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      Application of Molecular Methods in the Identification of Ingredients in Chinese Herbal Medicines

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          Abstract

          There are several kinds of Chinese herbal medicines originating from diverse sources. However, the rapid taxonomic identification of large quantities of Chinese herbal medicines is difficult using traditional methods, and the process of identification itself is prone to error. Therefore, the traditional methods of Chinese herbal medicine identification must meet higher standards of accuracy. With the rapid development of bioinformatics, methods relying on bioinformatics strategies offer advantages with respect to the speed and accuracy of the identification of Chinese herbal medicine ingredients. This article reviews the applicability and limitations of biochip and DNA barcoding technology in the identification of Chinese herbal medicines. Furthermore, the future development of the two technologies of interest is discussed.

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          A DNA barcode for land plants.

          Peter M. Hollingsworth, Laura L. Forrest, John Spouge … (2009)
          DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.
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            Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species

            Shilin Chen, Hui-min Yao, Jianping Han … (2010)
            Background The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL + matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over. Methodology/Principal Findings Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level. Conclusions The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.
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              Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants.

              De-Zhu Li, Lian-Ming Gao, Hong-Tao Li … (2011)
              A two-marker combination of plastid rbcL and matK has previously been recommended as the core plant barcode, to be supplemented with additional markers such as plastid trnH-psbA and nuclear ribosomal internal transcribed spacer (ITS). To assess the effectiveness and universality of these barcode markers in seed plants, we sampled 6,286 individuals representing 1,757 species in 141 genera of 75 families (42 orders) by using four different methods of data analysis. These analyses indicate that (i) the three plastid markers showed high levels of universality (87.1-92.7%), whereas ITS performed relatively well (79%) in angiosperms but not so well in gymnosperms; (ii) in taxonomic groups for which direct sequencing of the marker is possible, ITS showed the highest discriminatory power of the four markers, and a combination of ITS and any plastid DNA marker was able to discriminate 69.9-79.1% of species, compared with only 49.7% with rbcL + matK; and (iii) where multiple individuals of a single species were tested, ascriptions based on ITS and plastid DNA barcodes were incongruent in some samples for 45.2% of the sampled genera (for genera with more than one species sampled). This finding highlights the importance of both sampling multiple individuals and using markers with different modes of inheritance. In cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplify and sequence this subset of the marker. We therefore propose that ITS/ITS2 should be incorporated into the core barcode for seed plants.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Molecules
                Journal ID (iso-abbrev): Molecules
                Journal ID (publisher-id): molecules
                Title: Molecules : A Journal of Synthetic Chemistry and Natural Product Chemistry
                Publisher: MDPI
                ISSN (Electronic): 1420-3049
                Publication date (Electronic): 22 October 2018
                Publication date Collection: October 2018
                Volume: 23
                Issue: 10
                Electronic Location Identifier: 2728
                Affiliations
                [1 ]School of Computer and Information Engineering, Harbin University of Commerce, Harbin 150028, China
                [2 ]Life sciences and Environmental Sciences Development Center, Harbin University of Commerce, Harbin 150010, China; w1993817m@ 123456163.com (M.W.); 13212921382@ 123456163.com (L.Z.)
                [3 ]School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China; chunyu@ 123456hit.edu.cn
                Author notes
                [* ]Correspondence: hanke@ 123456hrbcu.edu.cn ; Tel.: +86-138-3611-6965
                Author information
                https://orcid.org/0000-0003-0279-4150
                Article
                Publisher ID: molecules-23-02728
                DOI: 10.3390/molecules23102728
                PMC ID: 6222746
                PubMed ID: 30360419
                SO-VID: 8b44884e-4fb9-476c-b0d7-152d31cdd794
                Copyright © © 2018 by the authors.
                License:

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 09 September 2018
                Date accepted : 20 October 2018
                Categories
                Subject: Review

                Keywords: bioinformatics,identification of chinese herbal medicines,biochip technology,dna barcoding technology
                Data availability:
                Keywords: bioinformatics, identification of chinese herbal medicines, biochip technology, dna barcoding technology

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