DNA Barcoding in Medicinal Plant Authentication: Principles, Applications and Future Perspectives

Plant medicinal provides therapy or medicine for the prevention and treatment of diseases. Many medicinal plants are used as source of therapy in modern medicine. However, correct identification of many medicinal plants is often difficult due to apparent morphology, extensive habitats and increasing adulteration in herbal products. Traditional taxonomy-based identification method is found sometimes unfruitful, especially when plant material is processed or chopped. Molecular approaches, especially DNA barcodes using small portions of plant DNA, have been proposed as efficient and reliable techniques for identification and authenticity assessment of medicinal plant species. This review discusses the principles and applications of DNA barcoding technology for the identification and authentication of medicinal plants. We mainly focus on three commonly used barcode regions: rbcL and matK from chloroplast DNA, and the nuclear internal transcribed spacer (ITS). We describe the workflow of DNA extraction, PCR amplification and sequencing, and sequence analysis using bioinformatics tools. Case studies demonstrate the role of the DNA barcodes in detecting adulterants, in distinguishing closely related species and in quality control in the herbal medicine industry.

DNA barcoding; Medicinal plants; rbcL; matK

1. Abdi, G., Singh, S., Selvakumar, S., Dhar, S. K., Mudgal, G., Swaminathan, P., Jain, M., & Tarighat, M. A. (2024). DNA barcoding and its applications. In Advances in genomics (pp. 91–117). [Google Scholar] [Crossref]

2. Agidew, M. G. (2022). Phytochemical analysis of some selected traditional medicinal plants in Ethiopia. Bulletin of the National Research Centre, 46(1), 87. [Google Scholar] [Crossref]

3. Al-Khayri, J. M., Banadka, A., Rashmi, R., Nagella, P., Alessa, F. M., & Almaghasla, M. I. (2023). Cadmium toxicity in medicinal plants: An overview of the tolerance strategies, biotechnological and omics approaches to alleviate metal stress. Frontiers in Plant Science, 14, 1132827. [Google Scholar] [Crossref]

4. Antil, S., Abraham, J. S., Sripoorna, S., Maurya, S., Dagar, J., Makhija, S., Bhagat, P., Gupta, R., Sood, U., Lal, R., & Toteja, R. (2023). DNA barcoding, an effective tool for species identification: A review. Molecular Biology Reports, 50(1), 761–775. [Google Scholar] [Crossref]

5. Asiminicesei, D.-M., Fertu, D. I., & Gavrilescu, M. (2024). Impact of heavy metal pollution in the environment on the metabolic profile of medicinal plants and their therapeutic potential. Plants, 13(6), 913. [Google Scholar] [Crossref]

6. Azadnia, R., Al-Amidi, M. M., Mohammadi, H., Cifci, M. A., Daryab, A., & Cavallo, E. (2022). An AI based approach for medicinal plant identification using deep CNN based on global average pooling. Agronomy, 12(11), 2723. [Google Scholar] [Crossref]

7. Barcaccia, G., Lucchin, M., & Cassandro, M. (2016). DNA barcoding as a molecular tool to track down mislabeling and food piracy. Diversity, 8(1), 2. [Google Scholar] [Crossref]

8. CBOL Plant Working Group. (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences, 106(31), 12794–12797. [Google Scholar] [Crossref]

9. Chen, S., Yao, H., Han, J., Liu, C., Song, J., Shi, L., Zhu, Y., Ma, X., Gao, T., Pang, X., Luo, K., Li, Y., Li, X., Jia, X., Lin, Y., & Leon, C. (2010). Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS ONE, 5(1), e8613. [Google Scholar] [Crossref]

10. Coghlan, M. L., Haile, J., Houston, J., Murray, D. C., White, N. E., Moolhuijzen, P., Bellgard, M. I., & Bunce, M. (2012). Deep sequencing of plant and animal DNA contained within traditional Chinese medicines reveals legality issues and health safety concerns. PLoS Genetics, 8(4), e1002657. [Google Scholar] [Crossref]

11. Davis, C. C., & Choisy, P. (2024). Medicinal plants meet modern biodiversity science. Current Biology, 34(4), R158–R173. [Google Scholar] [Crossref]

12. de Boer, H. J., Ichim, M. C., & Newmaster, S. G. (2015). DNA barcoding and pharmacovigilance of herbal medicines. Drug Safety, 38(7), 611–620. [Google Scholar] [Crossref]

13. Duta-Cornescu, G., Constantin, N., Pojoga, D.-M., Nicuta, D., & Simon-Gruita, A. (2023). Somaclonal variation—Advantage or disadvantage in micropropagation of the medicinal plants. International Journal of Molecular Sciences, 24(1), 838. [Google Scholar] [Crossref]

14. Gaskin, J. F., Bon, M. C., Cock, M. J. W., Cristofaro, M., De Biase, A., De Clerck-Floate, R., Ellison, C. A., Hinz, H. L., Julien, M. H., & Sforza, R. F. H. (2011). Applying molecular-based approaches to classical biological control of weeds. Biological Control, 58(1), 1–21. [Google Scholar] [Crossref]

15. Galimberti, A., De Mattia, F., Losa, A., Bruni, I., Federici, S., Casiraghi, M., Martellos, S., & Labra, M. (2013). DNA barcoding as a new tool for food traceability. Food Research International, 50(1), 55–63. [Google Scholar] [Crossref]

16. Hajibabaei, M., Singer, G. A. C., Hebert, P. D. N., & Hickey, D. A. (2007). DNA barcoding: How it complements taxonomy, molecular phylogenetics and population genetics. Trends in Genetics, 23(4), 167–172. [Google Scholar] [Crossref]

17. Hebert, P. D. N., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences, 270(1512), 313–321. [Google Scholar] [Crossref]

18. Hollingsworth, P. M., Forrest, L. L., Spouge, J. L., Hajibabaei, M., Ratnasingham, S., van der Bank, M., et al. (2011). A DNA barcode for land plants. Proceedings of the National Academy of Sciences, 108(31), 12794–12797. [Google Scholar] [Crossref]

19. Ichim, M. C., de Boer, H. J., & van Andel, T. R. (2020). DNA barcoding in herbal product authentication: Combining molecular and chemical approaches. Frontiers in Pharmacology, 11, 1–10. [Google Scholar] [Crossref]

20. Ivanova, N. V., Kuzmina, M. L., Braukmann, T. W. A., Borisenko, A. V., & Zakharov, E. V. (2016). Authentication of herbal supplements using DNA barcoding and next-generation sequencing. Scientific Reports, 6, 1–11. [Google Scholar] [Crossref]

21. Kool, A., de Boer, H. J., Krüger, Å., Rydberg, A., Abbad, A., Björk, L., & Martin, G. (2012). Molecular identification of commercialized medicinal plants in southern Morocco. PLoS ONE, 7(6), e39459. [Google Scholar] [Crossref]

22. Kress, W. J., Wurdack, K. J., Zimmer, E. A., Weigt, L. A., & Janzen, D. H. (2005). Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences, 102(23), 8369–8374. [Google Scholar] [Crossref]

23. Kumar, S., Singh, B., & Sharma, M. (2022). DNA barcoding in medicinal plant identification: A review. Journal of Applied Biology & Biotechnology, 10(2), 1–10. [Google Scholar] [Crossref]

24. Laldingliani, T. B. C., Thangjam, N. M., Zomuanawma, R., Bawitlung, L., Pal, A., & Kumar, A. (2022). Ethnomedicinal study of medicinal plants used by Mizo tribes in Champhai district of Mizoram, India. Journal of Ethnobiology and Ethnomedicine, 18(1), 22. [Google Scholar] [Crossref]

25. Li, X., Yang, Y., Henry, R. J., Rossetto, M., Wang, Y., & Chen, S. (2020). Plant DNA barcoding: From gene to genome. Biological Reviews, 95(1), 1–19. [Google Scholar] [Crossref]

26. Liu, J., Yan, H., Newmaster, S. G., Pei, N., Ragupathy, S., & Ge, X. (2018). The use of DNA barcoding as a tool for the authentication of medicinal plants in traditional Chinese medicine. PLoS ONE, 13(2), e0192557. [Google Scholar] [Crossref]

27. Meusnier, I., Singer, G. A. C., Landry, J. F., Hickey, D. A., Hebert, P. D. N., & Hajibabaei, M. (2008). A universal DNA mini-barcode for biodiversity analysis. BMC Genomics, 9, 214. [Google Scholar] [Crossref]

28. Mishra, P., Kumar, A., Nagireddy, A., Mani, D. N., Shukla, A. K., Tiwari, R., & Sundaresan, V. (2016). DNA barcoding: An efficient tool to overcome authentication challenges in the herbal market. Plant Biotechnology Journal, 14(1), 8–21. [Google Scholar] [Crossref]

29. Nabi, M., Saghir, K., Ullah, F., Hussain, A., & Safeer, A. (2026). Challenges in botanical extract standardization: Adulteration, misidentification, and supply chain variability. In Botanical extracts (1st ed., pp. 1–12). [Google Scholar] [Crossref]

30. Newmaster, S. G., Grguric, M., Shanmughanandhan, D., Ramalingam, S., & Ragupathy, S. (2013). DNA barcoding detects contamination and substitution in North American herbal products. BMC Medicine, 11, 222. [Google Scholar] [Crossref]

31. Nwozo, O. S., Effiong, E. M., Aja, P. M., & Awuchi, C. G. (2023). Antioxidant, phytochemical, and therapeutic properties of medicinal plants: A review. International Journal of Food Properties, 26(1), 359–388. [Google Scholar] [Crossref]

32. Parveen, I., Gafner, S., Techen, N., Murch, S. J., & Khan, I. A. (2016). DNA barcoding for the identification of botanicals in herbal medicine and dietary supplements. Critical Reviews in Biotechnology, 36(5), 1–12. [Google Scholar] [Crossref]

33. Pomerantz, A., Peñafiel, N., Arteaga, A., Bustamante, L., Pichardo, F., Coloma, L. A., et al. (2018). Real-time DNA barcoding in a rainforest using nanopore sequencing. GigaScience, 7(4), giy033. [Google Scholar] [Crossref]

34. Raclariu, A. C., Heinrich, M., Ichim, M. C., & de Boer, H. (2018). Benefits and limitations of DNA barcoding and metabarcoding in herbal product authentication. Phytochemical Analysis, 29(2), 123–128. [Google Scholar] [Crossref]

35. Raclariu, A. C., Ţebrencu, C. E., Ichim, M. C., Ciupercă, O. T., Brysting, A. K., & de Boer, H. (2018). DNA barcoding reveals illegal trade of protected plant species. Frontiers in Plant Science, 9, 1–12. [Google Scholar] [Crossref]

36. Ratnasingham, S., & Hebert, P. D. N. (2007). BOLD: The Barcode of Life Data System. Molecular Ecology Notes, 7(3), 355–364. [Google Scholar] [Crossref]

37. Seberg, O., & Petersen, G. (2009). How many loci does it take to DNA barcode a crocus? PLoS ONE, 4(2), e4598. [Google Scholar] [Crossref]

38. Seethapathy, G. S., Ganesh, D., Santhosh Kumar, J. U., Senthilkumar, U., Newmaster, S. G., Ragupathy, S., & Ravikanth, G. (2015). Assessing product adulteration using DNA barcoding. Genome, 58(10), 411–420. [Google Scholar] [Crossref]

39. Sgamma, T., Lockie-Williams, C., Kreuzer, M., Williams, S., Scheyhing, U., Koch, E., Slater, A., & Howard, C. (2017). DNA barcoding for industrial quality assurance. Planta Medica, 83(14–15), 1117–1129. [Google Scholar] [Crossref]

40. Sharma, P., Joshi, N., & Tripathi, R. (2021). Authentication of medicinal plants using molecular markers. Plant Gene, 26, 100281. [Google Scholar] [Crossref]

41. Sucher, N. J., & Carles, M. C. (2008). Genome-based approaches to the authentication of medicinal plants. Planta Medica, 74(6), 603–623. [Google Scholar] [Crossref]

42. Taberlet, P., Bonin, A., Zinger, L., & Coissac, E. (2018). Environmental DNA: For biodiversity research and monitoring. Oxford University Press. [Google Scholar] [Crossref]

43. Travadi, T., Sharma, S., Pandit, R., Joshi, C., Joshi, M., & Joshi, P. (2023). Advancing herbal product authentication. Journal of Applied Biology & Biotechnology, 11(5), 1–12. [Google Scholar] [Crossref]

44. Urumarudappa, S. K. J., et al. (2025). Authentication methods for phytochemicals. Journal of Dietary Supplements, 22(5), 680–721. [Google Scholar] [Crossref]

45. von Cräutlein, M., Korpelainen, H., Pietiläinen, M., & Rikkinen, J. (2011). DNA barcoding: A tool for improved taxon identification. Biodiversity and Conservation, 20(2), 373–389. [Google Scholar] [Crossref]

46. World Health Organization. (2013). WHO traditional medicine strategy 2014–2023. World Health Organization. [Google Scholar] [Crossref]

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