A phylogenetic analysis of three group I introns found in the nuclear small subunit ribosomal RNA gene of the ballistoconidiogenous anamorphic yeast-like fungus Tilletiopsis flava

Severe pneumonia with a massive pleural effusion in a child caused by Tilletiopsis minor: the first case from Saudi Arabia

Tilletiopsis minor, a blastoconidia-forming yeast, was isolated from a 4-year-old boy suffering from severe pneumonia. Chest x-rays revealed the progression of widespread and multiple nodular lesions, nonsymmetrical interstitial and airspace infiltrates, and consolidations. Creamy yellow, irregular, wrinkled yeast-like organisms were isolated from the pleural fluid specimens when cultured on Sabouraud dextrose agar for 5 days and incubated at 30°C. Microscopically, the organisms showed broad, irregular filaments with blastoconidia but no budding cells. Manual bench tests and automated phenotypic analyses failed to recognize the organism. This unique and rare organism (AB7-11; DSM 29469) was identified using the sequence analysis of the internal transcribed spacer region of the nuclear ribosomal DNA. It showed a precise alignment with the type strains of T minor. Subsequent to this diagnosis, and the earlier nonre.sponse to vancomycin and meropenem, the patient was put on liposomal amphotericin. However, the condition continued to deteriorate, and then, intravenous voriconazole was added to control the infection. Finally, the patient's condition improved, and he was discharged in good condition after 1 month of stay in the hospital.

A group I intron-like sequence in the nuclear small ribosomal subunit gene of the ophiostomatoid fungus Gondwanamyces proteae

During a phylogenetic study of ophiostomatoid fungi, a group I intron-like sequence was noted in the SSU rDNA gene of Gondwanamyces proteae. Secondary structure and sequence characteristics assigned the intron to the I E class. We then examined 27 related Group I-like sequences deposited in GenBank, and as a result 15 additional and previously uncategorized I E rDNA introns were identified. This study, with other recent publications, suggests that the I E class might represent a major family of group I introns that are located within the nuclear SSU and, to some extent LSU, genes in fungi.

Nucleotide structure of the Scytalidium hyalinum and Scytalidium dimidiatum 18S subunit ribosomal RNA gene: evidence for the insertion of a group IE intron in the rDNA gene of S. dimidiatum

The molds Scytalidium dimidiatum (Nattrassia mangiferae synanamorph) and Scytalidium hyalinum are responsible for dermatomycosis in humans. We sequenced their 18S subunit ribosomal RNA gene to identify these species with molecular biology-based methods. The coding sequences differed by a single polymorphism (A in S. dimidiatum, G in S. hyalinum). Moreover, we found an insert at position 1199 in the 18S rRNA gene sequence of S. dimidiatum. Its potential secondary structure was characteristic of a group IE intron. Bioinformatic and phylogenic group IE intron analyses generated four main homogeneous clusters. The S. dimidiatum intron is original and not related with other known IE group introns.

A structural and phylogenetic analysis of the group IC1 introns in the order Bangiales (Rhodophyta)

Our previous study of the North American biogeography of Bangia revealed the presence of two introns inserted at positions 516 and 1506 in the nuclear-encoded SSU rRNA gene. We subsequently sequenced nuclear SSU rRNA in additional representatives of this genus and the sister genus Porphyra in order to examine the distribution, phylogeny, and structural characteristics of these group I introns. The lengths of these introns varied considerably, ranging from 467 to 997 nt for intron 516 and from 509 to 1,082 nt for intron 1506. The larger introns contained large insertions in the P2 domain of intron 516 and the P1 domain of intron 1506 that correspond to open reading frames (ORFs) with His-Cys box homing endonuclease motifs. These ORFs were found on the complementary strand of the 1506 intron in Porphyra fucicola and P. umbilicalis (HG), unlike the 516 intron in P. abbottae, P. kanakaensis, P. tenera (SK), Bangia fuscopurpurea (Helgoland), and B. fuscopurpurea (MA). Frameshifts were noted in the ORFs of the 516 introns in P. kanakaensis and B. fuscopurpurea (HL), and all ORFs terminated prematurely relative to the amino acid sequence for the homing endonuclease I-Ppo I. This raises the possibility that these sequences are pseudogenes. Phylogenies generated using sequences of both introns and the 18S rRNA gene were congruent, which indicated long-term immobility and vertical inheritance of the introns followed by subsequent loss in more derived lineages. The introns within the florideophyte species Hildenbrandia rubra (position 1506) were included to determine relationships with those in the Bangiales. The two sequences of intron 1506 analyzed in Hildenbrandia were positioned on a well-supported branch associated with members of the Bangiales, indicating possible common ancestry. Structural analysis of the intron sequences revealed a signature structural feature in the P5b domain of intron 516 that is unique to all Bangialean introns in this position and not seen in intron 1506 or other group IC1 introns.

Sequence insertions and ITS data provide congruent information on Roccella canariensis and R. tuberculata (Arthoniales, Euascomycetes) phylogeny

Four Roccella species, R. canariensis, R. fimbriata, R. montagnei, and R. tuberculata, were found to possess sequence insertions in up to four locations in the first half of the SSU rDNA. Insertions from one of these positions have been classified as group I introns, while the others may represent degenerative forms of group I introns or messenger RNA introns. Two of the insertion-containing taxa, R. canariensis and R. tuberculata, differ only in their dispersal strategy: R. canariensis is sexual, producing only fruiting bodies and R. tuberculata is sterile, producing only vegetative propagules, i.e., soredia. Because insertions occurred in specimens of both taxa, they were used to examine the phylogenetic relationships between and within the two species. The sequence insertions from each of the four positions were aligned and cladistically analyzed separately. Internal transcribed spacers (ITS) were additionally sequenced to study the phylogeny of all R. canariensis and R. tuberculata specimens. Three other Roccella species (R. babingtonii, R. fimbriata, and R. montagnei) and Dirina catalinariae were used as outgroups in this parsimony analysis. Sequence insertions were found to be potentially useful in phylogenetic studies, although due to the sequence dissimilarity, homology relations were difficult to establish above the species level and in some cases even within the species. The phylogenies obtained from the insertion matrices were totally consistent with the ITS data and the insertions were concluded to have been inherited. When the insertion and ITS data were combined for total evidence, R. canariensis and R. tuberculata did not form distinct lineages in the phylogenetic tree, but appeared mixed in well-supported groups containing both sorediate and fertile specimens.