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DNA Barcoding for Herbal Medicines
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DNA Barcoding for Herbal Medicines

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 43387

Special Issue Editors

Prof. Dr. Adrian Slater

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Guest Editor
Biomolecular Technology Group, Leicester School of Allied Health Science, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK
Interests: plant molecular biology and biotechnology; DNA barcoding of medicinal plants; herbal medicine authentication
Dr. Tiziana Sgamma

E-Mail Website
Guest Editor
Biomolecular Technology Group, Leicester School of Allied Health Science, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK
Interests: herbal medicines; DNA barcoding; authentication; industrial quality assurance
Dr. Caroline Howard

E-Mail Website
Guest Editor
Biomolecular Technology Group, Leicester School of Allied Health Science, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK
Interests: regulatory standards; monograph elaboration; industrial and scientific quality control and quality assurance; herbal drugs; international pharmacopoeias

Special Issue Information

The potential for applying DNA barcoding to the authentication of herbal medicines was recognised at an early stage in the development of DNA barcodes for plant identification. Since then, there has been a steady stream of publications demonstrating the feasibility of using various barcode regions to distinguish a wide range of medicinal plants from related species and potential adulterant plants. Following the recommendations that the primary plant DNA barcodes should be the plastid rbcL and matK genes, along with the psbA-trnH intergenic spacer region, there have been many studies published demonstrating the virtues of one or another barcode for discriminating between members of a particular group of plants. There have also been convincing arguments made to reconsider other plant barcode regions for herbal medicine authentication, notably the nuclear ribosomal internal transcribed spacer (ITS) region, and particularly the ITS2 sub-region. 

In the meantime, the translation of these academic studies into useful quality control assays and standards by the herbal medicine industry and regulatory institutions has been relatively slow. The authentication of the plant raw materials (herbal drugs) used for production of herbal medicines has traditionally used morphological and chemical testing to identify the correct plant species and to detect adulterants. The industry has proved resistant to claims that DNA testing could replace these, particularly following the (mis)use of DNA barcoding by the New York Attorney General to test commercial products.   

One aim of this Special Issue on DNA barcoding for herbal medicines is to capture these recent advances in the translation of academic DNA barcoding studies into industrial QC protocols and regulatory standards. We therefore invite research and review papers from industrial laboratories describing “real-life” DNA testing of raw materials and the impact this has had on quality control procedures. We are also interested in reporting the introduction of DNA standards into regulations and pharmacopoeial monographs in different parts of the world and whether there are any opportunities for standardisation of methods and reference barcode sequences. Research papers on the application of new technologies to DNA authentication will also be welcomed, from next-generation sequencing (and beyond) metabarcoding studies to the application of “in-the-field” methods, as well as methods targeting “mini-barcodes”. Conventional DNA barcoding papers that focus on practical issues in discriminating medicinal plants from known adulterants will also be accepted.

Prof. Adrian Slater
Dr. Tiziana Sgamma
Dr. Caroline Howard
Guest Editors

Manuscript Submission Information

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Keywords

  • DNA barcode
  • herbal medicine
  • authentication
  • rbcL
  • matK
  • psbA- trnH
  • ITS2
  • RNA secondary structure
  • metabarcoding

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Published Papers (9 papers)

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Research

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12 pages, 2241 KiB  
Article
The Cultural and Commercial Value of Tulsi (Ocimum tenuiflorum L.): Multidisciplinary Approaches Focusing on Species Authentication
by Sukvinder Kaur Bhamra, Michael Heinrich, Mark R. D. Johnson, Caroline Howard and Adrian Slater
Plants 2022, 11(22), 3160; https://doi.org/10.3390/plants11223160 - 18 Nov 2022
Cited by 12 | Viewed by 8641
Abstract
Tulsi (Holy basil, Ocimum tenuiflorum L., Lamiaceae), native to Asia, has become globalised as the cultural, cosmetic, and medicinal uses of the herb have been popularised. DNA barcoding, a molecular technique used to identify species based on short regions of DNA, can discriminate [...] Read more.
Tulsi (Holy basil, Ocimum tenuiflorum L., Lamiaceae), native to Asia, has become globalised as the cultural, cosmetic, and medicinal uses of the herb have been popularised. DNA barcoding, a molecular technique used to identify species based on short regions of DNA, can discriminate between different species and identify contaminants and adulterants. This study aimed to explore the values associated with Tulsi in the United Kingdom (UK) and authenticate samples using DNA barcoding. A mixed methods approach was used, incorporating social research (i.e., structured interviews) and DNA barcoding of Ocimum samples using the ITS and trnH-psbA barcode regions. Interviews revealed the cultural significance of Tulsi: including origins, knowledge exchange, religious connotations, and medicinal uses. With migration, sharing of plants and seeds has been seen as Tulsi plants are widely grown in South Asian (SA) households across the UK. Vouchered Ocimum specimens (n = 33) were obtained to create reference DNA barcodes which were not available in databases. A potential species substitution of O. gratissimum instead of O. tenuiflorum amongst SA participants was uncovered. Commercial samples (n = 47) were difficult to authenticate, potentially due to DNA degradation during manufacturing processes. This study highlights the cultural significance of Tulsi, despite a potential species substitution, the plant holds a prestigious place amongst SA families in the UK. DNA barcoding was a reliable way to authenticate Ocimum species. Full article
(This article belongs to the Special Issue DNA Barcoding for Herbal Medicines)
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11 pages, 463 KiB  
Article
Enhancing Testing Laboratory Engagement in Plant DNA Barcoding through a Routine Workflow—A Case Study on Chinese Materia Medica (CMM)
by Wai-Yan Ha, Ka-Lok Wong, Wai-Yee Ma, Yuk-Yu Lau and Wing-Han Chan
Plants 2022, 11(10), 1317; https://doi.org/10.3390/plants11101317 - 16 May 2022
Cited by 1 | Viewed by 2152
Abstract
Introduction of DNA standards into Pharmacopoeia in different parts of the world enables identification of herbal materials in a complementary manner. However, little has been discussed about the quality requirements for a testing laboratory to implement DNA barcoding methods for herbal materials, which [...] Read more.
Introduction of DNA standards into Pharmacopoeia in different parts of the world enables identification of herbal materials in a complementary manner. However, little has been discussed about the quality requirements for a testing laboratory to implement DNA barcoding methods for herbal materials, which has limited the test method to be developed as a routine service. To encourage the engagement of testing laboratory in application of DNA barcode, a practical workflow including the components of analytical run and the corresponding quality control plan was suggested and employed to address a real-life challenge faced by the differentiation of plant-derived Chinese Materia Medica (CMM), Herba Potentillae Chinensis (Wei ling Cai), Herba Potentillae Discoloris (Fan Bai Cai), Radix Pulsatillae (Bai Tou Weng), and Radix Arnebiae (Zi Cao), which share similar morphological characteristics and multiple species involved. The ITS2 barcode results indicated that there are significant differences among the four CMM, together with quality control plan data to ensure the measurement traceability and validity of test results. Full article
(This article belongs to the Special Issue DNA Barcoding for Herbal Medicines)
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13 pages, 988 KiB  
Article
Assessment of ITS2 Region Relevance for Taxa Discrimination and Phylogenetic Inference among Pinaceae
by Joanna Sokołowska, Hanna Fuchs and Konrad Celiński
Plants 2022, 11(8), 1078; https://doi.org/10.3390/plants11081078 - 15 Apr 2022
Cited by 9 | Viewed by 3352
Abstract
The internal transcribed spacer 2 (ITS2) is one of the best-known universal DNA barcode regions. This short nuclear region is commonly used not only to discriminate taxa, but also to reconstruct phylogenetic relationships. However, the efficiency of using ITS2 in these applications depends [...] Read more.
The internal transcribed spacer 2 (ITS2) is one of the best-known universal DNA barcode regions. This short nuclear region is commonly used not only to discriminate taxa, but also to reconstruct phylogenetic relationships. However, the efficiency of using ITS2 in these applications depends on many factors, including the family under study. Pinaceae represents the largest family of extant gymnosperms, with many species of great ecological, economic, and medical importance. Moreover, many members of this family are representatives of rare, protected, or endangered species. A simple method for the identification of Pinaceae species based on DNA is necessary for their effective protection, authentication of products containing Pinaceae representatives, or phylogenetic inference. In this study, for the first time, we conducted a comprehensive study summarizing the legitimacy of using the ITS2 region for these purposes. A total of 368 sequences representing 71 closely and distantly related taxa of the seven genera and three subfamilies of Pinaceae were characterized for genetic variability and divergence. Intra- and interspecies distances of ITS2 sequences as well as rates of sequence identification and taxa discrimination among Pinaceae at various taxonomic levels, i.e., the species complex, genus, subfamily, and family, were also determined. Our study provides a critical assessment of the suitability of the ITS2 nuclear DNA region for taxa discrimination among Pinaceae. The obtained results clearly show that its usefulness for this purpose is limited. Full article
(This article belongs to the Special Issue DNA Barcoding for Herbal Medicines)
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10 pages, 623 KiB  
Article
DNA Barcoding of Two Thymelaeaceae Species: Daphne mucronata Royle and Thymelaea hirsuta (L.) Endl
by Almuthanna K. Alkaraki, Maisam A. Aldmoor, Jamil N. Lahham and Mohammed Awad
Plants 2021, 10(10), 2199; https://doi.org/10.3390/plants10102199 - 16 Oct 2021
Cited by 7 | Viewed by 2862
Abstract
Daphne mucronata Royle and Thymelaea hirsuta (L.) Endl both belong to the Thymelaeaceae family. Both species are used traditionally to treat several diseases along with various daily applications by Jordanian Bedouins. Traditionally, those species are identified through personal proficiency, which could be misleading [...] Read more.
Daphne mucronata Royle and Thymelaea hirsuta (L.) Endl both belong to the Thymelaeaceae family. Both species are used traditionally to treat several diseases along with various daily applications by Jordanian Bedouins. Traditionally, those species are identified through personal proficiency, which could be misleading due to human errors or lack of expertise. This study aims to investigate an effective DNA barcoding method to identify and characterize Daphne mucronata Royle and Thymelaea hirsuta plant species at the molecular level. Daphne mucronata Royle and Thymelaea hirsuta were collected from the ancient city of Petra in the Southern part of Jordan. Sequences of candidate DNA barcodes were amplified (rbcL, matK, and rpoC1), sequenced, and aligned to the blastn database. Moreover, the obtained sequences were compared with available sequences of related species at the GenBank database. Our results showed that DNA barcoding successfully identifies the two plant species using any of chloroplast genes (rbcL, matK, or rpoC1). The results emphasize the ability of DNA barcoding for identifying and characterizing different plant species through the recruitment of different barcode loci in molecular identification. Full article
(This article belongs to the Special Issue DNA Barcoding for Herbal Medicines)
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12 pages, 2601 KiB  
Article
Licorice Germplasm Resources Identification Using DNA Barcodes Inner-Variants
by Qianwen Liu, Shuai Guo, Xiasheng Zheng, Xiaofeng Shen, Tianyi Zhang, Baosheng Liao, Wenrui He, Haoyu Hu, Ruiyang Cheng and Jiang Xu
Plants 2021, 10(10), 2036; https://doi.org/10.3390/plants10102036 - 28 Sep 2021
Cited by 12 | Viewed by 2648
Abstract
Based on the gradual transformation from wild growth to artificial cultivation, the accurate authentication of licorice seeds contributes to the first committed step of its quality control and is pivotal to ensure the clinical efficacy of licorice. However, it is still challenging to [...] Read more.
Based on the gradual transformation from wild growth to artificial cultivation, the accurate authentication of licorice seeds contributes to the first committed step of its quality control and is pivotal to ensure the clinical efficacy of licorice. However, it is still challenging to obtain genetically stable licorice germplasm resources due to the multi-source, multi-heterozygous, polyploid, and hybrid characteristics of licorice seeds. Here, a new method for determining the heterozygosity of licorice seed mixture, based on the various sites, and finding the composition characteristics of licorice seed is preliminarily designed and proposed. Namely, high-throughput full-length multiple DNA barcodes(HFMD), based on ITS multi-copy variation exist, the full-length amplicons of ITS2, psbA-trnH and ITS are directly sequenced by rDNA through the next-generation sequence(NGS) and single-molecule real-time (SMRT) technologies. By comparing the three sequencing methods, our results proved that SMRT sequencing successfully identified the complete gradients of complex mixed samples with the best performance. Meanwhile, HFMD is a brilliant and feasible method for evaluating the heterozygosity of licorice seeds. It shows a perfect interpretation of DNA barcoding and can be applied in multi-base multi-heterozygous and polyploid species. Full article
(This article belongs to the Special Issue DNA Barcoding for Herbal Medicines)
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14 pages, 21401 KiB  
Article
DNA Barcode Authentication of Devil’s Claw Herbal Dietary Supplements
by Genelle L. Diaz-Silveira, Joan Deutsch and Damon P. Little
Plants 2021, 10(10), 2005; https://doi.org/10.3390/plants10102005 - 24 Sep 2021
Cited by 4 | Viewed by 3084
Abstract
Devil’s claw is the vernacular name for a genus of medicinal plants that occur in the Kalahari Desert and Namibia Steppes. The genus comprises two distinct species: Harpagophytum procumbens and H. zeyheri. Although the European pharmacopeia considers the species interchangeable, recent studies [...] Read more.
Devil’s claw is the vernacular name for a genus of medicinal plants that occur in the Kalahari Desert and Namibia Steppes. The genus comprises two distinct species: Harpagophytum procumbens and H. zeyheri. Although the European pharmacopeia considers the species interchangeable, recent studies have demonstrated that H. procumbens and H. zeyheri are chemically distinct and should not be treated as the same species. Further, the sale of H. zeyheri as an herbal supplement is not legal in the United States. Four markers were tested for their ability to distinguish H. procumbens from H. zeyheri: rbcL, matK, nrITS2, and psbA-trnH. Of these, only psbA-trnH was successful. A novel DNA mini-barcode assay that produces a 178-base amplicon in Harpagophytum (specificity = 1.00 [95% confidence interval = 0.80–1.00]; sensitivity = 1.00 [95% confidence interval = 0.75–1.00]) was used to estimate mislabeling frequency in a sample of 23 devil’s claw supplements purchased in the United States. PCR amplification failed in 13% of cases. Among the 20 fully-analyzable supplements: H. procumbens was not detected in 75%; 25% contained both H. procumbens and H. zeyheri; none contained only H. procumbens. We recommend this novel mini-barcode region as a standard method of quality control in the manufacture of devil’s claw supplements. Full article
(This article belongs to the Special Issue DNA Barcoding for Herbal Medicines)
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17 pages, 3405 KiB  
Article
Integrated Approach for Species Identification and Quality Analysis for Labisia pumila Using DNA Barcoding and HPLC
by Auni Aqilah Ahmad Tarmizi, Alina Wagiran, Faezah Mohd Salleh, Lee Suan Chua, Farah Izana Abdullah, Rosnani Hasham and Suraiya Binte Mostafiz
Plants 2021, 10(4), 717; https://doi.org/10.3390/plants10040717 - 7 Apr 2021
Cited by 9 | Viewed by 3888
Abstract
Labisia pumila is a precious herb in Southeast Asia that is traditionally used as a health supplement and has been extensively commercialized due to its claimed therapeutic properties in boosting a healthy female reproductive system. Indigenous people used these plants by boiling the [...] Read more.
Labisia pumila is a precious herb in Southeast Asia that is traditionally used as a health supplement and has been extensively commercialized due to its claimed therapeutic properties in boosting a healthy female reproductive system. Indigenous people used these plants by boiling the leaves; however, in recent years it has been marketed as powdered or capsuled products. Accordingly, accuracy in determination of the authenticity of these modern herbal products has faced great challenges. Lack of authenticity is a public health risk because incorrectly used herbal species can cause adverse effects. Hence, any measures that may aid product authentication would be beneficial. Given the widespread use of Labisia herbal products, the current study focuses on authenticity testing via an integral approach of DNA barcoding and qualitative analysis using HPLC. This study successfully generated DNA reference barcodes (ITS2 and rbcL) for L. pumila var. alata and pumila. The DNA barcode that was generated was then used to identify species of Labisia pumila in herbal medicinal products, while HPLC was utilized to determine their quality. The findings through the synergistic approach (DNA barcode and HPLC) implemented in this study indicate the importance of both methods in providing the strong evidence required for the identification of true species and to examine the authenticity of such herbal medicinal products. Full article
(This article belongs to the Special Issue DNA Barcoding for Herbal Medicines)
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12 pages, 2521 KiB  
Article
Differentiation of Hedyotis diffusa and Common Adulterants Based on Chloroplast Genome Sequencing and DNA Barcoding Markers
by Mavis Hong-Yu Yik, Bobby Lim-Ho Kong, Tin-Yan Siu, David Tai-Wai Lau, Hui Cao and Pang-Chui Shaw
Plants 2021, 10(1), 161; https://doi.org/10.3390/plants10010161 - 15 Jan 2021
Cited by 21 | Viewed by 3728
Abstract
Chinese herbal tea, also known as Liang Cha or cooling beverage, is popular in South China. It is regarded as a quick-fix remedy to relieve minor health problems. Hedyotis diffusa Willd. (colloquially Baihuasheshecao) is a common ingredient of cooling beverages. H. diffusa is [...] Read more.
Chinese herbal tea, also known as Liang Cha or cooling beverage, is popular in South China. It is regarded as a quick-fix remedy to relieve minor health problems. Hedyotis diffusa Willd. (colloquially Baihuasheshecao) is a common ingredient of cooling beverages. H. diffusa is also used to treat cancer and bacterial infections. Owing to the high demand for H. diffusa, two common adulterants, Hedyotis brachypoda (DC.) Sivar and Biju (colloquially Nidingjingcao) and Hedyotis corymbosa (L.) Lam. (colloquially Shuixiancao), are commonly encountered in the market. Owing to the close similarity of their morphological characteristics, it is difficult to differentiate them. Here, we sequenced the complete chloroplast genomes of the three species of Hedyotis using next-generation sequencing (NGS). By comparing the complete chloroplast genomes, we found that they are closely related in the subfamily Rubioideae. We also discovered that there are significant differences in the number and repeating motifs of microsatellites and complex repeats and revealed three divergent hotspots, rps16-trnQ intergenic spacer, ndhD and ycf1. By using these species-specific sequences, we propose new DNA barcoding markers for the authentication of H. diffusa and its two common adulterants. Full article
(This article belongs to the Special Issue DNA Barcoding for Herbal Medicines)
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Review

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26 pages, 2875 KiB  
Review
Challenges in Medicinal and Aromatic Plants DNA Barcoding—Lessons from the Lamiaceae
by Nazia Nazar, Caroline Howard, Adrian Slater and Tiziana Sgamma
Plants 2022, 11(1), 137; https://doi.org/10.3390/plants11010137 - 5 Jan 2022
Cited by 35 | Viewed by 10132
Abstract
The potential value of DNA barcoding for the identification of medicinal plants and authentication of traded plant materials has been widely recognized; however, a number of challenges remain before DNA methods are fully accepted as an essential quality control method by industry and [...] Read more.
The potential value of DNA barcoding for the identification of medicinal plants and authentication of traded plant materials has been widely recognized; however, a number of challenges remain before DNA methods are fully accepted as an essential quality control method by industry and regulatory authorities. The successes and limitations of conventional DNA barcoding are considered in relation to important members of the Lamiaceae. The mint family (Lamiaceae) contains over one thousand species recorded as having a medicinal use, with many more exploited in food and cosmetics for their aromatic properties. The family is characterized by a diversity of secondary products, most notably the essential oils (EOs) produced in external glandular structures on the aerial parts of the plant that typify well-known plants of the basil (Ocimum), lavender (Lavandula), mint (Mentha), thyme (Thymus), sage (Salvia) and related genera. This complex, species-rich family includes widely cultivated commercial hybrids and endangered wild-harvested traditional medicines, and examples of potential toxic adulterants within the family are explored in detail. The opportunities provided by next generation sequencing technologies to whole plastome barcoding and nuclear genome sequencing are also discussed with relevant examples. Full article
(This article belongs to the Special Issue DNA Barcoding for Herbal Medicines)
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