scholarly journals Molecular authentication of Euphorbia schimperiana Scheele using internal transcribed spacer sequences of nuclear ribosomal DNA

2021 ◽  
Vol 28 (1) ◽  
pp. 125-130
Author(s):  
Mesfer M Alqahtani ◽  
M Ajmal Ali ◽  
M Oliur Rahman ◽  
Fahad M Al Hemaid ◽  
Sidanand V Kambhar ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Molecular Phylogenetics ◽  
Taxonomic Status ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Universal Primers ◽  
Important Species ◽  
Discrimination Ability ◽  
Plant Taxon

The Internal Transcribed Spacers (ITS) sequences of nuclear ribosomal DNA (nrDNA) are commonly used in plant molecular phylogenetics for the molecular based taxonomic identification and DNA barcoding because of shorter length and easy to amplify by using the universal primers, and further has discrimination ability to distinguish the taxon at lower taxonomic level. The present molecular phylogenetic analysis of ITS nrDNA sequences focuses to determine the taxonomic status of an unresolved medicinally important species Euphorbia schimperiana Scheele of the family Euphorbiaceae reported from Saudi Arabia. The combined length of the entire ITS region in E. schimperiana is 644 nucleotides. The study reveals that E. schimperiana shows a close proximity with the members of the subgenus Esula. Bangladesh J. Plant Taxon. 28(1): 125-130, 2021 (June)

scholarly journals Inclusion of Kickxia abhaica D.A. Sutton in the genus Nanorrhinum (Plantaginaceae): Evidence from its nuclear ribosomal DNA sequences

2018 ◽  
Vol 25 (2) ◽  
pp. 209-214
Author(s):  
M. Ajmal Ali
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Molecular Phylogenetics ◽  
Taxonomic Status ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Universal Primers ◽  
Discrimination Power ◽  
Molecular Phylogenetic ◽  
Endemic Taxon

The nuclear ribosomal DNA (nrDNA) internal transcribed spacers (ITS) sequences is extensively used in the plant molecular phylogenetics for plant taxonomic identification and DNA barcoding purposes because the nrDNA ITS gene is easy to amplify by using the universal primers, its length is shorter and thus easy to sequence, and has strong discrimination power to distinguish the taxon at the species level. The present molecular phylogenetic analysis of ITS nrDNA sequences focuses to determine the taxonomic status of an unresolved endemic taxon Kickxia abhaica D.A. Sutton (Family Plantaginaceae, tribe Antirrhineae) reported from Saudi Arabia. The analysis supports the transfer of K. abhaica under the genus Nanorrhinum.

PCR Amplification of Ribosomal DNA for Species Identification in the Plant Pathogen Genus Phytophthora

1998 ◽  
Vol 64 (3) ◽  
pp. 948-954 ◽  
Author(s):  
Jean B. Ristaino ◽  
Michael Madritch ◽  
Carol L. Trout ◽  
Gregory Parra
Keyword(s):  
Ribosomal Dna ◽  
Plant Pathogen ◽  
Pcr Amplification ◽  
Its Region ◽  
Restriction Enzymes ◽  
Internal Transcribed Spacers ◽  
Important Species ◽  
Major Species ◽  
Field Samples ◽  
Taxonomic Groups

ABSTRACT We have developed a PCR procedure to amplify DNA for quick identification of the economically important species from each of the six taxonomic groups in the plant pathogen genusPhytophthora. This procedure involves amplification of the 5.8S ribosomal DNA gene and internal transcribed spacers (ITS) with the ITS primers ITS 5 and ITS 4. Restriction digests of the amplified DNA products were conducted with the restriction enzymesRsaI, MspI, and HaeIII. Restriction fragment patterns were similar after digestions with RsaI for the following species: P. capsici andP. citricola; P. infestans,P. cactorum, and P. mirabilis;P. fragariae, P. cinnamomi, andP. megasperma from peach; P. palmivora, P. citrophthora, P. erythroseptica, and P. cryptogea; andP. megasperma from raspberry and P. sojae. Restriction digests with MspI separatedP. capsici from P. citricola and separated P. cactorum from P. infestans and P. mirabilis. Restriction digests with HaeIII separated P. citrophthorafrom P. cryptogea, P. cinnamomi fromP. fragariae and P. megasperma on peach, P. palmivora from P. citrophthora, and P. megasperma on raspberry from P. sojae. P. infestans and P. mirabilis digests were identical and P. cryptogea and P. erythroseptica digests were identical with all restriction enzymes tested. A unique DNA sequence from the ITS region I in P. capsici was used to develop a primer called PCAP. The PCAP primer was used in PCRs with ITS 1 and amplified only isolates of P. capsici,P. citricola, and P. citrophthoraand not 13 other species in the genus. Restriction digests withMspI separated P. capsici from the other two species. PCR was superior to traditional isolation methods for detection of P. capsici in infected bell pepper tissue in field samples. The techniques described will provide a powerful tool for identification of the major species in the genusPhytophthora.

Phylogeny of Sisymbrium (Brassicaceae) based on ITS sequences of nuclear ribosomal DNA

2002 ◽  
Vol 80 (9) ◽  
pp. 1002-1017 ◽  
Author(s):  
Suzanne I Warwick ◽  
Ihsan A Al-Shehbaz ◽  
Robert A Price ◽  
Connie Sauder
Keyword(s):  
Ribosomal Dna ◽  
New World ◽  
Sequence Data ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Maximum Parsimony Analysis ◽  
Rrna Gene ◽  
Old World ◽  
5.8S Rrna Gene

The genus Sisymbrium as currently circumscribed includes about 94 species disjunctly distributed in the Old (41 spp.) and the New World (53 spp.). Sisymbrium has been variously delimited, with several segregate genera proposed (subtribe Sisymbriinae) primarily for the new World taxa, including Schoenocrambe, Coelophragmus, and Mostacillastrum. Using sequence data from the internal transcribed spacers of nuclear ribosomal DNA and the 5.8S rRNA gene (collectively, ITS region), we examined the evolutionary relationships of Old and New World Sisymbrium species with its segregate genera and the validity of O.E. Schulz's classical sectional treatment of Sisymbrium. Sequence data were obtained from 33 Sisymbrium species, representing all 14 sections and two Sisymbrium species formerly assigned to segregate genera Coelophragmus and Mostacillastrum (subtribe Sisymbriinae), and two putative Sisymbrium species currently assigned to Neotorularia. Sequence data were also obtained from 26 taxa from segregate or related genera includingSchoenocrambe, Werdermannia (subtribe Sisymbriinae), eight genera in the Thelypodieae, Sibara (tribe Arabideae) and Pringlea (tribe Pringleeae), four members of the tribe Brassiceae, and three other Neotorularia species. Results from maximum parsimony analysis showed a polyphyletic origin for Sisymbrium and did not correspond well to Schulz's sectional classification. Sisymbrium species were split into three major clades: Old World Sisymbrium (including Neotorularia aculeolata, Neotorularia afghanica, and the type species of Schoenocrambe, Schoenocrambe linifolia, the sole New World member of this Old World clade); New World Sisymbrium (along with the remaining New World taxa) and designated as the New World Thelypodieae alliance; and the tribe Brassiceae ( including Sisymbrium supinum and Sisymbrium thellungii).Key words: Sisymbrium, Schoenocrambe, ITS, Thelypodieae, taxonomy, Brassicaceae.

scholarly journals Application of internal transcribed spacer of nuclear ribosomal DNA for identification of Echinops mandavillei Kit Tan

2014 ◽  
Vol 21 (1) ◽  
pp. 33-42 ◽  
Author(s):  
Fahad M.A. Al-Hemaid ◽  
M. Ajmal Ali ◽  
Joongku Lee ◽  
Gábor Gyulai ◽  
Arun K. Pandey
Keyword(s):  
Ribosomal Dna ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Local Alignment ◽  
The Novel ◽  
Search Tool ◽  
Plant Taxon ◽  
High Level

The present study explored the use of internal transcribed spacers (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA (nrDNA) for identification of Echinops mandavillei Kit Tan, an endemic species to Saudi Arabia. The sequence similarity search using Basic Local Alignment Search Tool (BLAST) and phylogenetic analyses of the ITS sequence of E. mandavillei Kit Tan showed high level of sequence similarity (98%) with E. glaberrimus DC. (section Ritropsis). The novel primary sequence and the secondary structure of ITS2 of E. mandavillei could have a potential use for molecular genotyping.DOI: http://dx.doi.org/10.3329/bjpt.v21i1.19256Bangladesh J. Plant Taxon. 21(1): 33-42, 2014 (June)

Phylogenetic Analysis of Black Peper (Piper Spp.) Population Collected in Different Locations of Vietnam Based on the ITSU1-4 Gene Region

2021 ◽  
Author(s):  
Sonexay Rasphone ◽  
Long Thanh Dang ◽  
Hoan Nguyen ◽  
Ngoc Quang Nguyen ◽  
Oanh Thi Duong ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Ribosomal Dna ◽  
Maximum Likelihood Method ◽  
Dna Barcode ◽  
Population Expansion ◽  
Nuclear Ribosomal Dna ◽  
Likelihood Method ◽  
Gene Region ◽  
Universal Primers ◽  
Intraspecific Distance

Abstract Background: The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. To compare and find out the analysis genetic diversity difference some pepper individuals collected in different localities in Vietnam when using the ITS of nuclear ribosomal DNA. The ITS gene region from the nuclear genomes were tested for their suitability as DNA barcoding regions of thirty-nine pepper individuals. Universal primers were used, and sequenced products were analyzed using the Maximum Likelihood method and Tamura-Nei model in the MEGA X program.Results: We did not observe high variability in intraspecific distance within the ITSu1-4 gene region between individuals, ranged from 0.000 to 0.155 (mean = 0.033). The size of the gene region has fluctuated from 667 to 685 bp between different individuals with the percentage (G + C) contained in the ITSu1-4 gene region was ranged from 54.776% to 60.805%, mean = 60.174%. The values of Fu’s Fs, D, Fu and Li’s D* and F* were negative as well (Fs = -0.209, D = -1.824; P < 0.05, D* = -1.205; not significant, P > 0.10 and F* = -1.699; not significant, 0.10 > P > 0.05), indicating an excess of recently derived haplotypes and suggesting that either population expansion or background selection has occurred. The value Strobeck’s S the obtained between individuals in a population is high (S = 0.684). The results of evolutionary relationships of taxa obtained 3 groups with the highest value of Fst is shown in the pairs of groups II and III (Fst = 0.151), and the lowest is in groups II and I (Fst = 0.015). All of the new sequences have been deposited in GeneBank under the following accession numbers MZ636718 to MZ636756.Conclusions: This database is an important resource for researchers working on Species of pepper in Vietnam and also provides a tool to create ITSu1-4 databases for any given taxonomy.

scholarly journals Phylogenetics of Taxus Using the Internal Transcribed Spacers of Nuclear Ribosomal DNA and Plastid trnL-F Regions

Horticulturae ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 19
Author(s):  
Patricia Coughlan ◽  
James C. Carolan ◽  
Ingrid L. I. Hook ◽  
Lisa Kilmartin ◽  
Trevor R. Hodkinson
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Its Region ◽  
Single Species ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Trnl Intron ◽  
Group Status ◽  
Haplotype Networks

Taxus is a genus of trees and shrubs with high value in horticulture and medicine as a source of the anticancer drug paclitaxel. The taxonomy of the group is complex due to the lack of diagnostic morphological characters and the high degree of similarity among species. Taxus has a wide global geographic distribution and some taxonomists recognize only a single species with geographically defined subgroups, whereas others have described several species. To address these differences in taxonomic circumscription, phylogenetic analyses were conducted on DNA sequences using Maximum Likelihood, Bayesian Inference and TCS haplotype networks on single and combined gene regions obtained for the nuclear ribosomal ITS region and the plastid trnL intron and trnL-F intergenic spacer. Evidence is presented for the sister group status of Pseudotaxus to Taxus and the inclusion of Amentotaxus, Austrotaxus, Cephalotaxus and Torreya within Taxaceae. Results are consistent with the taxonomic recognition of nine species: T. baccata, T. brevifolia, T. canadensis, T. cuspidata, T. floridana, T. fuana, T. globosa, T. sumatrana and T. wallichiana, but evidence is found for less species distinction and considerable reticulation within the T. baccata, T. canadensis and T. cuspidata group. We compare the results to known taxonomy, biogeography, present new leaf anatomical data and discuss the origins of the hybrids T. ×media and T. ×hunnewelliana.

Characterization of Trichuris trichiura from humans and T. suis from pigs in China using internal transcribed spacers of nuclear ribosomal DNA

2012 ◽  
Vol 88 (1) ◽  
pp. 64-68 ◽  
Author(s):  
G.H. Liu ◽  
W. Zhou ◽  
A.J. Nisbet ◽  
M.J. Xu ◽  
D.H. Zhou ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Sequence Variation ◽  
Animal Health ◽  
Trichuris Trichiura ◽  
Its Rdna ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Economic Losses ◽  
Molecular Characteristics ◽  
Rdna Sequences

AbstractTrichuris trichiura and Trichuris suis parasitize (at the adult stage) the caeca of humans and pigs, respectively, causing trichuriasis. Despite these parasites being of human and animal health significance, causing considerable socio-economic losses globally, little is known of the molecular characteristics of T. trichiura and T. suis from China. In the present study, the entire first and second internal transcribed spacer (ITS-1 and ITS-2) regions of nuclear ribosomal DNA (rDNA) of T. trichiura and T. suis from China were amplified by polymerase chain reaction (PCR), the representative amplicons were cloned and sequenced, and sequence variation in the ITS rDNA was examined. The ITS rDNA sequences for the T. trichiura and T. suis samples were 1222–1267 bp and 1339–1353 bp in length, respectively. Sequence analysis revealed that the ITS-1, 5.8S and ITS-2 rDNAs of both whipworms were 600–627 bp and 655–661 bp, 154 bp, and 468–486 bp and 530–538 bp in size, respectively. Sequence variation in ITS rDNA within and among T. trichiura and T. suis was examined. Excluding nucleotide variations in the simple sequence repeats, the intra-species sequence variation in the ITS-1 was 0.2–1.7% within T. trichiura, and 0–1.5% within T. suis. For ITS-2 rDNA, the intra-species sequence variation was 0–1.3% within T. trichiura and 0.2–1.7% within T. suis. The inter-species sequence differences between the two whipworms were 60.7–65.3% for ITS-1 and 59.3–61.5% for ITS-2. These results demonstrated that the ITS rDNA sequences provide additional genetic markers for the characterization and differentiation of the two whipworms. These data should be useful for studying the epidemiology and population genetics of T. trichiura and T. suis, as well as for the diagnosis of trichuriasis in humans and pigs.

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