title: Occurrence and characteristics of group 1 introns found at three different positions within the 28S ribosomal RNA gene of the dematiaceous Phialophora verrucosa: phylogenetic and secondary structural implications.
abstract: BACKGROUND
  Group 1 introns (ribozymes) are among the most ancient and have the broadest phylogenetic distribution among the known self-splicing ribozymes. Fungi are known to be rich in rDNA group 1 introns. In the present study, five sequences of the 28S ribosomal RNA gene (rDNA) regions of pathogenic dematiaceous Phialophora verrucosa were analyzed using PCR by site-specific primers and were found to have three insertions, termed intron-F, G and H, at three positions of the gene. We investigated the distribution of group 1 introns in this fungus by surveying 34 strains of P. verrucosa and seven strains of Phialophora americana as the allied species.
  
  
  RESULTS
  Intron-F's (inserted at L798 position) were found in 88% of P. verrucosa strains, while intron-G's (inserted at L1921) at 12% and intron-H's (inserted at L2563) at 18%. There was some correlation between intron distribution and geographic location. In addition, we confirmed that the three kinds of introns are group 1 introns from results of BLAST search, alignment analysis and Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR). Prediction of secondary structures and phylogenetic analysis of intron sequences identified introns-F and G as belonging to subgroup IC1. In addition, intron-H was identified as IE.
  
  
  CONCLUSIONS
  The three intron insertions and their insertion position in the 28S rDNA allowed the characterization of the clinical and environmental isolates of P. verrucosa and P. americana into five genotypes. All subgroups of introns-F and G and intron-H were characterized and observed for the first time in both species.
authors.affiliation: Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan. kayokotakizawa@office.chiba-u.jp
authors.forename: Kayoko
authors.initials: K
authors.lastname: Takizawa
authors.forename: Toko
authors.initials: T
authors.lastname: Hashizume
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Kamei
mesh_terms: D017931:DNA Primers / Q000235:genetics; D004783:Environmental Microbiology; D005838:Genotype; D006801:Humans; D007438:Introns; D008969:Molecular Sequence Data; D016533:Mycological Typing Techniques; D009181:Mycoses / Q000382:microbiology; D009690:Nucleic Acid Conformation; D010676:Phialophora / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D012339:RNA, Ribosomal, 28S / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
chemical_list: D017931:DNA Primers; D012339:RNA, Ribosomal, 28S