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

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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ITS1-gene 5.8S rRNA-ITS2 and trnL-trnF sequence variability during the divergence of Elymus L. species of the flora of Siberia and Russian Far East

Biological Communications ◽

10.21638/spbu03.2015.401 ◽

2015 ◽

Author(s):

Kseniya Dobryakova ◽

Nikolay Nosov

Keyword(s):

Comparative Analysis ◽

Phylogenetic Trees ◽

Russian Far East ◽

Far East ◽

Nuclear Genome ◽

Rrna Gene ◽

5.8S Rrna Gene ◽

5.8S Rrna ◽

Molecular Phylogenetic ◽

Elymus Species

The phylogenetic relationship of Elymus species were analyzed by molecular phylogenetic methods. Comparative analysis of the sequences ITS1-5.8S rRNA gene-ITS2 of the nuclear genome species of genus Elymus and kinship group showed that the species of the genus Elymus have 3 haplotypes. Нaplotype A was found in Elymus species (sections: Turczaninovia, Goulardia и Elymus) and Elytrigia geniculata; haplotype B was found in Elymus species (sections: Turczaninovia, Goulardia); haplotype C (sections: Goulardia и Clinelymopsis) and E. repens. Comparative analysis of the sequences trnL-trnF of the chloroplast genome of genus Elymus related species showed that the species of the genus Elymus form strongly supported clade. The phylogenetic trees were constructed using Bayesian method. Refs 22. Figs 2. Tables 3.

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A Real-Time PCR Assay Based on 5.8S rRNA Gene (5.8S rDNA) for Rapid Detection of Candida from Whole Blood Samples

Mycopathologia ◽

10.1007/s11046-015-9977-z ◽

2015 ◽

Vol 181 (5-6) ◽

pp. 405-413 ◽

Cited By ~ 4

Author(s):

Yi Guo ◽

Jing-xian Yang ◽

Guo-wei Liang

Keyword(s):

Real Time Pcr ◽

Whole Blood ◽

Rapid Detection ◽

Rrna Gene ◽

Pcr Assay ◽

Blood Samples ◽

5.8S Rdna ◽

5.8S Rrna Gene ◽

5.8S Rrna ◽

Whole Blood Samples

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

Clinical and Diagnostic Laboratory Immunology ◽

10.1128/cdli.8.3.503-508.2001 ◽

2001 ◽

Vol 8 (3) ◽

pp. 503-508 ◽

Cited By ~ 7

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.

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Species-specific duplex PCR for the detection of Pratylenchus penetrans

Nematology ◽

10.1163/156854109x428016 ◽

2009 ◽

Vol 11 (6) ◽

pp. 847-857 ◽

Cited By ~ 21

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.

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

Journal of Veterinary Diagnostic Investigation ◽

10.1177/104063870301500417 ◽

2003 ◽

Vol 15 (4) ◽

pp. 390-394 ◽

Cited By ~ 22

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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