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

BackgroundGroup 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.ResultsIntron-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.ConclusionThe 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.

Multiple Group I Introns in the Small-Subunit rDNA of Botryosphaeria dothidea: Implication for Intraspecific Genetic Diversity

“…A similar phenomenon has been reported in Exophiala dermatitidis and Phialophora verrucosa [6], [7]. In E. dermatitidis , the invasive genotype A and B strains from the natural environment were differentiated by the distribution of ribosomal introns.…”

“…Additionally, a minority of the reported group I introns have open reading frames (ORFs) for encoding homing endonucleases (HEs), which fall into these four families - LAGLIDADG, GIY-YIG, His-Cys box and NHN - based on the conserved motifs [5]. Frequently found in the rDNA region of fungi, these highly variable group I introns have been used increasingly as a molecular genotyping tool to explore the population diversity of this lineage [6], [7].…”

Biodiversity and human-pathogenicity ofPhialophora verrucosaand relatives inChaetothyriales

“…Notes — The strain taken by several authors as representative for the species, CBS 281.35 was derived from a verrucous dermatosis of the legs of a human chromoblastomycosis patient, USA. The isolate was first described as Phialophora verrucosa by Schol-Schwarz (1970) as representative of that species, but later it was redescribed as P. americana by Yamagishi (in Yamagishi et al 1997 ), Untereiner (in Untereiner et al 2008 ) and Takizawa (in Takizawa et al 2011 ). The species was also reported as Capronia semiimmersa from a herbarium specimen by Candousseau & Sulmont (1971) .…”

“…No multi-locus verification is available for the P. verrucosa / P. americana complex ( Untereiner et al 2008 ) . Molecular typing of mitochondrial DNA using restriction fragment length polymorphisms (RFLP) suggested that P. verrucosa comprised three groups, while analyses of group 1 introns in the 28S ribosomal RNA gene divided the species into five genotypes ( Yamagishi et al 1997 , Takizawa et al 2011 ). Given this genetic variation a study of phylogenetic relationships is overdue.…”

Detection of Introns in Eukaryotic Small Subunit Ribosomal RNA Gene Sequences

“…SSU-rRNA gene sequences may contain numerous selfsplicing introns of variable lengths [4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23]. e SSU-rRNA genes can thus be enlarged to up to 3.5 kb.…”