title: Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages.
abstract: BACKGROUND
  Pseudogymnoascus spp. is a wide group of fungi lineages in the family Pseudorotiaceae including an aggressive pathogen of bats P. destructans. Although several lineages of P. spp. were shown to produce ascospores in culture, the vast majority of P. spp. demonstrates no evidence of sexual reproduction. P. spp. can tolerate a wide range of different temperatures and salinities and can survive even in permafrost layer. Adaptability of P. spp. to different environments is accompanied by extremely variable morphology and physiology.
  
  
  RESULTS
  We sequenced genotypes of 14 strains of P. spp., 5 of which were extracted from permafrost, 1 from a cryopeg, a layer of unfrozen ground in permafrost, and 8 from temperate surface environments. All sequenced genotypes are haploid. Nucleotide diversity among these genomes is very high, with a typical evolutionary distance at synonymous sites dS ≈ 0.5, suggesting that the last common ancestor of these strains lived >50 Mya. The strains extracted from permafrost do not form a separate clade. Instead, each permafrost strain has close relatives from temperate environments. We observed a strictly clonal population structure with no conflicting topologies for ~99% of genome sequences. However, there is a number of short (~100-10,000 nt) genomic segments with the total length of 67.6 Kb which possess phylogenetic patterns strikingly different from the rest of the genome. The most remarkable case is a MAT-locus, which has 2 distinct alleles interspersed along the whole-genome phylogenetic tree.
  
  
  CONCLUSIONS
  Predominantly clonal structure of genome sequences is consistent with the observations that sexual reproduction is rare in P. spp. Small number of regions with noncanonical phylogenies seem to arise due to some recombination events between derived lineages of P. spp., with MAT-locus being transferred on multiple occasions. All sequenced strains have heterothallic configuration of MAT-locus.
authors.affiliation: Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. leushkin@gmail.com.|Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127994, Russia. leushkin@gmail.com.
authors.forename: Evgeny V
authors.initials: EV
authors.lastname: Leushkin
authors.affiliation: Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. maria.log@gmail.com.|Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127994, Russia. maria.log@gmail.com.|A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia. maria.log@gmail.com.
authors.forename: Maria D
authors.initials: MD
authors.lastname: Logacheva
authors.affiliation: Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. alekseypenin@gmail.com.|Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127994, Russia. alekseypenin@gmail.com.|Department of Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. alekseypenin@gmail.com.
authors.forename: Aleksey A
authors.initials: AA
authors.lastname: Penin
authors.affiliation: Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. rsutormin@gmail.com.|Lawrence Berkeley National Laboratory, Berkeley, 94710, CA, USA. rsutormin@gmail.com.
authors.forename: Roman A
authors.initials: RA
authors.lastname: Sutormin
authors.affiliation: Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. jalgard@gmail.com.|Department of Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. jalgard@gmail.com.
authors.forename: Evgeny S
authors.initials: ES
authors.lastname: Gerasimov
authors.affiliation: G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, 142290, Russia. gak@dol.ru.
authors.forename: Galina A
authors.initials: GA
authors.lastname: Kochkina
authors.affiliation: G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, 142290, Russia. nei@dol.ru.
authors.forename: Natalia E
authors.initials: NE
authors.lastname: Ivanushkina
authors.affiliation: G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, 142290, Russia. ovvasilenko@gmail.com.
authors.forename: Oleg V
authors.initials: OV
authors.lastname: Vasilenko
authors.affiliation: Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. kondrash@umich.edu.|Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA. kondrash@umich.edu.
authors.forename: Alexey S
authors.initials: AS
authors.lastname: Kondrashov
authors.affiliation: G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, 142290, Russia. smovkm@gmail.com.
authors.forename: Svetlana M
authors.initials: SM
authors.lastname: Ozerskaya
mesh_terms: D001203:Ascomycota / Q000145:classification / Q000235:genetics / Q000502:physiology*; D060965:Clonal Evolution; D019143:Evolution, Molecular; D016681:Genome, Fungal; D010802:Phylogeny; D012100:Reproduction, Asexual; D017422:Sequence Analysis, DNA; D013045:Species Specificity