title: Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analyses.
abstract: Yeasts of the artificial genus Candida include plant endophytes, insect symbionts, and opportunistic human pathogens. Phylogenies based on rRNA gene and actin sequences confirmed that the genus is not monophyletic, and the relationships among Candida species and allied teleomorph genera are not clearly resolved. Protein-coding genes have been useful to resolve taxonomic positions among a broad range of fungi. Over 70 taxa of the genus Candida and its allied sexually reproducing genera were therefore selected, and their phylogenetic relationships were investigated using nuclear sequences of the largest subunit and second largest subunit of RNA polymerase II gene, actin, the second subunit of the mitochondrial cytochrome oxidase gene, and D1/D2 LSU rRNA gene. The DNA sequences were analysed by maximum parsimony and Bayesian inference, resulting in the recognition of six major phylogenetic groups (A-F). Group A contains six facultative pathogenic Candida species, which seem to have derived from nonpathogenic species, while Group B contains species of Clavispora, Metschnikowia, and Pichia guilliermondii. Species of Debaryomyces form an independent group C that is related to groups A and B. Pichia fermentans and other environmental species are concentrated in Group D. Group E, containing Pichia anomala, may be a sibling to group F, which is represented by the Saccharomyces species complex.
authors.affiliation: Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Hospital, Westmead Millennium Institute, Westmead, NSW, Australia.
authors.forename: Clement K M
authors.initials: CK
authors.lastname: Tsui
authors.forename: Heide-Marie
authors.initials: HM
authors.lastname: Daniel
authors.forename: Vincent
authors.initials: V
authors.lastname: Robert
authors.forename: Wieland
authors.initials: W
authors.lastname: Meyer
mesh_terms: D000199:Actins / Q000235:genetics; D001203:Ascomycota / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D016000:Cluster Analysis; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D003576:Electron Transport Complex IV / Q000235:genetics; D005656:Fungal Proteins / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012319:RNA Polymerase II / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D000199:Actins; D004271:DNA, Fungal; D004275:DNA, Ribosomal; D021903:DNA, Ribosomal Spacer; D005656:Fungal Proteins; C117108:cytochrome C oxidase subunit II; D003576:Electron Transport Complex IV; D012319:RNA Polymerase II