Taxonomic affiliation was indicated by letters in parentheses; namely, [A], Fungi/Ascomycota; [Ac], Acanthamoebidae; [C], Chlorophyta; [H], Heterolobosea; [M], Mycetozoa and [R], Rhodophyta. Secondary structure modeling The secondary structures are proposed from modeling by Michel et al. [14, 26, 43] and computational
analysis was done using the Mfold web server available at http://mfold.rna.albany.edu/ and GENETYX Ver.9 software, with BMS202 molecular weight manual adjustments. The pairing segments of P1-P10 locations are indicated in Figure 4 and 5. Moreover, the model was manually optimized based on previous studies of group 1 introns [17, 45–47]. Acknowledgements This study was supported in part by the National BioResource Project of the Ministry of Education, Culture, Sports, Science and Technology, Japan. Electronic supplementary material Additional file 1: Schematic representation of the large ribosomal subunit 28S gene. The hatched and dotted selleck compound boxes selleck correspond to the group 1 intron of P. verrucosa inserted
at positions 798, 1921 and 2563 relative to the 23S rDNA of the E. coli J01965 sequence. The numbering in the parentheses is relative to the ITS and 28S rDNA sequence of P. verrucosa. (PDF 31 KB) Additional file 2: Partial alignment of IC1 introns of P. verrucosa and selected introns from the database. Highly conserved sequences of the elements of P, Q, R and S and the pairing segment P3 are also shown. Intron insertion positions relative to E. coli are given after the sample ID or taxon name. * indicates the insertion position relative to the 18S rDNA of the S. cerevisiae sequence. Letters PTK6 in parentheses indicate taxonomic affiliation: [A], Fungi/Ascomycota; [Ac], Acanthamoebidae; [C], Chlorophyta; [H], Heterolobosea; [M], Mycetozoa; [R], Rhodophyta. (PDF 32 KB) Additional file 3: Alignment of intron-F used for the phylogenetic analysis and the modeling of secondary structure. The gaps were marked with dashes. The highly conserved (ribozymatic core) regions of the P, Q, R and S were marked with dotted lines. Boxed nucleotides participate
in the pairing segments of P1-P10 of the secondary structure model. (PDF 36 KB) Additional file 4: Alignment of intron-G used for the phylogenetic analysis and the modeling of secondary structure. The gaps were marked with dashes. The highly conserved (ribozymatic core) regions of the P, Q, R and S were marked with dotted lines. Boxed nucleotides participate in the pairing segments of P1-P10 of the secondary structure model. (PDF 37 KB) References 1. Medlar EM: A new fungus, Phialophora verrucosa , pathogenic for men. Mycologia 1915, 7:200–203.CrossRef 2. Yamagishi Y, Kawasaki K, Ishizaki H: Mitochondrial DNA analysis of Phialophora verrucosa . Mycoses 1997,40(9–10):329–334.PubMedCrossRef 3. Botterel F, Desterke C, Costa C, Bretagne S: Analysis of microsatellite markers of Candida albicans used for rapid typing. J Clin Microbiol 2001,39(11):4076–4081.