Phylogeny of yeasts and related filamentous fungi within Pucciniomycotina determined from multigene sequence analyses

Abstract

In addition to rusts, the subphylum Pucciniomycotina (Basidiomycota) includes a large number of unicellular or dimorphic fungi which are usually studied as yeasts. Ribosomal DNA sequence analyses have shown that the current taxonomic system of the pucciniomycetous yeasts which is based on phenotypic criteria is not concordant with the molecular phylogeny and many genera are polyphyletic. Here we inferred the molecular phylogeny of 184 pucciniomycetous yeast species and related filamentous fungi using maximum likelihood, maximum parsimony and Bayesian inference analyses based on the sequences of seven genes, including the small subunit ribosomal DNA (rDNA), the large subunit rDNA D1/D2 domains, the internal transcribed spacer regions (ITS 1 and 2) of rDNA including the 5.8S rDNA gene; the nuclear protein-coding genes of the two subunits of DNA polymerase II (RPB1 and RPB2) and the translation elongation factor 1-α (TEF1); and the mitochondrial gene cytochrome b (CYTB). A total of 33 monophyletic clades and 18 single species lineages were recognised among the pucciniomycetous yeasts employed, which belonged to four major lineages corresponding to Agaricostilbomycetes, Cystobasidiomycetes, Microbotryomycetes and Mixiomycetes. These lineages remained independent from the classes Atractiellomycetes, Classiculomycetes, Pucciniomycetes and Tritirachiomycetes formed by filamentous taxa in Pucciniomycotina. An updated taxonomic system of pucciniomycetous yeasts implementing the ‘One fungus = One name’ principle will be proposed based on the phylogenetic framework presented here.

DNA barcoding analysis of more than 9 000 yeast isolates contributes to quantitative thresholds for yeast species and genera delimitation

“…Recent studies (Liu et al., 2015, Wang et al., 2015a, Wang et al., 2015b, Wang et al., 2015c) have revised the generic taxonomy of basidiomycetous yeasts that until recently was not concordant with the molecular phylogeny particularly as it relates to genus circumscriptions. To evaluate the revision of Basidiomycota and the current classification of yeasts at the genus level, reference sequences of CBS strains (datasets C1 and C2) were clustered to predict taxonomic thresholds that give the best match to the generic taxonomy of yeasts before and after the revision.…”

“…Except for 6 % and 9.5 % of yeast species sharing the same ITS and LSU sequences respectively, the high quality of clustering produced in different datasets shows that current yeast species can be clearly separated using ITS and LSU barcodes. Our analyses also showed that recent studies (Liu et al., 2015, Wang et al., 2015a, Wang et al., 2015b, Wang et al., 2015c) have made a significant improvement to the generic taxonomy of basidiomycetous yeasts. The taxonomic thresholds predicted to distinguish current yeast genera were 96.31 % for ITS and 97.11 % for LSU.…”

“…For the analysis presented in this paper, all the barcodes of yeast strains that were added to the database until June 2015, were included. The species names of the strains were also updated with the new names obtained from recent large-scale reclassifications in Basidiomycota (Liu et al., 2015, Wang et al., 2015a, Wang et al., 2015b, Wang et al., 2015c). …”

Fungal evolution: diversity, taxonomy and phylogeny of the Fungi

“…There are more than 8,400 described species of Pucciniomycotina, classified in 10 classes (Agaricostilbomycetes, Atractiellomycetes, Classiculomycetes, Cryptomycocolacomycetes, Cystobasidiomycetes, Microbotryomycetes, Mixiomycetes, Pucciniomycetes, Spiculogloeomycetes and Tritirachiomycetes), 20 orders and 35 families (Aime et al ., ; Schell, Lee, & Aime, ; Wang et al ., , c ). Some members of the group, particularly in the Pucciniomycetes, have very large genomes (Tavares et al ., ) and several have highly complex life cycles (e.g.…”

Basidiomycota isolated from the Mediterranean Sea – Phylogeny and putative ecological roles

“…Eleven datasets were assembled on the basis of BLASTn results and of recent phylogenetic studies that included allied taxa, as follows: Psathyrellaceae (Nagy et al, 2013;Orstadius et al, 2015), Peniophoraceae (Hallenberg et al, 1996), Ustilaginaceae (Wang et al, 2015a), Sporidiobolaceae (Wang et al, 2015b), Schizophyllaceae (Siqueira et al, 2016), Polyporales (Phleboid clade and Trametes) (Binder et al, 2013;Justo and Hibbett, 2011;Miettinen et al, 2016), Holtermanniales (Liu et al, 2015;Wuczkowski et al, 2011) and Wallemiales (Jancic et al, 2015) (Table 2; Table S1-S9).…”