1
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Du P, He HY, Wu NY, Cao T, Cui BK. Medicinal Value, Genetic Diversity, and Genetic Relationship Analysis of Auricularia cornea (Agaricomycetes) Based on ITS, ISSR, and SRAP Markers. Int J Med Mushrooms 2024; 26:43-57. [PMID: 38780422 DOI: 10.1615/intjmedmushrooms.2024053182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Wild resources of Auricularia cornea (A. polytricha) are abundant in China, and genetic diversity and genetic relationships analysis of A. cornea can provide basis for germplasm resource utilization and innovation and molecular marker-assisted breeding. In this study, 22 Auricularia strains collected were identified as A. cornea based on ITS sequence analysis, and its genetic diversity was examined by ISSR and SRAP markers. The results showed that a total of 415 bands were amplified by 11 selected ISSR primers, with an average amplification of 37.73 bands per primer, and the mean values of Ne, I, and H were 1.302, 0.368, and 0.219, respectively. A total of 450 bands were amplified by 10 SRAP primers, with an average of 45 bands per primer, and the average of Ne, I, and H were 1.263, 0.302, and 0.183, respectively. The unweighted pair-group method with arithmetic means analysis based on ISSR-SRAP marker data revealed that the genetic similarity coefficient between the tested strains was 0.73-0.97, and the strains could be divided into five groups at 0.742, which had a certain correlation with regional distribution. The results of PCOA and population structure analysis based on ISSR-SRAP data also produced similar results. These results demonstrate the genetic diversity and distinctness among wild A. cornea and provide a theoretical reference for the classification, breeding, germplasm innovation, utilization, and variety protection of A. cornea resources.
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Affiliation(s)
- Ping Du
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing 408100, P.R. China
| | - Hong-Yan He
- College of Modern Agriculture and Bioengineering, Yangtze Normal University, Chongqing 408100, P.R. China
| | - Ni-Ya Wu
- College of Modern Agriculture and Bioengineering, Yangtze Normal University, Chongqing 408100, P.R. China
| | - Tianxu Cao
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing 408100, P.R. China
| | - Bao-Kai Cui
- Institute of Microbiology, Beijing Forestry University, Beijing, China
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2
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Dai J, Liu Q, Xu X, Tan Z, Lin Y, Gao X, Zhu S. Comparative and phylogenetic analysis of the complete chloroplast genomes of Uncaria (Rubiaceae) species. FRONTIERS IN PLANT SCIENCE 2023; 14:1271689. [PMID: 38186595 PMCID: PMC10766718 DOI: 10.3389/fpls.2023.1271689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024]
Abstract
The genus Uncaria is famous for its high medicinal value. However, the high morphological similarities and unclear interspecific genetic relationships have posed challenges to the classification and identification of Uncaria species. Here, we newly sequenced six chloroplast genomes of Uncaria species: U. hirsuta, U. rhynchophylla, U. rhynchophylloides, U. homomalla, U. sinensis, and U. lancifolia. Comparisons among the chloroplast genomes of Uncaria species showed their conservation in structure, gene content, and order. Ten highly variable loci could be potentially used as specific molecular markers in the identification of Uncaria species. The third position of codons tended to use A/U base, and natural selection contributed more to the formation of codon usage bias in comparison to mutation pressure. Four genes (rbcL, ndhF, rps8, and ycf2) were detected to be subjected to positive selection. Phylogenetic analysis showed that the genus Uncaria was a monophyletic group, belonging to the tribe Naucleeae. Moreover, U. sinensis was not a variant of U. rhynchophylla. U. rhynchophylloides and U. rhynchophylla were not the same species. The results of the comparative and phylogenetic analysis provide valuable references for further research studies of classification, identification, breeding improvement, and phylogenetic relationships in Uncaria species.
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Affiliation(s)
- Jiangpeng Dai
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Qiaozhen Liu
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xingyuan Xu
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Zhijie Tan
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yuexia Lin
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiaoxia Gao
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Shuang Zhu
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
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Castro AA, Nunes R, Carvalho LR, Targueta CP, Dos Santos Braga-Ferreira R, de Melo-Ximenes AA, Corvalán LCJ, Bertoni BW, Pereira AMS, de Campos Telles MP. Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily. Sci Rep 2023; 13:8390. [PMID: 37225737 DOI: 10.1038/s41598-023-34334-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/27/2023] [Indexed: 05/26/2023] Open
Abstract
Uncaria species are used in traditional medicine and are considered of high therapeutic value and economic importance. This work describes the assembly and annotation of the chloroplast genomes of U. guianensis and U. tomentosa, as well as a comparative analysis. The genomes were sequenced on MiSeq Illumina, assembled with NovoPlasty, and annotated using CHLOROBOX GeSeq. Addictionaly, comparative analysis were performed with six species from NCBI databases and primers were designed in Primer3 for hypervariable regions based on the consensus sequence of 16 species of the Rubiaceae family and validated on an in-silico PCR in OpenPrimeR. The genome size of U. guianensis and U. tomentosa was 155,505 bp and 156,390 bp, respectively. Both Species have 131 genes and GC content of 37.50%. The regions rpl32-ccsA, ycf1, and ndhF-ccsA showed the three highest values of nucleotide diversity within the species of the Rubiaceae family and within the Uncaria genus, these regions were trnH-psbA, psbM-trnY, and rps16-psbK. Our results indicates that the primer of the region ndhA had an amplification success for all species tested and can be promising for usage in the Rubiaceae family. The phylogenetic analysis recovered a congruent topology to APG IV. The gene content and the chloroplast genome structure of the analyzed species are conserved and most of the genes are under negative selection. We provide the cpDNA of Neotropical Uncaria species, an important genomic resource for evolutionary studies of the group.
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Affiliation(s)
- Andrezza Arantes Castro
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Rhewter Nunes
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil.
- Instituto Federal de Goiás - Campus Cidade de Goiás (IFG), Goiás, GO, 74600-000, Brazil.
| | - Larissa Resende Carvalho
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Cíntia Pelegrineti Targueta
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Ramilla Dos Santos Braga-Ferreira
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Amanda Alves de Melo-Ximenes
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | - Leonardo Carlos Jeronimo Corvalán
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
| | | | | | - Mariana Pires de Campos Telles
- Laboratório de Genética and Biodiversidade (LGBio), Instituto de Ciências Biológicas - Universidade Federal de Goiás (UFG), Goiânia, GO, 74045-155, Brazil
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás (PUC - GO), Goiânia, GO, 74605-050, Brazil
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Abdel-Hamid AME, Elenazy HH, Abdel-Hameed UK. DNA barcoding of some taxa of genus Acacia and their phylogenetic relationship. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1938702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Amal M. E. Abdel-Hamid
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, Egypt
- Department of Biology, College of Sciences and Arts, Taibah University, Al Ula, Kingdom of Saudi Arabia
| | - Hanaa H. Elenazy
- Department of Biology, College of Science, Taibah University, Al Madinah, Kingdom of Saudi Arabia
| | - Usama K. Abdel-Hameed
- Department of Biology, College of Science, Taibah University, Al Madinah, Kingdom of Saudi Arabia
- Department of Botany, Faculty of Science, Ain Shams University, Cairo, Egypt
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Gai Y, Yang N, Chen J. Inhibitory Activity of 8 Alkaloids on P-gp and Their Distribution in Chinese Uncaria Species. Nat Prod Commun 2020. [DOI: 10.1177/1934578x20973506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
P-glycoprotein (P-gp) inhibition conduces to improving the ability of chemicals to cross through blood-brain barrier (BBB). The hook-bearing branch of Uncaria is used as a traditional herbal medicine for the treatment of hypertension, headache, stroke, and Alzheimer’s disease in recent years. In this study, the inhibitory effects of 8 alkaloids sourced from Uncaria plants on P-gp were evaluated. Meanwhile, the content of 8 alkaloids in 8 Chinese Uncaria species was quantified simultaneously by high-performance liquid chromatography analysis. Western blotting, real-time quantitative reverse transcription-polymerase chain reaction, and flow cytometry were used to evaluate the P-gp levels in MCF-7/adriamycin-resistant (ADR) cells. It was shown that hirsuteine and hirsutine, selected from 8 candidate alkaloids, could remarkably suppressed P-gp level and function in MCF-7/ADR cells when using Verapamil as positive control. By tracking their chemical distribution in 8 Chinese Uncaria species, we found that hirsuteine and hirsutine were much more abundant in Uncaria rhynchophylla and Uncaria hirsuta than in any other 6 species. And a chemical content profile of these alkaloids was plotted within 8 Chinese species.
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Affiliation(s)
- Yanan Gai
- Research Center of Medicinal Plants, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Nannan Yang
- Research Center of Medicinal Plants, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jian Chen
- Research Center of Medicinal Plants, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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6
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Leong F, Hua X, Wang M, Chen T, Song Y, Tu P, Chen XJ. Quality standard of traditional Chinese medicines: comparison between European Pharmacopoeia and Chinese Pharmacopoeia and recent advances. Chin Med 2020; 15:76. [PMID: 32742301 PMCID: PMC7388521 DOI: 10.1186/s13020-020-00357-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022] Open
Abstract
Traditional Chinese medicine (TCM) are becoming more and more popular all over the world. However, quality issues of TCM may lead to medical incidents in practice and therefore quality control is essential to TCM. In this review, the state of TCM in European Pharmacopoeia are compared with that in Chinese Pharmacopoeia, and herbal drugs that are not considered as TCM and not elaborated by TCM working party at European Directorate for the Quality of Medicines & Health Care (EDQM) but present in both European Pharmacopoeia and Chinese Pharmacopoeias are also discussed. Different aspects in quality control of TCM including origins, identification, tests and assays, as well as sample preparation, marker selection and TCM processing are covered to address the importance of establishing comprehensive quality standard of TCM. Furthermore, advanced analytical techniques for quality control and standard establishment of TCM are also reviewed.
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Affiliation(s)
- Fong Leong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao People's Republic of China
| | - Xue Hua
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao People's Republic of China
| | - Mei Wang
- LU-European Center for Chinese Medicine and Natural Compounds, Institute of Biology, Leiden University, Sylviusweg72, 2333BE Leiden, The Netherlands
| | - Tongkai Chen
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405 China
| | - Yuelin Song
- Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Pengfei Tu
- Modern Research Center for Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029 China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191 China
| | - Xiao-Jia Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao People's Republic of China
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7
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Zhu S, Li Q, Chen S, Wang Y, Zhou L, Zeng C, Dong J. Phylogenetic analysis of Uncaria species based on internal transcribed spacer (ITS) region and ITS2 secondary structure. PHARMACEUTICAL BIOLOGY 2018; 56:548-558. [PMID: 30392423 PMCID: PMC6225500 DOI: 10.1080/13880209.2018.1499780] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 06/22/2018] [Accepted: 07/06/2018] [Indexed: 05/31/2023]
Abstract
CONTEXT The plant genus Uncaria (Rubiaceae), also known as Gouteng, is the source of an important traditional Chinese medicine. Misidentification and adulteration of Gouteng affect the safety and efficacy of the medication. Phylogenetic relationships among the species of this genus are unknown. OBJECTIVE The present study sought to detect the phylogenetic relationships based on internal transcribed spacer (ITS) region of all 12 species of Uncaria recorded in the Flora of China. MATERIALS AND METHODS Accession of seven species of Uncaria served as reference samples. ITS region was used for polymerase chain reaction (PCR) amplification of the reference samples representing 39 specimens. Distance analysis, species discrimination, and secondary structure of ITS2 were used to assess the ability of ITS sequence in authenticating. The phylogenetic relationships were detected using three methods: Bayesian inference (BI), maximum likelihood (ML), and neighbor joining (NJ). RESULTS Five species of traditional Chinese medicine Gouteng were well resolved in molecular phylogenetic tree. Besides, Uncaria lancifolia Hutch. was closer to U. rhynchophylloides F.C. How and U. sessilifructus Roxb. was closer to U. laevigata Wall. within the tree. Further, we also found that ITS2 secondary structure can be a candidate tool in distinguishing two closely related species U. yunnanensis K.C.Hsia and U. lanosa Wall. For accurate identification of different species of Uncaria based on species-specific nucleotide sites, a consensus sequences database with all 12 species is established. DISCUSSIONS AND CONCLUSIONS The results are able to discriminate Uncaria species and illustrate the phylogenetic relationships, which are essential for the investigation of adulterants and misidentifications of Uncaria.
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Affiliation(s)
- Shuang Zhu
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Qiwei Li
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Shanchong Chen
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Yesheng Wang
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Lin Zhou
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Changqing Zeng
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Jun Dong
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
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8
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Jiao J, Huang W, Bai Z, Liu F, Ma C, Liang Z. DNA barcoding for the efficient and accurate identification of medicinal polygonati rhizoma in China. PLoS One 2018; 13:e0201015. [PMID: 30021015 PMCID: PMC6051646 DOI: 10.1371/journal.pone.0201015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/06/2018] [Indexed: 12/23/2022] Open
Abstract
Polygonati rhizoma (PR), a traditional medicinal and edible product with various bioactive components (Polygonatum polysaccharides, saponins, phenols, and flavonoids), is widely consumed in China. However, other species with morphological characteristics similar to those of the actual components are being used to replace or adulterate PR, causing issues with quality control and product safety. The morphological similarity of PR and its substitutes makes classic morphological identification challenging. To address this issue, DNA barcoding-based identification using ITS2 and psbA-trnH sequences was applied in this study to evaluate the efficiency and accuracy of this approach in identifying PR samples collected from 39 different regions in China. The identification of PR by this method was confirmed by other methods (phylogeny-based and character-based methods), and all the samples were clearly and accurately distinguished. This study highlights the efficient and accurate nature of DNA barcoding in PR identification. Applying this technique will provide a means to differentiate PR from other altered formulations, thus improving product quality and safety for consumers of PR and its products.
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Affiliation(s)
- Jie Jiao
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenli Huang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Zhenqing Bai
- College of Life Science, Yan'an University, Yan'an, Shaanxi, China
| | - Feng Liu
- Research Department, Buchang Pharma, Xi’an, Shaanxi, China
| | - Cunde Ma
- Research Department, Buchang Pharma, Xi’an, Shaanxi, China
| | - Zongsuo Liang
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
- College of Life Science, Zhejiang SCI-TECH University, Hangzhou, Zhejiang, China
- * E-mail:
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9
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Assessment of three plastid DNA barcode markers for identification of Clinacanthus nutans (Acanthaceae). 3 Biotech 2018; 8:62. [PMID: 29354373 DOI: 10.1007/s13205-018-1092-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/04/2018] [Indexed: 01/26/2023] Open
Abstract
This study was conducted to determine the feasibility of using three plastid DNA regions (matK, trnH-psbA, and rbcL) as DNA barcodes to identify the medicinal plant Clinacanthus nutans. In this study, C. nutans was collected at several different locations. Total genomic DNA was extracted, amplified by polymerase chain reaction (PCR), and sequenced using matK, trnH-psbA, and rbcL, primers. DNA sequences generated from PCR were submitted to the National Center for Biotechnology Information's (NCBI) GenBank. Identification of C. nutans was carried out using NCBI's Basic Local Alignment Search Tool (BLAST). The rbcL and trnH-psbA regions successfully identified C. nutans with sequencing rates of 100% through BLAST identification. Molecular Evolutionary Genetics Analysis (MEGA) 6.0 was used to analyze interspecific and intraspecific divergence of plastid DNA sequences. rbcL and matK exhibited the lowest average interspecific distance (0.0487 and 0.0963, respectively), whereas trnH-psbA exhibited the highest average interspecific distance (0.2029). The R package Spider revealed that trnH-psbA correctly identified Barcode of Life Data System (BOLD) 96%, best close match 79%, and near neighbor 100% of the species, compared to matK (BOLD 72%; best close match 64%; near neighbor 78%) and rbcL (BOLD 77%; best close match 62%; near neighbor 88%). These results indicate that trnH-psbA is very effective at identifying C. nutans, as it performed well in discriminating species in Acanthaceae.
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Zhao B, Huang Y, Chen Q, Chen Q, Miao H, Zhu S, Zeng C. Characteristic component profiling and identification of different Uncaria species based on high-performance liquid chromatography-photodiode array detection tandem ion trap and time of flight mass spectrometry coupled with rDNA ITS sequence. Biomed Chromatogr 2017; 32. [PMID: 29034541 DOI: 10.1002/bmc.4119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/28/2017] [Accepted: 10/01/2017] [Indexed: 01/11/2023]
Abstract
Uncaria is a multi-source herb and its species identification has become a bottleneck in quality control. To study the identification method of different Uncaria species herbs through HPLC-MS coupled with rDNA Internal Transcribed Spacer (rDNA ITS) sequence, both plant morphological traits and molecular identification were used to determine the species of every collected Uncaria herb. The genetic analysis of different Uncaria species was performed using their rDNA ITS sequence as a molecular marker. Meanwhile, the phylogenetic relationships of 22 samples from six Uncaria species were divided and classified clearly. By optimizing the chromatographic conditions, a practical HPLC method to differentiate various varieties of Uncaria herbs was set up based on a set of characteristic components across each species. A high-performance liquid chromatography-photodiode array detector tandem ion trap and time of flight mass spectrometry technique combined with reference substances was utilized to derive 21 characteristic compounds containing six groups of six Uncaria species in China. Thus, this study provides a feasible method to solve the current problem of confusion in Uncaria species, and makes a significant step forward in the appropriate clinical use, in-depth research and further utilization of different Uncaria species.
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Affiliation(s)
- Bingqiang Zhao
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Yanjun Huang
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Qiulan Chen
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Qizhao Chen
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Hui Miao
- School of Pharmaceutical Science, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shuang Zhu
- College of Bioscience and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Changqing Zeng
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China.,National Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicine Digital Quality Evaluation Technology, School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
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11
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Wang DY, Wang Q, Wang YL, Xiang XG, Huang LQ, Jin XH. Evaluation of DNA barcodes in Codonopsis (Campanulaceae) and in some large angiosperm plant genera. PLoS One 2017; 12:e0170286. [PMID: 28182623 PMCID: PMC5300163 DOI: 10.1371/journal.pone.0170286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 01/03/2017] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding is expected to be one of the most promising tools in biological taxonomy. However, there have been no agreements on which core barcode should be used in plants, especially in species-rich genera with wide geographical distributions. To evaluate their discriminatory power in large genera, four of the most widely used DNA barcodes, including three plastid regions (matK, rbcL, trnH-psbA) and nuclear internal transcribed spacer (nrITS), were tested in seven species-rich genera (Ficus, Pedicularis, Rhodiola, Rhododendron,Viburnum, Dendrobium and Lysimachia) and a moderate size genus, Codonopsis. All of the sequences from the aforementioned seven large genera were downloaded from NCBI. The related barcodes for Codonopsis were newly generated in this study. Genetics distances, DNA barcoding gaps and phylogenetic trees of the four single barcodes and their combinations were calculated and compared in the seven genera. As for single barcode, nrITS has the most variable sites, the clearest intra- and inter-specific divergences and the highest discrimination rates in the seven genera. Among the combinations of barcodes, ITS+matK performed better than all the single barcodes in most cases and even the three- and four-loci combinations in the seven genera. Therefore, we recommend ITS+matK as the core barcodes for large plant genera.
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Affiliation(s)
- De-Yi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ying-Li Wang
- Baotou Medical College, Donghe District, Baotou City, Inner Mongolia, China
| | - Xiao-Guo Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lu-Qi Huang
- National Resource Centre for Chinese Materia Medica, China Academy of Chinese Medical Science, Beijing, China
| | - Xiao-Hua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Science (CAS-SEABRI), Menglun, Mengla, Yunnan, China
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