scholarly journals Internal Transcribed Spacer Regions of rRNA Genes of Pneumocystis carinii from Monkeys

2001 ◽  
Vol 8 (3) ◽  
pp. 503-508 ◽  
Author(s):  
John Y. C. Hsueh ◽  
Rudolf P. Bohm ◽  
Peter J. Didier ◽  
Xing Tang ◽  
Mark E. Lasbury ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Pneumocystis Carinii ◽  
Distinct Species ◽  
Its2 Sequence ◽  
Rrna Genes ◽  
Its2 Region ◽  
Rrna Gene ◽  
5.8S Rrna Gene ◽  
Sequence Variations ◽  
5.8S Rrna

ABSTRACT Analysis of sequence variations among isolates ofPneumocystis carinii f. sp. macacae from 14 Indian rhesus monkeys (Macaca mulatta) at the internal transcribed spacer (ITS) regions of the nuclear rRNA gene was undertaken. Like those from P. carinii f. sp.hominis, the ITS sequences from various P. carinii f. sp. macacae isolates were not identical. Two major types of sequences were found. One type of sequence was shared by 13 isolates. These 13 sequences were homologous but not identical. Variations were found at 13 of the 180 positions in the ITS1 region and 28 of the 221 positions in the ITS2 region. These sequence variations were not random but exhibited definite patterns when the sequences were aligned. According to this sequence variation, ITS1 sequences were classified into three types and ITS2 sequences were classified into five types. The remaining specimen had ITS1 and ITS2 sequences substantially different from the others. Although some specimens had the same ITS1 or ITS2 sequence, all 14 samples exhibited a unique whole ITS sequence (ITS1 plus ITS2). The 5.8S rRNA gene sequences were also analyzed, and only two types of sequences that differ by only one base were found. Unlike P. carinii f. sp. hominis infections in humans, none of the monkey lung specimens examined in this study were found to be infected by more than one type of P. carinii f. sp. macacae. These results offer insights into the genetic differences between P. carinii organisms which infect distinct species.

scholarly journals Combined Molecular and Biochemical Approach Identifies Aspergillus japonicus and Aspergillus aculeatus as Two Species

2001 ◽  
Vol 67 (2) ◽  
pp. 521-527 ◽  
Author(s):  
Lucie Pařenicová ◽  
Pernille Skouboe ◽  
Jens Frisvad ◽  
Robert A. Samson ◽  
Lone Rossen ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Aspergillus Aculeatus ◽  
Aspergillus Japonicus ◽  
5.8S Rrna Gene ◽  
Black Aspergilli ◽  
5.8S Rrna ◽  
Metabolite Profiles

ABSTRACT We examined nine Aspergillus japonicus isolates and 10Aspergillus aculeatus isolates by using molecular and biochemical markers, including DNA sequences of the ITS1-5.8S rRNA gene-ITS2 region, restriction fragment length polymorphisms (RFLP), and secondary-metabolite profiles. The DNA sequence of the internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene could not be used to distinguish between A. japonicus and A. aculeatus but did show that these two taxa are more closely related to each other than to other species of black aspergilli.Aspergillus niger pyruvate kinase (pkiA) and pectin lyase A (pelA) and Agaricus bisporus 28S rRNA genes, which were used as probes in the RFLP analysis, revealed clear polymorphism between these two taxa. The A. niger pkiA and pelA probes placed six strains in anA. japonicus group and 12 isolates in an A. aculeatus group, which exhibited intraspecific variation when they were probed with the pelA gene. The secondary-metabolite profiles supported division of the isolates into the two species and differed from those of other black aspergilli. The strains classified as A. japonicus produced indole alkaloids and a polar metabolite, while the A. aculeatusisolates produced neoxaline, okaramins, paraherquamidelike compounds, and secalonic acid. A. aculeatus CBS 114.80 showed specific RFLP patterns for all loci examined. The secondary-metabolite profile of strain CBS 114.80 also differed from those of A. japonicus and A. aculeatus. Therefore, this strain probably represents a third taxon. This study provides unambiguous criteria for establishing the taxonomic positions of isolates of black aspergilli, which are important in relation to industrial use and legal protection of these organisms.

Sequence analysis of the ribosomal DNA internal transcribed spacer region in some scallop species (Mollusca: Bivalvia: Pectinidae)

Genome ◽  
2003 ◽  
Vol 46 (4) ◽  
pp. 595-604 ◽  
Author(s):  
Ana Insua ◽  
María J López-Piñón ◽  
Ruth Freire ◽  
Josefina Méndez
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Internal Transcribed Spacers ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Region ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
Aequipecten Opercularis

The internal transcribed spacer (ITS) region of the ribosomal DNA from the European scallops Aequipecten opercularis, Mimachlamys varia, Hinnites distortus, and Pecten maximus was PCR amplified and sequenced. For each species, three or five clones were examined. The size ranged between 636 and 713 bp (ITS1, 209–276 bp; 5.8S rRNA gene, 157 bp; ITS2, 270–294 bp) and GC content ranged between 47 and 50% (ITS1, 43–49%; 5.8S rRNA gene, 56–57%; ITS2, 44–49%). Variation within repeats was minimal; only clones from M. varia and P. maximus displayed a few variable sites in ITS2. Among scallops, including Chlamys farreri whose ITS sequence appears in databases, significant variation was observed in both ITS1 and ITS2. Phylogenetic analysis using ITS1, ITS2, or both spacer sequences always yielded trees with similar topology. Aequipecten opercularis and P. maximus grouped in one clade and the other three scallops (C. farreri, M. varia, and H. distortus) in another, where M. varia and H. distortus are the more closely related species. These results provide new insights into the evolutionary relationships of scallop species and corroborate the close evolutionary relationship between the tribes Aequipectinini and Pectinini previously deduced from 18S rDNA sequences.Key words: scallops, Pectinidae, ribosomal DNA, internal transcribed spacers, phylogeny.

Comparative sequence analysis of 5·8S rRNA genes and internal transcribed spacer (ITS) regions of trichomonadid protozoa

Parasitology ◽  
1997 ◽  
Vol 115 (2) ◽  
pp. 111-119 ◽  
Author(s):  
R. S. J. FELLEISEN
Keyword(s):  
Sequence Analysis ◽  
Internal Transcribed Spacer ◽  
Trichomonas Vaginalis ◽  
Comparative Sequence Analysis ◽  
Rrna Genes ◽  
Its2 Region ◽  
Rrna Gene ◽  
Molecular Biological Analysis ◽  
Future Revision ◽  
High Degree

The taxonomic situation in the genus Tritrichomonas is the subject of controversial discussion: potentially T. foetus and T. suis, the tritrichomonads from cattle and swine, respectively, could belong to the same species. In order to shed some light on this question, a molecular biological analysis was performed. The 5·8S rRNA gene and the flanking internal transcribed spacer regions (ITS1 and ITS2) of 12 different isolates of 3 Tritrichomonas species T. foetus, T. suis and T. mobilensis were enzymatically amplified by PCR and subcloned. Also, the corresponding regions of the trichomonads Trichomonas vaginalis, T. tenax, T. gallinae and Pentatrichomonas hominis were included in this study. Sequence analysis of cloned fragments was used to compare the parasite isolates. The genus Tritrichomonas exhibited an extremely high degree of homogeneity. All T. foetus and T. suis isolates had identical sequences, and only 1 substitution was found in the ITS2 region of T. mobilensis. In contrast, the genus Trichomonas shared more diversity. The results obtained in this study support a possible future revision of the taxonomic classification of tritrichomonads.

scholarly journals Genotyping ofPneumocystis jiroveciiby Use of a New Simplified Nomenclature System Based on the Internal Transcribed Spacer Regions and 5.8S rRNA Gene of the rRNA Operon

2019 ◽  
Vol 57 (6) ◽  
Author(s):  
Ting Xue ◽  
Zhuang Ma ◽  
Fan Liu ◽  
Wei-Qin Du ◽  
Li He ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Rrna Operon ◽  
Rrna Gene ◽  
Length Variation ◽  
Nomenclature System ◽  
Content Type ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
Its1 And Its2 ◽  
New System

ABSTRACTGenotyping based on internal transcribed spacer 1 (ITS1) and ITS2 of the rRNA operon has played an important role in understanding the transmission and epidemiology ofPneumocystis jirovecii, one of the major opportunistic pathogens in individuals with AIDS and other immunocompromised individuals. The widespread use of this typing system has resulted in several problems, including inconsistent genotype nomenclatures, difficult data transferability, and complicated interpretation of the length variation in multiple homopolymeric tracts. The aim of this study was to establish a new, simplified genotype nomenclature system forP. jiroveciibased on the ITS1 and ITS2 sequences. We first analyzed the complete ITS1, 5.8S rRNA gene, and ITS2 sequences (termed ITS1-5.8S-ITS2) in 27 recentP. jiroveciiisolates from China and identified 18 unique genotypes. Subsequently, we performed a comprehensive classification of more than 400 ITS1- and ITS2-related sequences from GenBank and an in-depth evaluation of the length variation of multiple homopolymeric tracts within ITS1-5.8S-ITS2. Integration of the results from these analyses led to a new, simplified genotype nomenclature system including 62 unique ITS1-5.8S-ITS2 genotypes, simply designated types 1 through 62. This new system offers several advantages over traditional ITS1- and ITS2-based typing systems, including a simpler analysis and interpretation process, a higher discriminative power, and no limitation in assigning potential new genotypes. This new system is expected to facilitate the standardization ofP. jiroveciigenotyping and easy data exchanges across different laboratories.

scholarly journals Comparison of the 5.8S rRNA Gene and Internal Transcribed Spacer Regions of Trichomonadid Protozoa Recovered from the Bovine Preputial Cavity

2003 ◽  
Vol 15 (1) ◽  
pp. 14-20 ◽  
Author(s):  
R. L. Walker ◽  
D. C. Hayes ◽  
S. J. Sawyer ◽  
R. W. Nordhausen ◽  
K. A. Van Hoosear ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Internal Transcribed Spacer ◽  
Rrna Gene ◽  
Tritrichomonas Foetus ◽  
Similarity Matrix ◽  
Multiple Sequence ◽  
Internal Transcribed Spacer Regions ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
High Degree

Sequence analysis of the 5.8S rRNA gene and the internal transcribed spacer regions (ITSRs) was used to compare trichomonadid protozoa ( n = 39) of varying morphologies isolated from the bovine preputial cavity. A multiple sequence alignment was performed with bovine isolate sequences and other trichomonadid protozoa sequences available in GenBank. As a group, Tritrichomonas foetus isolates ( n = 7) had nearly complete homology. A similarity matrix showed low homology between the T. foetus isolates and other trichomonads recovered from cattle (<70%). Two clusters of trichomonads other than T. foetus were identified. Eighteen isolates comprised 1 group. These isolates shared >99% homology among themselves and with Pen-tatrichomonas hominis. The other non– T. foetus cluster ( n = 14) did not exhibit a high degree of homology (<87%) with other bovine isolates or any of the trichomonad sequences available in GenBank. The sequence homology among isolates in that cluster was >99%, except for 1 isolate that varied from the others in both ITSRs (∼2% dissimilarity). Sequence analysis of the 5.8S rRNA gene and ITSRs was useful for comparing trichomonadid protozoa isolated from the bovine preputial cavity and demonstrated that 2 distinct types of trichomonads constituted the non– T. foetus isolates recovered from the bovine preputial cavity.

scholarly journals Study of Spanish Grape Mycobiota and Ochratoxin A Production by Isolates of Aspergillus tubingensis and Other Members of Aspergillus Section Nigri

2005 ◽  
Vol 71 (8) ◽  
pp. 4696-4702 ◽  
Author(s):  
Angel Medina ◽  
Rufino Mateo ◽  
Laura López-Ocaña ◽  
Francisco Manuel Valle-Algarra ◽  
Misericordia Jiménez
Keyword(s):  
Liquid Chromatography ◽  
Ochratoxin A ◽  
Pcr Amplification ◽  
Rrna Genes ◽  
Its2 Region ◽  
Rrna Gene ◽  
Aspergillus Tubingensis ◽  
Isolation Frequency ◽  
5.8S Rrna ◽  
Grape Varieties

ABSTRACT The native mycobiota of five grape varieties grown in Spain has been studied. Four (Bobal, Tempranillo, Garnacha, and Monastrell) were red varieties and one (Moscatel) was white. The main fungal genera isolated were Alternaria, Cladosporium, and Aspergillus. The isolation frequency of Aspergillus spp. section Nigri in contaminated samples was 82%. Ochratoxin A (OTA) production was assessed using yeast extract-sucrose broth supplemented with 5% bee pollen. Cultures of 205 isolates from this section showed that 74.2% of Aspergillus carbonarius and 14.3% of Aspergillus tubingensis isolates produced OTA at levels ranging from 1.2 to 3,530 ng/ml and from 46.4 to 111.5 ng/ml, respectively. No Aspergillus niger isolate had the ability to produce this toxin under the conditions assayed. Identification of the A. niger aggregate isolates was based on PCR amplification of 5.8S rRNA genes and its two intergenic spacers, internal transcribed spacer 1 (ITS1) and ITS2, followed by digestion with restriction endonuclease RsaI of the PCR products. The restriction patterns were compared with those from strains of A. niger CECT 2807 and A. tubingensis CECT 20393, held at the Spanish Collection of Type Cultures. DNA sequencing of the ITS1-5.8S rRNA gene-ITS2 region of the OTA-producing isolates of A. tubingensis matched 99 to 100% with the nucleotide sequence of strain A. tubingensis CBS 643.92. OTA determination was accomplished by liquid chromatography with fluorescence detection. OTA confirmation was carried out by liquid chromatography coupled to ion trap mass spectrometry. The results showed that there are significant differences with regard to the isolation frequency of ochratoxinogenic fungi in the different grape varieties. These differences were uncorrelated to berry color. The ability of A. tubingensis to produce OTA and the influence of grape variety on the occurrence of OTA-producing fungi in grapes are described in this report for the first time.

scholarly journals The ITS1-5.8S rRNA gene -ITS2 sequence variability during the divergence of sweet-grass species (gen us Glyceria R. Br.)

2011 ◽  
Vol 9 (4) ◽  
pp. 63-69
Author(s):  
Alexander V Rodionov ◽  
Armen R Kotsinyan ◽  
Alexander A Gnutikov ◽  
Marina A Dobroradova ◽  
Eduard M Machs
Keyword(s):  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Its2 Sequence ◽  
Grass Species ◽  
Rrna Gene ◽  
Sequence Variability ◽  
5.8S Rdna ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
Haplotype A

Comparative analysis of the sequence ITS1-5.8S rRNA gene-ITS2 of the nuclear genome of 13 species of genus Glyceria, 4 species of Melica and a species of monotypic genus Pleuropogon showed that the species of the genus Glyceria have 3 haplotypes: 1) Haplotype A was found only in species of the subgenus Glyceria section Glyceria (G. septentrionalis, G. fluitans, G. declinata, G. occidentalis, G. notata, G. borealis, G. leptostachya) and in Pleuropogon sabinii; 2) Haplotype C is characteristic of the subgenus Hydropoa, section Hydropoa (G. grandis, G. х amurensis, G. triflora, G. maxima) and sect. Lithuanicae (G. leptolepis); 3) Haplotype B is found in the species of the subgenus Hydropoa sections Striatae (G. elata, G. striata, G. neogaea, G. canadensis), Scolochloiformes (G. alnasteretum, G. spiculosa) and G. lithuanica of sect. Lithuanicae. Species carring haplotype B are located at the base of the phylogenetic tree of the genus Glyceria and/or clustered with low bootstrap indices. On the phylogenetic trees inferred by the analysis of the sequences ITS and 5.8S rDNA both sect. Glyceria and sect. Hydropoa represented two sister monophyly branches. The species Pleuropogon sabinii belong to the branch of subgenus Glyceria as a sister monotypic branch to the branch of the sect. Glyceria.

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