title: Phylogenetic relationship within the Erythrobasidium clade: molecular phylogenies, secondary structure, and intron positions inferred from partial sequences of ribosomal RNA and elongation factor-1alpha genes.
abstract: Phylogenetic relationships within the Erythrobasidium clade as a lineage of the urediniomycetous yeasts were examined using partial regions of 18S rDNA, 5.8S rDNA, 26S rDNA, internal transcribed spacers (ITSs), and elongation factor (EF)-1alpha. Combined data analysis of all segments successfully yielded a reliable phylogeny and confirmed the cohesion of species characterized by Q-10(H2) as a major ubiquinone. Differences in secondary structure predicted for a variable region in 26S rDNA corresponded to major divergences in the phylogenetic tree based on the primary sequence. The common presence of a shortened helix in this region was considered to be evidence of monophyly for species with Q-10(H2), Sakaguchia dacryoides, Rhodotorula lactosa, and Rhodotorula lamellibrachiae, although it was not as strongly supported by the combined data tree. The information on intron positions in the EF-1alpha gene had potential usefulness in the phylogenetic inference between closely related species.
authors.affiliation: Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan. nagahama@jamstec.go.jp
authors.forename: Takahiko
authors.initials: T
authors.lastname: Nagahama
authors.forename: Makiko
authors.initials: M
authors.lastname: Hamamoto
authors.forename: Takashi
authors.initials: T
authors.lastname: Nakase
authors.forename: Shigeru
authors.initials: S
authors.lastname: Shimamura
authors.forename: Koki
authors.initials: K
authors.lastname: Horikoshi
mesh_terms: D001487:Basidiomycota / Q000145:classification* / Q000235:genetics*; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000737:chemistry / Q000235:genetics; D020459:Genes, rRNA; D007438:Introns / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020648:Peptide Elongation Factor 1 / Q000235:genetics*; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D012340:RNA, Ribosomal, 5.8S / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D004271:DNA, Fungal; D004275:DNA, Ribosomal; D021903:DNA, Ribosomal Spacer; D020648:Peptide Elongation Factor 1; D012335:RNA, Ribosomal; D012337:RNA, Ribosomal, 18S; D012340:RNA, Ribosomal, 5.8S; C065096:RNA, ribosomal, 26S