RRC ID 41114
著者 Takashima M, Manabe R, Iwasaki W, Ohyama A, Ohkuma M, Sugita T.
タイトル Selection of Orthologous Genes for Construction of a Highly Resolved Phylogenetic Tree and Clarification of the Phylogeny of Trichosporonales Species.
ジャーナル PLoS One
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.
巻・号 10(8)
ページ e0131217
公開日 2015-1-1
DOI 10.1371/journal.pone.0131217
PII PONE-D-14-45138
PMID 26241762
PMC PMC4524599
MeSH Amino Acid Sequence Basidiomycota / chemistry Basidiomycota / genetics* Fungal Proteins / chemistry Fungal Proteins / genetics* Genes, Fungal* Molecular Sequence Data Phylogeny*
IF 2.74
引用数 7
WOS 分野 MICROBIOLOGY
リソース情報
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