Skip to main content
SpringerLink
Log in

Identification of medicinal Dendrobium species by phylogenetic analyses using matK and rbcL sequences

  • Original Paper
  • Published:
Journal of Natural Medicines Aims and scope Submit manuscript

Abstract

Species identification of five Dendrobium plants was conducted using phylogenetic analysis and the validity of the method was verified. Some Dendrobium plants (Orchidaceae) have been used as herbal medicines but the difficulty in identifying their botanical origin by traditional methods prevented their full modern utilization. Based on the emerging field of molecular systematics as a powerful classification tool, a phylogenetic analysis was conducted using sequences of two plastid genes, the maturase-coding gene (matK) and the large subunit of ribulose 1,5-bisphosphate carboxylase-coding gene (rbcL), as DNA barcodes for species identification of Dendrobium plants. We investigated five medicinal Dendrobium species, Dendrobium fimbriatum, D. moniliforme, D. nobile, D. pulchellum, and D. tosaense. The phylogenetic trees constructed from matK data successfully distinguished each species from each other. On the other hand, rbcL, as a single-locus barcode, offered less species discriminating power than matK, possibly due to its being present with little variation. When results using matK sequences of D. officinale that was deposited in the DNA database were combined, D. officinale and D. tosaense showed a close genetic relationship, which brought us closer to resolving the question of their taxonomic identity. Identification of the plant source as well as the uniformity of the chemical components is critical for the quality control of herbal medicines and it is important that the processed materials be validated. The methods presented here could be applied to the analysis of processed Dendrobium plants and be a promising tool for the identification of botanical origins of crude drugs.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Wood HP (2006) The Dendrobiums. Gantner Verlag, Ruggel

    Google Scholar 

  2. Baker MLB, Charles O (1996) Orchid species culture: Dendrobium. Timber Press, Portland

    Google Scholar 

  3. Bao XS, Shun QS, Chen LZ (2001) The medicinal plants of Dendrobium (Shi-hu) in China. Shanghai Medicinal University Press and Fudan University Press, Shanghai (in Chinese)

    Google Scholar 

  4. Lin P, Bi Z, Xu H, Wang Z, Xu L (2003) Advances in studies on pharmacology of plants from Dendrobium Sw. Chin Tradit Herb Drugs 34(11)Suppl.:19–22 (in Chinese)

    Google Scholar 

  5. Chinese Pharmacopoeia Committee of People’s Republic of China (ed) (2005) The Pharmacopoeia of the People’s Republic of China: I. Chemical Industry Press, Beijing (in Chinese)

    Google Scholar 

  6. Tsi Z, Chen S, Luo Y, Zhu G (eds) (1999) Flora, Reipublicae Popularis Sinicae. Angiospermae, Monocotyledoneae, Orchidaceae (3), Tomus 19. Science Press, Beijing (in Chinese)

    Google Scholar 

  7. Institute of Botany, Academy of Science (ed) (1976) Iconographia Cormophytorum Sinicorum Tomus V. Science Press, Beijing (in Chinese)

    Google Scholar 

  8. Hilu K, Liang H (1997) The matK gene: sequence variation and application in plant systematics. Am J Bot 84:830–839

    Article  CAS  Google Scholar 

  9. Wilson CA (2004) Phylogeny of Iris based on chloroplast matK gene and trnK intron sequence data. Mol Phylogenet Evol 33:402–412

    Article  CAS  PubMed  Google Scholar 

  10. Kress WJ, Erickson DL (2007) A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE 2:e508

    Article  PubMed  Google Scholar 

  11. Hasebe M, Omori T, Nakazawa M, Sano T, Kato M, Iwatsuki K (1994) rbcL gene sequences provide evidence for the evolutionary lineages of leptosporangiate ferns. Proc Natl Acad Sci USA 91:5730–5734

    Article  CAS  PubMed  Google Scholar 

  12. Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, Husband BC, Percy DM, Hajibabaei M, Barrett SCH (2008) Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. PLoS ONE 3:e2802

    Article  PubMed  Google Scholar 

  13. Steven GN, Subramanyam R (2009) Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae). Mol Ecol Res 9(Suppl. 1):172–180

    Article  Google Scholar 

  14. Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V (2008) DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci USA 105:2923–2928

    Article  CAS  PubMed  Google Scholar 

  15. CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106:12794–12797

    Article  Google Scholar 

  16. Hebert PD, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc Biol Sci 270:313–321

    Article  CAS  PubMed  Google Scholar 

  17. Vogler AP, Monaghan MT (2007) Recent advances in DNA taxonomy. J Zool Syst Evol Res 45:1–10

    Article  Google Scholar 

  18. Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, Haidar N, Savolainen V (2005) Land plants and DNA barcodes: short-term and long-term goals. Philos Trans R Soc Lond B Biol Sci 360:1889–1895

    Article  CAS  PubMed  Google Scholar 

  19. Topik H, Yukawa T, Ito M (2005) Molecular phylogenetics of subtribe Aeridinae (Orchidaceae): insights from plastid matK and nuclear ribosomal ITS sequences. J Plant Res 118:271–284

    Article  CAS  PubMed  Google Scholar 

  20. 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 22:4673–4680

    Article  CAS  PubMed  Google Scholar 

  21. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  22. Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 101:11030–11035

    Article  CAS  PubMed  Google Scholar 

  23. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  CAS  PubMed  Google Scholar 

  24. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  25. Suzuki H, Keimatsu S, Ito K (1934) Nachtrag zum “Chin-Shih-Hu”. Yakugakuzasshi 54(9):820–823 (in Japanese)

    CAS  Google Scholar 

  26. Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 84:9054–9058

    Article  CAS  PubMed  Google Scholar 

  27. Ding G, Zhang D, Feng Z, Fan W, Ding X, Li X (2008) SNP, ARMS and SSH authentication of medicinal Dendrobium officinale KIMURA et MIGO and application for identification of Fengdou drugs. Biol Pharm Bull 31(4):553–557

    Article  CAS  PubMed  Google Scholar 

  28. Kimura K (1936) Pharmacological study of Dendrobiinae plants as the Chinese drug shih-hu. J Shanghai Sci Inst Sect III 3(Suppl. 1):1–60 (in Japanese)

    Google Scholar 

  29. Kimura K, Migo H (1936) New species of Dendrobium from the Chinese drug shih-hu. J Shanghai Sci Inst Sect III 3:121–124

    Google Scholar 

  30. Karasawa K (2003) Species Orchidacearum I text. Japan Broadcasting Publishing, Tokyo (in Japanese)

    Google Scholar 

Download references

Acknowledgments

We are grateful to Dr. Setsuko Sekita of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University for her helpful comments. We thank Dr. Li Heng of Kunming Institute of Botany and Dr. Kohji Karasawa for their advice on Orchid taxonomy. We also thank Dr. Masayuki Hatta of Ochanomizu University for his help in interpreting the phylogenetic trees. Our thank goes to Dr. Yuko Shimamura of Ochanomizu University for her technical advice. We appreciate the kind sample offering from Mr. Toraichiro Seki and The Hiroshima Botanical Garden. Part of this research was financially supported by the Ministry of Health, Labor and Welfare.

Author information

Authors and Affiliations

  1. Laboratory of Food Chemistry, Faculty of Humanities and Sciences, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo, 112-8610, Japan

    Haruka Asahina & Yasujiro Morimitsu

  2. Institute of Environmental Science for Human Life, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo, 112-8610, Japan

    Motoyoshi Satake

  3. Faculty of Pharmaceutical Sciences, Showa Pharmaceutical University, 3 Higashi-Tamagawagakuen, Machida City, Tokyo, 194-8543, Japan

    Junichi Shinozaki & Kazuo Masuda

Authors
  1. Haruka Asahina
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Junichi Shinozaki
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kazuo Masuda
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yasujiro Morimitsu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Motoyoshi Satake
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Haruka Asahina.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Asahina, H., Shinozaki, J., Masuda, K. et al. Identification of medicinal Dendrobium species by phylogenetic analyses using matK and rbcL sequences. J Nat Med 64, 133–138 (2010). https://doi.org/10.1007/s11418-009-0379-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11418-009-0379-8

Keywords

Search

Navigation