title: Selection of Orthologous Genes for Construction of a Highly Resolved Phylogenetic Tree and Clarification of the Phylogeny of Trichosporonales Species.
abstract: The order Trichosporonales (Tremellomycotina, Basidiomycota) includes various species that have clinical, agricultural and biotechnological value. Thus, understanding why and how evolutionary diversification occurred within this order is extremely important. This study clarified the phylogenetic relationships among Tricosporonales species. To select genes suitable for phylogenetic analysis, we determined the draft genomes of 17 Trichosporonales species and extracted 30 protein-coding DNA sequences (CDSs) from genomic data. The CDS regions of Trichosporon asahii and T. faecale were identified by referring to mRNA sequence data since the intron positions of the respective genes differed from those of Cryptococcus neoformans (outgroup) and are not conserved within this order. A multiple alignment of the respective gene was first constructed using the CDSs of T. asahii, T. faecale and C. neoformans, and those of other species were added and aligned based on codons. The phylogenetic trees were constructed based on each gene and a concatenated alignment. Resolution of the maximum-likelihood trees estimated from the concatenated dataset based on both nucleotide (72,531) and amino acid (24,173) sequences were greater than in previous reports. In addition, we found that several genes, such as phosphatidylinositol 3-kinase TOR1 and glutamate synthase (NADH), had good resolution in this group (even when used alone). Our study proposes a set of genes suitable for constructing a phylogenetic tree with high resolution to examine evolutionary diversification in Trichosporonales. These can also be used for epidemiological and biogeographical studies, and may also serve as the basis for a comprehensive reclassification of pleomorphic fungi.
authors.affiliation: Japan Collection of Microorganisms, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki, 305-0074, Japan.
authors.forename: Masako
authors.initials: M
authors.lastname: Takashima
authors.affiliation: Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Suehiro-cho, Tsurumiku, Yokohama, Kanagawa, 230-0045, Japan.
authors.forename: Ri-ichiroh
authors.initials: R
authors.lastname: Manabe
authors.affiliation: Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Yayoi, Bunkyoku, Tokyo, 113-0032, Japan.
authors.forename: Wataru
authors.initials: W
authors.lastname: Iwasaki
authors.affiliation: Planning, in silico biology, inc., SOHO Station 706, 24-8 Yamashita-cho, Naka-ku, Yokohama, Kanagawa, 231-0023 Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Ohyama
authors.affiliation: Japan Collection of Microorganisms, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki, 305-0074, Japan.
authors.forename: Moriya
authors.initials: M
authors.lastname: Ohkuma
authors.affiliation: Department of Microbiology, Meiji Pharmaceutical University, Kiyose, Tokyo, 204-8588, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Sugita
mesh_terms: D000595:Amino Acid Sequence; D001487:Basidiomycota / Q000737:chemistry / Q000235:genetics*; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics*; D005800:Genes, Fungal; D008969:Molecular Sequence Data; D010802:Phylogeny
chemical_list: D005656:Fungal Proteins