Phylogeny of tremellomycetous yeasts and related dimorphic and filamentous basidiomycetes reconstructed from multiple gene sequence analyses

• Published in: Studies in mycology Vol. 81; no. 1; pp. 1 - 26
• Main Authors: Liu, X.-Z., Wang, Q.-M., Theelen, B., Groenewald, M., Bai, F.-Y., Boekhout, T.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.06.2015; Westerdijk Fungal Biodiversity Institute; Centraalbureau voor Schimmelcultures; CBS Fungal Biodiversity Centre
• Subjects: algorithms; anamorphs; Basidiomycota; Bayesian theory; chemotaxonomy; Cystofilobasidiales; cytochrome b; data collection; DNA-directed RNA polymerase; Filobasidiales; Fungi; genes; Identification and classification; internal transcribed spacers; mitochondria; monophyly; Multigene Phylogeny; polyphyly; ribosomal DNA; ribosomal RNA; sequence analysis; teleomorphs; transcription (genetics); translation (genetics); Tremellales; Tremellomycetes; Yeast fungi; Yeasts; Fungi; Yeasts; Tremellomycetes; Multigene phylogeny; Basidiomycota
• ISSN: 0166-0616; 1872-9797
• DOI: 10.1016/j.simyco.2015.08.001

The Tremellomycetes (Basidiomycota) contains a large number of unicellular and dimorphic fungi with stable free-living unicellular states in their life cycles. These fungi have been conventionally classified as basidiomycetous yeasts based on physiological and biochemical characteristics. Many currently recognised genera of these yeasts are mainly defined based on phenotypical characters and are highly polyphyletic. Here we reconstructed the phylogeny of the majority of described anamorphic and teleomorphic tremellomycetous yeasts using Bayesian inference, maximum likelihood, and neighbour-joining analyses based on the sequences of seven genes, including three rRNA genes, namely the small subunit of the ribosomal DNA (rDNA), D1/D2 domains of the large subunit rDNA, and the internal transcribed spacer regions (ITS 1 and 2) of rDNA including 5.8S rDNA; and four protein-coding genes, namely the two subunits of the RNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial gene cytochrome b (CYTB). With the consideration of morphological, physiological and chemotaxonomic characters and the congruence of phylogenies inferred from analyses using different algorithms based on different data sets consisting of the combined seven genes, the three rRNA genes, and the individual protein-coding genes, five major lineages corresponding to the orders Cystofilobasidiales, Filobasidiales, Holtermanniales, Tremellales, and Trichosporonales were resolved. A total of 45 strongly supported monophyletic clades with multiple species and 23 single species clades were recognised. This phylogenetic framework will be the basis for the proposal of an updated taxonomic system of tremellomycetous yeasts that will be compatible with the current taxonomic system of filamentous basidiomycetes accommodating the ‘one fungus, one name’ principle.