DNA Barcoding of Medicinal Orchid Dendrobium discolor Lindl. Tanimbar Using rbcL and ITS genes

Dian Al Ghifari Perwitasari, Siti Rohimah, Tri Ratnasari, Bambang Sugiharto, Mukhamad Su'udi

Abstract


Dendrobium discolor Lindl., Tanimbar is one of the medicinal orchids that has been used to treat skin diseases. Morphologically, D. discolor Tanimbar shows similarities with D. discolor Merauke and D. bigibbum, making it challenging to identify. DNA barcoding using ribulose-1,5-bisphosphate carboxylase large (rbcL) and Internal Transcribed Spacer (ITS) markers expected to be used to identify D. discolor accurately. This study aimed to identify potential DNA sequences as barcodes for the identification of medicinal orchid D. discolor Tanimbar using molecular markers rbcL and ITS. The DNA genome of D. discolor Tanimbar was isolated and used as a template in the PCR reaction. The resulting amplicons were then sequenced. The results showed that the rbcL gene sequence of D. discolor had high homology with D. salaccense (Accession: LC193510.1, Prect. Ident  :   99.45 %),   whereas   the   ITS   had  high homology with D. nindii (Accession: AY239985.1 Identification: 98.67 %). Bioinformatics analysis showed that the rbcL gene sequence from D. discolor had more homology sequence than the ITS. However, the ITS sequence was more specific and could differentiate to species level. Based on the results of this study, the ITS sequence can be recommended as a molecular marker for the identification of the medicinal orchid D. discolor Tanimbar.


Keywords


Dendrobium bigibbum; Merauke; bioinformatics; molecular identification

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References


Adams, P.B. (2015) Dendrobium bigibbum (sect. Phalaenanthe) in Australia - Analysis of Diagnostic Characters, Review of Taxa and A New Classification. Kew Bulletin. 70 (2), Springer-Verlag London Ltd. doi:10.1007/s12225-015-9565-x.

Baker, S.S. (2018) Using DNA Barcoding to Identify Duckweed Species as Part of An Undergraduate Ecology Course. ACS Symposium Series. 1276, 67-79. doi:10.1021/bk-2018-1276.ch005.

Bulpitt, C.J. (2005) The Uses and Misuses of Orchids in Medicine. Quaterly Journal of Medicine. 98 (9), 625-631. doi:10.1093/qjmed/hci094.

Burke, J.M., Bayly, M.J., Adams, P.B. & Ladiges, P.Y. (2008) Molecular Phylogenetic Analysis of Dendrobium (Orchidaceae), with Emphasis on the Australian Section Dendrocoryne, and Implications for Generic Classification. Australian Systematic Botany. 21 (1), 1-14. doi:10.1071/SB07038.

Cheng, T., Xu, C., Lei, L., Li, C., Zhang, Y. & Shiliang, Z. (2016) Barcoding the Kingdom Plantae: New PCR Primers for ITS Regions of plants with Improved Universality and Specificity. Molecular Ecology Resources. 16 (1), 138-149. doi:10.1111/1755-0998.12438.

Cribb, P.J. (1983) A Revision of Dendrobium sect. Latouria (Orchidaceae). Kew Bulletin. 38 (2), 229. doi:10.2307/4108109.

Cribb, P.J. (1986) A Revision of Dendrobium sect. Spatulata (Orchidaceae). Kew Bulletin. 41 (3), 615-692. doi:10.2307/4108109.

Doyle, J.J. & Doyle, J.L. (1990) Isolation of DNA from Small Amounts of Plant Tissues. BRL Focus. 12, 13-15.

Ekman, S. (1999) PCR Optimization and Troubleshooting, with Special Reference to the Amplification of Ribosomal DNA in Lichenized Fungi. Lichenologist. 31 (5), 517-531. doi:10.1006/lich.1999.0226.

Erzurumlu, G.S., Sultana, N., Vural, M. & Serce, S. (2018) Genetic and Phenotypic Variation among Turkish Terrestrial Orchid Species as Revealed by RAPD and Morphological Characteristics. Turkish Journal of Agriculture and Forestry. 42 (4), 227-236. doi:10.3906/tar-1711-37.

Fazekas, A.J., Kesanakurti, P.R., Burgess, K.S., Percy, D.M., Graham, S.W., Barrett, S.C.H., Newmaster, S.G., Hajibabaei, M. & Husband, B.C. (2009) Are Plant Species Inherently Harder to Discriminate than Animal Species Using DNA Barcoding Markers? Molecular Ecology Resources. 9 (SUPPL. 1), John Wiley & Sons, Ltd, 130-139. doi:10.1111/j.1755-0998.2009.02652.x.

Fernando, S.S. & Ormerod, P. (2008) An Annotated Checklist of the Orchids of Sri Lanka. Rheedea. 18 (1), 1-28.

Frederick, M.A., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. & Struhl, K. (2003) Current Protocols in Molecular Biology. Massachusetts, John Wiley & Sons, Inc.

Ghorbani, A., Saeedi, Y. & de Boer, H.J. (2017) Unidentifiable by Morphology: DNA Barcoding of Plant Material in Local Markets in Iran. PLoS ONE. 12 (4). doi:10.1371/journal.pone.0175722.

Govaerts, R. (2003) World Checklist of Monocotyledons Database in ACCESS: 1- 71827 (WCSP). London, The Board of Trustees of the Royal Botanic Gardens, Kew.

Han, R., Xie, D., Tong, X., Zhang, W., Liu, G., Peng, D. & Yu, N. (2018) Transcriptomic Landscape of Dendrobium huoshanense and Its Genes Related to Polysaccharide Biosynthesis. Acta Societatis Botanicorum Poloniae. 87 (1), 1-11. doi:10.5586/asbp.3574.

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. In: Proceedings of the National Academy of Sciences of the United States of America. 91 (12), pp. 5730-5734. doi:10.1073/pnas.91.12.5730.

Hebert, P.D.N., Cywinska, A., Ball, S.L. & Dewaard, J.R. (2003) Biological Identifications Through DNA Barcodes. In: Proceedings of the Royal Society of London. Series B: Biological Sciences. 270 (1512), London, pp. 313-321. doi:10.1098/rspb.2002.2218.

Hollingsworth, P.M., Forrest, L.L., Spouge, J.L., Hajibabaei, M., Ratnasingham, S., & Fazekas, A. (2009) A DNA Barcode for Land Plants. In: Proceedings of the National Academy of Sciences. 106 (31), pp. 12794-12797.

Hollingsworth, P.M., Graham, S.W. & Little, D.P. (2011) Choosing and Using A Plant DNA Barcode. PLoS ONE. 6 (5), 1-13. doi:10.1371/journal.pone.0019254.

Hossain, M.M. (2011) Therapeutic Orchids: Traditional Uses and Recent Advances - An Overview. Fitoterapia. 82 (2), Elsevier B.V., 102-140. doi:10.1016/j.fitote.2010.09.007.

Jeanmougin, F., Thompson, J., Gouy, M. & Higgins, D. (1998) Multiple Sequence Alignment with Clustal X. Trendsin Biochemical Sciences. 23 (10), 403-405. doi:https://doi.org/10.1016/S0968-0004(98)01285-7.

Joshi, G.C., Tewari, L.M., Lohani, N., Upreti, K., Jalal, J.S. & Tewari, G. (2009) Diversity Of Orchids In Uttarakhand and Their Conservation Strategy with Special Reference to Their Medicinal Importance. Report and Opinion. 1 (3), 47-52.

Kartikaningrum, S., Widiastoety, D. & Effendie, K. (2004) Karakterisasi Tanaman Hias: Anggrek & Anthurium. Bogor, Sekretariat Komisi Nasional Plasma Nutfah.

Kim, H.M., Oh, S., Bhandari, G.S., Kim, C. & Park, C. (2014) DNA Barcoding of Orchidaceae in Korea. Molecular Ecology Resources. 14 (3), 499-507. doi:10.1111/1755-0998.12207.

Kishor, R. & Devi, H.S. (2009) Induction of Multiple Shoots in A Monopodial Orchid Hybrid (Aerides vandarum Reichb.f × Vanda stangeana Reichb.f) Using Thidiazuron and Analysis of Their Genetic Stability. Plant Cell, Tissue and Organ Culture. 97 (2), 121-129. doi:10.1007/s11240-009-9506-1.

Kress, W.J. & Erickson, D.L. (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 (6), e508. doi:10.1371/journal.pone.0000508.

Kumar, S., Nei, M., Dudley, J. & Tamura, K. (2008) MEGA: A Biologist-Centric Software for Evolutionary Analysis of DNA and Protein Sequences. Briefings in Bioinformatics. 9 (4), 299-306. doi:https://doi.org/10.1093/bib/bbn017.

Liddle, D.J. & Forster, P.I. (1990) The Recognition of Subspecies in Dendrobium discolor Lindley (Orchidaceae). Austrobaileya. 3 (2), Queensland Herbarium, 319-321. doi:10.2307/41738767.

Liu, H., Fang, C., Zhang, T., Guo, L. & Ye, Q. (2019) Molecular Authentication and Differentiation of Dendrobium Species by rRDNA ITS Region Sequence Analysis. AMB Express. 9 (1), Springer Berlin Heidelberg. doi:10.1186/s13568-019-0767-8.

Lokho, A. (2013) Diversity of Dendrobium Sw. Its Distributional Patterns and Present Status in the Northeast India. International Journal of Scientific and Research Publications. 3 (5), 1-9.

Malik, S., Priya, A. & Babbar, S.B. (2019) Employing Barcoding Markers to Authenticate Selected Endangered Medicinal Plants Traded in Indian Markets. Physiology and Molecular Biology of Plants. 25 (2), Springer India, 327–337. doi:10.1007/s12298-018-0610-8.

Meshoul, S., Layeb, A. & Batouche, M. (2005) A Quantum Evolutionary Algorithm for Effective Multiple Sequence Alignment. In: Bento, C., Cardoso, A. & Dias, G. (eds.) Progress in Artificial Intelligence. 3808 LNCS, Berlin, Springer, pp. 260-271. doi:10.1007/11595014_26.

Miftakhurohmah, Mariana, M. & Wahyuno, D. (2016) Deteksi Piper Yellow Mottle Virus (PYMoV) Penyebab Penyakit Kerdil pada Tanaman Lada secara Polymerase Chain Reaction (PCR). Bul Littro. 27 (1), 77. doi:10.21082/bullittro.v27n1.2016.77-83.

Millar, A. (1978) Orchids of Papua New Guinea. Portland, Oregon, Timber Press.

Misener, S. & Krawetz, S.A. (2000) Bioinformatics Methods and Protocols. Methods in. Totowa, New Jersey, Humana Press.

Pant, B. (2013) Medicinal Orchids and Their Uses: Tissue Culture A Potential Alternative for Conservation. African Journal of Plant Science. 7 (10), 448-467. doi:10.5897/ajps2013.1031.

Parveen, I., Singh, H.K., Malik, S., Raghuvanshi, S. & Babba, S.B. (2017) Evaluating Five Different Loci (rbcL, rpoB, rpoC1, matK and ITS) for DNA Barcoding of Indian Orchids. Genome. 60 (8), 665-671.

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. doi:10.1002/pca.2732.

Saitou, N. & Nei, M. (1987) The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees. Molecular Biology and Evolution. 4 (4), Oxford University Press (OUP), 406-425. doi:10.1093/oxfordjournals.molbev.a040454.

Schuiteman, A. (2013) A Guide to Dendrobium of New Guinea. Kinabalu, Natural History Publications.

Seidenfaden, G., Wood, J. & Holttum, R. (1992) The Orchids of Peninsular Malaysia and Singapore. Fredensborg, Olsen & Olsen.

Subedi, A., Kunwar, B., Choi, Y., Dai, Y., van Andel, T., Chaudhary, R.P., de Boer, H.J. & Gravendeel, B. (2013) Collection and Trade of Wild-harvested Orchids in Nepal. Journal of Ethnobiology and Ethnomedicine. 9 (1), 1–10. doi:10.1186/1746-4269-9-64.

Taberlet, P., Gielly, L., Pautou, G. & Bouvet, J. (1991) Universal Primers for Amplification of Three Non-Coding Regions of Chloroplast DNA. Plant Molecular Biology. 17, pp. 1105-1109.

Teoh, E.S. (2016) Medicinal Orchids of Asia. Medicinal Orchids of Asia. Singapore, Springer Nature. doi:10.1007/978-3-319-24274-3.

Wang, H., Qi, M. & Cutler, A.J. (1993) A Simple Method of Preparing Plant Samples for PCR. Nucleic Acids Research. 21 (17), 4153-4154. doi:10.1093/nar/21.17.4153.

Wang, X., Chen, X., Yang, P., Wang, L. & Han, J. (2017) Barcoding the Dendrobium (Orchidaceae) Species and Analysis of the Intragenomic Variation Based on the Internal Transcribed Spacer 2. BioMed Research International. 2017, 2734960. doi:10.1155/2017/2734960.

Williams, N.H. & Whitten, W.M. (1999) Molecular Phylogeny and Floral Fragrances of Male Euglossine Bee-Pollinated Orchids: A Study Of Stanhopea (Orchidaceae). Plant Species Biology. 14, 129-136. doi:10.1046/j.1442-1984.1999.00016.x.

Xu, S., Li, D., Li, J., Xiang, X., Jin, W., Huang, W., Jin, X. & Huang, L. (2015) Evaluation of the DNA Barcodes in Dendrobium (Orchidaceae) from Mainland Asia. PLoS ONE. 10 (1), 1-12. doi:10.1371/journal.pone.0115168.




DOI: http://dx.doi.org/10.21082/bullittro.v31n1.2020.8-20

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