title: 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.
authors.affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Q-M
authors.initials: QM
authors.lastname: Wang
authors.affiliation: CBS Fungal Biodiversity Center (CBS-KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
authors.forename: M
authors.initials: M
authors.lastname: Groenewald
authors.affiliation: Japan Collection of Microorganisms, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan.
authors.forename: M
authors.initials: M
authors.lastname: Takashima
authors.affiliation: CBS Fungal Biodiversity Center (CBS-KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
authors.forename: B
authors.initials: B
authors.lastname: Theelen
authors.affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: P-J
authors.initials: PJ
authors.lastname: Han
authors.affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: X-Z
authors.initials: XZ
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CBS Fungal Biodiversity Center (CBS-KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China.
authors.forename: T
authors.initials: T
authors.lastname: Boekhout
authors.affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CBS Fungal Biodiversity Center (CBS-KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
authors.forename: F-Y
authors.initials: FY
authors.lastname: Bai
keywords: Basidiomycota; Fungi; Multigene phylogeny; Pucciniomycotina; Yeasts