Internal transcribed spacer sequence-based identification and phylogenic relationship of I-Tiao-Gung originating from Flemingia and Glycine (Leguminosae) in Taiwan

Wu, Chin-Tung; Hsieh, Chang-Chi; Lin, Wen‐Chuan; Tang, Chuan-Yi; Yang, Chao‐Hsun; Huang, Yu‐Chun; Ko, Yu-Jen

doi:10.1016/j.jfda.2013.08.002

Cited by 14 publications

(7 citation statements)

References 9 publications

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“…A further description of insertions, deletions, and repeats should be included as if there was any difference between them that could help to authenticate them from the others. 14 , 15 Finally, in case of undiscrimination by K2P distance, different species were grouped in the same branch in the phylogenetic tree. This means that sequences of these accessions were identical.…”

Section: Methodsmentioning

confidence: 99%

In Silico Study on Molecular Sequences for Identification ofPaphiopedilumSpecies

Huynh

Tran

et al. 2018

Evol Bioinform Online

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Our study searched all available sequences of Paphiopedilum from NCBI (National Center for Biotechnology Information) and tested for their species resolution capability in single as well as in combination forms. A total of 28 loci were applied for analyses in the study. From the nuclear genome, the highest resolution was of LFY, followed by ACO, DEF4, and RAD51. These 4 loci were found to be even better than the popular region ITS for Paphiopedilum identification. Among the chloroplast regions, the intergenic spacer atpB-rbcL gave the highest species resolution (76.7%), followed by matK, trnL, rpoC2, and ycf1. The divergence of CHS, XDH, 18S, Nad1, ccsA, rbcL, and ycf2 was very low and should not be used as identifying markers for Paphiopedilum. In addition, 2-locus combinations could improve significantly the resolving capability for the genus, in which 14/36 data sets could be resolved completely (100%) with interspecies relationships. The indel information was also effective supporting data for molecular discrimination of species.

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Section: Methodsmentioning

confidence: 99%

In Silico Study on Molecular Sequences for Identification ofPaphiopedilumSpecies

Huynh

Tran

et al. 2018

Evol Bioinform Online

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“…Genetic identification achieved by hybridization, polymerase chain reaction (PCR), and sequencing techniques is considered more objective, precise, and reliable method for identifying and authenticating herbal species [ 9 , 10 ]. Internal transcribed spacer (ITS) regions, which are rapidly evolving regions of nuclear ribosomal DNA, have been widely used for the identification of plant materials, and phylogenetic analysis using ITS regions has been conducted to investigate the genetic variability of complicated herbal species [ 11 – 13 ]. It has been reported that the four species of Atractylodes ( A. japonica , A. macrocephala , A. lancea , and A. chinensis ) can be distinguished by their different genotypes on ITS sequences [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Medicinal Categorization of Atractylodes japonica Koidz. by Using Internal Transcribed Spacer Sequencing Analysis and HPLC Fingerprinting Combined with Statistical Tools

Doh

Lee

2016

Evidence-Based Complementary and Alternative Medicine

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Atractylodes rhizomes have been used as the herbal medicine “Changchul” or “Baekchul,” according to their clinical purpose, in Korea, China, and Japan. Among the Atractylodes species, the medicinal use of Atractylodes japonica has been controversial, as it is categorized as both Changchul and Baekchul in those countries, and, moreover, parts of the rhizome have been differently used, depending on age of the plant, in Korea. Chromatographic fingerprinting by using HPLC combined with chemometric analyses and internal transcribed spacer (ITS) sequencing analysis were conducted to classify and identify 34 crude drugs derived from Atractylodes rhizomes. The identification of the samples, authenticated by their morphological features as A. japonica Koidz. (Changchul and Baekchul), A. chinensis Koidz., and A. macrocephala Koidz., was confirmed as A. japonica, A. chinensis, and A. macrocephala by ITS sequencing. The results from chemometric analyses showed that the chemical components of the crude drugs from A. japonica were significantly different from those from A. macrocephala but were similar to those from A. chinensis. The analyses also suggested that the categorization by age of A. japonica as Changchul or Baekchul is not recommended. The results indicate that A. japonica should be categorized as “Changchul” and should not be further categorized by age.

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“…Fragments with a length of 595 to 622 were replicated and the cluster analyses of two species were placed in separate clusters. It was also concluded that ITS can be useful for intraspecific evaluation (Wu et al, 2013). Using ITS sequencing data in the nuclear ribosomal DNA as well as plastid DNA sequencing (psbA-trnH intergenic spacer regions) and morphological markers (the number of edges and seam width of fruit), the phylogenetic relationships between 39 species of Bunium were studied and the results showed that the genome Bunium has more than one subtype.…”

Section: Discussionmentioning

confidence: 99%

Assesment of molecular diversity of internal transcribed spacer region in some lines and landrace of Persian clover (Trifolium resupinatum L.)

Ansari

Solouki

Fakheri

et al. 2018

Potr. S. J. F. Sci.

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Clover which is an herbaceous, annual, and self-pollinated plant belongs to fabaceae family (legumes) and has become naturalized in Iran, Asia Minor and the Mediterranean eastern suburban countries. The aim of the present study is ITS molecular evaluation of the nuclear ribosomal genes of lines and landraces of Persian Clover. The sequences were aligned using ClustalW method and by MegAlign software and the dendrogram of different phylogenetic and matrix relationships between the sequences were drawn. The results showed little genetic diversity between the lines and the landrace. The conserved sequence of the analyzed gene in the Persian clover is 561 base. Totally, 740 loci (69 and 671 loci, respectively, with and without removal and addition), 9 Singletons, and 5 haplotypes were identified. The highest rate of transfer was observed in pyrimidine (%16.3). The numerical value of the ratio (dN/dS) was 0.86, and since it was less than 1, the pure selection on the studied gene happened. The lines and landraces were not separated based on their geographic locations. In general, the results indicated that the highest rate of the regional diversity belonged to the clover plants in Lorestan region. Moreover, ITS markers did not seem suitable enough for evaluating the intra-species genetic variation, but it was quite well-suited for inter-species or intergeneric evaluation.

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Internal transcribed spacer sequence-based identification and phylogenic relationship of I-Tiao-Gung originating from Flemingia and Glycine (Leguminosae) in Taiwan

Cited by 14 publications

References 9 publications

In Silico Study on Molecular Sequences for Identification ofPaphiopedilumSpecies

In Silico Study on Molecular Sequences for Identification ofPaphiopedilumSpecies

Evaluation of Medicinal Categorization of Atractylodes japonica Koidz. by Using Internal Transcribed Spacer Sequencing Analysis and HPLC Fingerprinting Combined with Statistical Tools

Assesment of molecular diversity of internal transcribed spacer region in some lines and landrace of Persian clover (Trifolium resupinatum L.)

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