A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved ‘natural’ hybrid genomes

Abstract

To construct a backbone tree consisting of basidiomycetous yeasts, draft genome sequences from 25 species of Trichosporonales (Tremellomycetes, Basidiomycota) were generated. In addition to the hybrid genomes of Trichosporon coremiiforme and Trichosporon ovoides that we described previously, we identified an interspecies hybrid genome in Cutaneotrichosporon mucoides (formerly Trichosporon mucoides). This hybrid genome had a gene retention rate of ~55%, and its closest haploid relative was Cutaneotrichosporon dermatis. After constructing the C. mucoides subgenomes, we generated a phylogenetic tree using genome data from the 27 haploid species and the subgenome data from the three hybrid genome species. It was a high-quality tree with 100% bootstrap support for all of the branches. The genome-based tree provided superior resolution compared with previous multi-gene analyses. Although our backbone tree does not include all Trichosporonales genera (e.g. Cryptotrichosporon), it will be valuable for future analyses of genome data. Interest in interspecies hybrid fungal genomes has recently increased because they may provide a basis for new technologies. The three Trichosporonales hybrid genomes described in this study are different from well-characterized hybrid genomes (e.g. those of Saccharomyces pastorianus and Saccharomyces bayanus) because these hybridization events probably occurred in the distant evolutionary past. Hence, they will be useful for studying genome stability following hybridization and speciation events. Copyright © 2017 John Wiley & Sons, Ltd.

Convergent evolution of linked mating-type loci in basidiomycete fungi

“…The genome was assembled into 21 scaffolds with 5089 predicted genes. At 22.63 Mb, the assembly size is similar to that of strain JCM1457 (A2) (22.65 Mb, [50]). A k-mer analysis of the Illumina reads for CBS4282 showed a single peak as expected for a haploid genome (S1 Fig).…”

“…To verify that both MAT alleles, A1 and A2, can be found in different strains within a single species, we analyzed additional Vanrija humicola strains ( Table 2). V. humicola is a member of a phylogenetically early-branching lineage within the Trichosporonales, and the previously sequenced strain (JCM1457) carries the A2 allele (Figs 1 and 2) [50]. Several other strains obtained from culture collections were analyzed by RAPD genotyping, which revealed banding patterns similar to those from the type strain V. humicola JCM1457 (=CBS571, MAT A2) (S1 Fig).…”

“…Since 2015, genome sequences have been published for Trichosporonales species from the genera Apiotrichum, Cutaneotrichosporon, Takashimella, Trichosporon, and Vanrija [45][46][47][48][49][50][51][52] ( Table 1). We analyzed the genomes of 29 isolates that belong to 24 Trichosporonales species for the organization of the MAT loci, and found that all of them contain fused MAT loci, with both mating-type determining genes (STE3 and SXI) located ~55 kb apart from each other.…”

“…Recently, several Trichosporonales were studied with respect to their biotechnological properties, including the oil-accumulating C. oleaginosum, which was first isolated from a dairy plant, and has the ability to metabolize chitin-rich and other nonconventional substrates [41][42][43][44]. The sequenced C. oleaginosum strain is haploid, and similar in genome size and gene content to genomes from the sister order Tremellales, and this was also the case for several other Trichosporonales genomes that have since been sequenced [43,[45][46][47][48][49][50]. Interestingly, C. oleaginosum showed some similarities to C. neoformans in the organization of MAT loci.…”

“…A well-studied case of fused MAT loci is the one of Cryptococcus neoformans, a member of a group of closely related, pathogenic Cryptococcus species [1]. Fusion of the HD and P/R loci most likely occurred in the ancestor of the pathogenic Cryptococci, because other analyzed Tremellales species including the closely related, but non-pathogenic Cryptococcus Since the analysis of the first C. oleaginosum genome, several more Trichosporonales genomes were sequenced, although none were analyzed with respect to their MAT loci [45][46][47][48][49][50][51]. Here, we describe the sequencing of two additional Trichosporonales genomes for C. oleaginosum ATCC20508 and Vanrija humicola CBS4282, and the analysis of MAT loci organization in Trichosporonales genomes from 24 different species.…”