism. However, this rate has been measured only in a breeding experiment on Petri dishes, and it is unclear how this result translates to natural populations. Here, we used an experimental design that measures the rate of accumulation of de novo mutations in a linearly growing mycelium. We show that S. commune accumulates mutations at a uniform rate of 1.4·10−7 substitutions per nucleotide per meter of growth, which is 3 orders of magnitude higher than the corresponding rates in the oak Quercus robur and the fungus Armillaria gallica. This figure is consistent with the estimate obtained before, and suggests the lack of a dedicated germline in this system. If so, even a low per cell division mutation rate can translate into a very high per generation mutation rate when the number of cell divisions between consecutive meioses is large.

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“…Together with the published S. commune genome sequence (Ohm et al, 2010) expression of 67 % of the predicted genes was shown as well as a high abundance of antisense transcripts (42 % of the genes). Since then, a comprehensive genome study followed (Baranova et al, 2015) which revealed a high intraspecific diversity. Such high divergence requires that co-isogenic strains be used in transcriptomics and proteomics, as used previously (De Vries et al, 1980;De Vries and Wessels, 1984), or in studies on the metabolome (Menezes et al, 2015), such as the identification of volatile profiles.…”

Section: Introductionmentioning

confidence: 99%