title: Extraordinary Genetic Diversity in a Wood Decay Mushroom.
abstract: 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 United States 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 2 parental and 17 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.
authors.affiliation: School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia.
authors.forename: Maria A
authors.initials: MA
authors.lastname: Baranova
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Maria D
authors.initials: MD
authors.lastname: Logacheva
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Aleksey A
authors.initials: AA
authors.lastname: Penin
authors.affiliation: School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia.
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Seplyarskiy
authors.affiliation: Algorithmic Biology Lab, St. Petersburg Academic University of the Russian Academy of Sciences, St Petersburg, Russia.
authors.forename: Yana Y
authors.initials: YY
authors.lastname: Safonova
authors.affiliation: School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Sergey A
authors.initials: SA
authors.lastname: Naumenko
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Anna V
authors.initials: AV
authors.lastname: Klepikova
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Evgeny S
authors.initials: ES
authors.lastname: Gerasimov
authors.affiliation: School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Georgii A
authors.initials: GA
authors.lastname: Bazykin
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Michigan.
authors.forename: Timothy Y
authors.initials: TY
authors.lastname: James
authors.affiliation: School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia Department of Ecology and Evolutionary Biology, University of Michigan kondrash@umich.edu.
authors.forename: Alexey S
authors.initials: AS
authors.lastname: Kondrashov
mesh_terms: D000363:Agaricales / Q000235:genetics*; D014644:Genetic Variation; D009711:Nucleotides / Q000235:genetics; D011110:Polymorphism, Genetic; D014934:Wood / Q000382:microbiology*
chemical_list: D009711:Nucleotides
keywords: de novo mutation rate; genetic variation; hyperdiversity; population genetics