Extraordinary Genetic Diversity in a Wood Decay Mushroom

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

Populations of different species vary in the amounts of genetic diversity they possess. Nucleotide diversity π, the fraction of nucleotides that are different between two randomly chosen genotypes, has been known to range in eukaryotes between 0.0001 in Lynx lynx and 0.16 in Caenorhabditis brenneri. Here, we report the results of a comparative analysis of 24 haploid genotypes (12 from the USA, and 12 from European Russia) of a split-gill fungus Schizophyllum commune. The diversity at synonymous sites is 0.20 in the American population of S. commune, and 0.13 in the Russian population. This exceptionally high level of nucleotide diversity also leads to extreme amino acid diversity of protein-coding genes. Using whole-genome resequencing of two parental and seventeen offspring haploid genotypes, we estimate that the mutation rate in S. commune is high, at 2.0×10(-8) (95% CI 1.1×10(-8) to 4.1×10(-8)) per nucleotide per generation. Therefore, the high diversity of S. commune is primarily determined by its elevated mutation rate, although high effective population size likely also plays a role. Small genome size, ease of cultivation and completion of the life cycle in the laboratory, free-living haploid life stages and exceptionally high variability of S. commune make it a promising model organism for population, quantitative, and evolutionary genetics.