title: Phylogeny of tremellomycetous yeasts and related dimorphic and filamentous basidiomycetes reconstructed from multiple gene sequence analyses.
abstract: 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.
authors.affiliation: State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.
authors.forename: X-Z
authors.initials: XZ
authors.lastname: Liu
authors.affiliation: State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.
authors.forename: Q-M
authors.initials: QM
authors.lastname: Wang
authors.affiliation: CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands.
authors.forename: B
authors.initials: B
authors.lastname: Theelen
authors.affiliation: CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands.
authors.forename: M
authors.initials: M
authors.lastname: Groenewald
authors.affiliation: State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands.
authors.forename: F-Y
authors.initials: FY
authors.lastname: Bai
authors.affiliation: State Key Laboratory for Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; CBS Fungal Biodiversity Centre (CBS-KNAW), Uppsalalaan 8, Utrecht, The Netherlands; Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, PR China.
authors.forename: T
authors.initials: T
authors.lastname: Boekhout
keywords: Basidiomycota; Fungi; Multigene phylogeny; Tremellomycetes; Yeasts