title: Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity.
abstract: Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena.
authors.affiliation: School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia pamjat@mail.ru.
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Seplyarskiy
authors.affiliation: School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Maria D
authors.initials: MD
authors.lastname: Logacheva
authors.affiliation: School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, 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 of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Maria A
authors.initials: MA
authors.lastname: Baranova
authors.affiliation: School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Evgeny V
authors.initials: EV
authors.lastname: Leushkin
authors.affiliation: School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Moscow, Russia.
authors.forename: Natalia V
authors.initials: NV
authors.lastname: Demidenko
authors.affiliation: School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Moscow, Russia.
authors.forename: Anna V
authors.initials: AV
authors.lastname: Klepikova
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Pg. Lluís Companys, Barcelona, Spain.
authors.forename: Fyodor A
authors.initials: FA
authors.lastname: Kondrashov
authors.affiliation: School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI.
authors.forename: Alexey S
authors.initials: AS
authors.lastname: Kondrashov
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI.
authors.forename: Timothy Y
authors.initials: TY
authors.lastname: James
mesh_terms: D001482:Base Composition; D020029:Base Pairing; D003433:Crosses, Genetic; D003434:Crossing Over, Genetic; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D056426:Genetic Loci; D014644:Genetic Variation; D006238:Haploidy; D015810:Linkage Disequilibrium; D012567:Schizophyllum / Q000235:genetics*; D012641:Selection, Genetic
chemical_list: D004247:DNA
keywords: S. commune; hyperpolymorphic; negative selection; recombination