Nucleotide sequences of the 5.8S rRNA gene and internal transcribed spacer regions in carrot and broad bean ribosomal DNA

1989 ◽  
Vol 29 (4) ◽  
pp. 294-301 ◽  
Author(s):  
Yukihiko Yokota ◽  
Takefumi Kawata ◽  
Yoichi Iida ◽  
Atsushi Kato ◽  
Shigeyuki Tanifuji
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Broad Bean ◽  
Nucleotide Sequences ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Regions ◽  
5.8S Rrna Gene ◽  
5.8S Rrna

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.

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 Identification of Medically RelevantTrichosporon Species Based on Sequences of Internal Transcribed Spacer Regions and Construction of a Database forTrichosporon Identification

1999 ◽  
Vol 37 (6) ◽  
pp. 1985-1993 ◽  
Author(s):  
Takashi Sugita ◽  
Akemi Nishikawa ◽  
Reiko Ikeda ◽  
Takako Shinoda
Keyword(s):  
Sequence Analysis ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Comparative Sequence Analysis ◽  
Nucleotide Sequences ◽  
Its Sequences ◽  
Rrna Gene ◽  
Comparative Sequence ◽  
Internal Transcribed Spacer Regions ◽  
Molecular Phylogenetic

The nucleotide sequences of the internal transcribed spacer (ITS) 1 and 2 regions in the rRNA gene were determined by directly sequencing PCR-amplified fragments for all of the species (17 species and five varieties) in the genus Trichosporon. Comparative sequence analysis suggests that six medically relevant species, T. asahii, T. asteroides, T. cutaneum,T. inkin, T. mucoides, and T. ovoides, can be readily identified by their ITS sequences. In addition, the sequence analysis showed that conspecific strains have fewer than 1% nucleotide differences in the ITS 1 and 2 regions overall. Molecular phylogenetic trees are also presented.

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 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.

Species-specific duplex PCR for the detection of Pratylenchus penetrans

Nematology ◽  
2009 ◽  
Vol 11 (6) ◽  
pp. 847-857 ◽  
Author(s):  
Lieven Waeyenberge ◽  
Nicole Viaene ◽  
Maurice Moens
Keyword(s):  
Internal Control ◽  
Dna Sequences ◽  
Rrna Gene ◽  
Duplex Pcr ◽  
Specific Primers ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
Wide Range ◽  
Pcr Products ◽  
Species Specific

Abstract ITS1, the 5.8S rRNA gene and ITS2 of the rDNA region were sequenced from 20 different Pratylenchus species. Additionally, the same region was sequenced from seven populations of P. penetrans. After purifying, cloning and sequencing the PCR products, all sequences were aligned in order to find unique sites suitable for the design of species-specific primers for P. penetrans. Since ITS regions showed variability between and even within populations of P. penetrans, only three small DNA sequences were suitable for the construction of three potentially useful species-specific primers. New species-specific primers were paired with existing universal ITS primers and tested in all possible primer combinations. The best performing primer set, supplemented with a universal 28S rDNA primer set that served as an internal control, was tested in duplex PCR. The ideal annealing temperature, Mg2+ concentration and primer ratios were then determined for the most promising primer set. The optimised duplex PCR was subsequently tested on a wide range of different Pratylenchus spp. and 25 P. penetrans populations originating from all over the world. To test the sensitivity, the duplex PCR was conducted on DNA extracted from a single P. penetrans nematode mixed with varying amounts of nematodes belonging to another Pratylenchus species. Results showed that a reliable and sensitive P. penetrans species-specific duplex PCR was constructed.

scholarly journals Identification of Trichomonadid Protozoa from the Bovine Preputial Cavity by Polymerase Chain Reaction and Restriction Fragment Length Polymorphism Typing

2003 ◽  
Vol 15 (4) ◽  
pp. 390-394 ◽  
Author(s):  
Dawn C. Hayes ◽  
Rebecca R. Anderson ◽  
Richard L. Walker
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
Restriction Fragment Length

Accurate identification of the bovine pathogen Tritrichomonas foetus is sometimes complicated by the presence of other trichomonadid protozoa in clinical samples. A highly specific and reproducible approach for differentiating 3 common types of bovine trichomonadid protozoa found in the bovine preputial cavity, T. foetus, Pentatrichomonas hominis, and a Tetratrichomonas species, was developed using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. Universal trichomonadid protozoa primers, TFR1 and TFR2, were used to amplify the 5.8S rRNA gene and internal transcribed spacer regions (ITSRs), and the products were digested with the restriction enzyme HpyCH4IV. Restriction fragment length polymorphism analysis was performed on 55 trichomonad isolates from bovine preputial washing and scraping samples. The RFLP results correlated 100% with 5.8S rRNA gene and ITSR sequence results and PCR results with primers specific for T. foetus. The results of this study demonstrate that PCR and RFLP analysis can be used in lieu of DNA sequencing to identify the specific trichomonadid protozoa isolated from the bovine preputial cavity.

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