Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages

BMC Genomics

Svetlana M Ozerskaya²  Alexey S Kondrashov⁵  Oleg V Vasilenko²  Natalia E Ivanushkina²  Galina A Kochkina²  Evgeny S Gerasimov⁶  Roman A Sutormin³  Aleksey A Penin⁶  Maria D Logacheva⁴  Evgeny V Leushkin¹ 

[1] Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow 127994, Russia;G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino 142290, Russia;Lawrence Berkeley National Laboratory, Berkeley 94710, CA, USA;A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia;Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor 48109, MI, USA;Department of Biology, Lomonosov Moscow State University, Moscow 119992, Russia

关键词: MAT-locus;    Recombination;    Clonality;    Asexual fungus;   

Others  :  1203907
DOI  :  10.1186/s12864-015-1570-9

 received in 2014-12-16, accepted in 2015-04-23,  发布年份 2015

【 摘 要 】

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 >50Mya. 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.

【 授权许可】

   
2015 Leushkin et al.; licensee BioMed Central.

【 图 表 】

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