Journal of Natural Medicines

, Volume 67, Issue 2, pp 296–302 | Cite as

Identification of cortex herbs using the DNA barcode nrITS2

Original Paper


To discriminate the cortex herbs of Chinese Pharmacopoeia, the second internal transcribed spacer (ITS2) of ribosomal DNA of 51 samples belonging to 19 kinds of cortex herbs were analyzed in this paper. Sequence assembly was performed using the CodonCode Aligner. Phylogenetic study was performed using the molecular evolutionary genetics analysis (MEGA) 4.0 software in accordance with the Kimura 2-Parameter (K2P) model. Phylogenetic tree was constructed using the neighbor-joining (NJ) method. We found that the ITS2 sequences of the studied samples ranged from 207 to 256 bp in length and easy to be amplified. The intraspecific genetic distance of the cortex herbs was between 0 and 0.073, which was lower than their interspecific genetic distance (mean, 0.868; minimum, 0.101). In the cluster dendrogram, all the studied medicinal materials with several samples, were monophyletic. It is concluded that ITS2 barcode is suitable for the identification of cortex herbs of Chinese Pharmacopoeia, and it will play an important role in the field of identification of traditional Chinese medicine (TCM).


Cortex herbs DNA barcode ITS2 Traditional Chinese medicine 


  1. 1.
    Chinese Pharmacopoeia Committee of People’s Republic of China (2010) The Pharmacopoeia of the People’s Republic of China: I. Chemical Industry Press, Beijing (in Chinese)Google Scholar
  2. 2.
    Mao MR (1998) The empirical discrimination of 13 cortex herbs. Lishizhen Med Mater Med Res 9:236–237 (in Chinese)Google Scholar
  3. 3.
    Wang XF (2003) Studies on the microstructure of cortex herbs. China J Chin Mat Med 28:924–926 (in Chinese)Google Scholar
  4. 4.
    Chen SL, Song JY, Yao H, Shi LC, Luo K, Han JP (2009) Strategy and key technique of identification of Chinese herbal medicine using DNA barcoding. Chin J Nat Med 7:322–327 (in Chinese)CrossRefGoogle Scholar
  5. 5.
    Chen SL, Yao H, Song JY, Li XW, Liu C, Lu JW (2007) Use of DNA barcoding to identify Chinese medicinal materials. World Sci Technol Mod Tradit Chin Med 9:7–12 (in Chinese)Google Scholar
  6. 6.
    Chen SL, Yao H, Han JP, Liu C, Song JY, Shi LC, Zhu YJ, Ma XY, Gao T, Pang XH, Luo K, Li Y, Li XW, Jia XC, Lin YL, Leon C (2010) Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One 5(1):e8613PubMedCrossRefGoogle Scholar
  7. 7.
    Luo K, Chen SL, Chen KL, Song JY, Yao H, Ma XY, Zhu YJ, Pang XH, Yu H, Li XW, Liu Z (2010) Assessment of candidate plant DNA barcodes using the Rutaceae family. Sci China Life Sci 53:701–708PubMedCrossRefGoogle Scholar
  8. 8.
    Zhu YJ, Chen SL, Yao H, Tan R, Song JY, Luo K, Lu J (2010) DNA barcoding the medicinal plants of the genus Paris. Acta Pharm Sin 45:376–382 (in Chinese)Google Scholar
  9. 9.
    Gao T, Yao H, Song JY, Liu C, Zhu YJ, Ma XY, Pang XH, Xu HX, Chen SL (2010) Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2. J Ethnopharmacol 130:116–121PubMedCrossRefGoogle Scholar
  10. 10.
    Pang XH, Song JY, Zhu YJ, Xu HX, Huang LF, Chen SL (2010) Applying plant DNA barcodes for Rosaceae species identification. Cladistics 26:1–6CrossRefGoogle Scholar
  11. 11.
    Yao H, Song JY, Liu C, Luo K, Han JP, Li Y, Pang XH, Xu HX, Zhu YJ, Xiao PG, Chen SL (2010) Use of ITS2 region as the universal DNA barcode for plants and animals. PLoS One 5:e13102PubMedCrossRefGoogle Scholar
  12. 12.
    Gao T, Yao H, Song JY, Zhu YJ, Liu C, Chen SL (2010) Evaluating the Feasibility of Using Candidate DNA Barcodes in Discriminating Species of the Large Asteraceae Family. BMC Evol Biol 10:324PubMedGoogle Scholar
  13. 13.
    Pang XH, Song JY, Zhu YJ, Xie CX, Chen SL (2010) Using DNA barcoding to identify species within Euphorbiaceae. Planta Med 76:1784–1786PubMedCrossRefGoogle Scholar
  14. 14.
    Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102:8369–8374PubMedCrossRefGoogle Scholar
  15. 15.
    Eddy SR (1998) Profile hidden markov models. Bioinformatics 14:755–763PubMedCrossRefGoogle Scholar
  16. 16.
    Keller A, Schleicher T, Schultz J, Muller T, Dandekar T, Wolf M (2009) 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene 430:50–57PubMedCrossRefGoogle Scholar
  17. 17.
    Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673PubMedCrossRefGoogle Scholar
  18. 18.
    Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599PubMedCrossRefGoogle Scholar
  19. 19.
    Chase MW, Cowan RS, Hollingsworth PM, van den Berg C, Madrinan S, Petersen G, Seberg O, Jorgsensen T, Cameron KM, Carine M, Pedersen N, Hedderson TAJ, Conrad F, Salazar GA, Richardson JE, Hollingsworth ML, Barraclough TG, Kelly L, Wilkinson M (2007) A proposal for a standardized protocol to barcode all land plants. Taxon 56:295–299Google Scholar
  20. 20.
    Coleman AW (2007) Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucl Acids Res 35:3322–3329PubMedCrossRefGoogle Scholar
  21. 21.
    Jiang M, Yang J, Zhang C, Liu BY, Chan K, Cao HX, Lu AP (2010) Clinical studies with traditional Chinese medicine in the past decade and future research and development. Planta Med 76:2048–2064PubMedCrossRefGoogle Scholar

Copyright information

© The Japanese Society of Pharmacognosy and Springer 2012

Authors and Affiliations

  1. 1.The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of EducationInstitute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingPeople’s Republic of China
  2. 2.College of Chinese MedicineShandong University of Traditional Chinese MedicineJinanPeople’s Republic of China

Personalised recommendations