DNA Barcode Analysis of Dendrobium sp. Based On rbcL Sequence
DOI:
10.29303/jbt.v25i4.10177Published:
2025-10-21Downloads
Abstract
Morphological characterization of Dendrobium orchids needs to be supported by the utilization of DNA barcoding as a faster and more accurate approach. This study aims to identify the rbcL marker as a potential barcode for Dendrobium sp. collected from Jenggawah, Jember. The isolation of Dendrobium sp. genomic DNA was performed using the CTAB method, and the isolated DNA was amplified using PCR. The PCR products were used for sequencing analysis, and the sequence data were analyzed using several bioinformatics programs namely BLAST, ClustalX 2.1, and MEGA11. The results showed that the Dendrobium sp. sequence had a high level of homology with Calanthe alpina (MN192480.1), with a genetic similarity of 99.82%. The sequence analysis results of rbcL in Dendrobium sp. showed low genetic variation, which made rbcL less effective for use as a molecular marker at the species level. The rbcL barcode showed universal results for Dendrobium sp., so it needs to be supported by molecular identification using other markers such as matK and ITS for a more effective identification method in distinguishing between species.
Keywords:
Barcode, Dendrobium, Molecular marker, Orchid, PhylogeneticReferences
Ardalan, M.-R., & Rafieian-Kopaei, M. (2013). Is the safety of herbal medicines for kidneys under question? Journal of Nephropharmacology, 2(2), 11–12. http://www.ncbi.nlm.nih.gov/pubmed/28197435%0Ahttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5297543
Asahina, H., Shinozaki, J., Masuda, K., Morimitsu, Y., & Satake, M. (2010). Identification of medicinal Dendrobium species by phylogenetic analyses using matK and rbcL sequences. Journal of Natural Medicines, 64(2), 133–138. https://doi.org/10.1007/s11418-009-0379-8
Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J., Higgins, D. G., & Thompson, J. D. (2003). Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Research, 31(13), 3497–3500. https://doi.org/10.1093/nar/gkg500
Chung, H. H., Shi, S. K., Huang, B., & Chen, J. T. (2017). Enhanced agronomic traits and medicinal constituents of autotetraploids in anoectochilus formosanus hayata, a top-grade medicinal orchid. Molecules, 22(11). https://doi.org/10.3390/molecules22111907
De, L. C., Rao, A. N., Rajeevan, P. K., Srivastava, M., & Chhetri, G. (2015). Morphological Characterization in Dendrobium Species. Journal of Global Biosciences, 4(August), 1198–1215. www.mutagens.co.in
Ekman, S. (1999). PCR optimization and troubleshooting, with special reference to the amplification of ribosomal DNA in lichenized fungi. Lichenologist, 31(5), 517–531. https://doi.org/10.1006/lich.1999.0226
Hartati, S., Samanhudi, & Cahyono, O. (2022). Short Communication: Morphological characterization of five species of Dendrobium native to Indonesia for parent selection. Biodiversitas, 23(5), 2648–2654. https://doi.org/10.13057/biodiv/d230548
Ho, V. T., Tran, T. K. P., Vu, T. T. T., & Widiarsih, S. (2021). Comparison of matK and rbcL DNA barcodes for genetic classification of jewel orchid accessions in Vietnam. Journal of Genetic Engineering and Biotechnology, 19(1), 93. https://doi.org/10.1186/s43141-021-00188-1
Hollingsworth, P. M., Forrest, L. L., Spouge, J. L., Hajibabaei, M., Ratnasingham, S., van der Bank, M., Chase, M. W., Cowan, R. S., Erickson, D. L., Fazekas, A. J., Graham, S. W., James, K. E., Kim, K. J., John Kress, W., Schneider, H., van AlphenStahl, J., Barrett, S. C. H., van den Berg, C., Bogarin, D., … Little, D. P. (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America, 106(31), 12794–12797. https://doi.org/10.1073/pnas.0905845106
Kasutjianingati, K., & Firgiyanto, R. (2018). Characterization of Morphology from Orchid Vanda sp. as a Genetic Information Source for Preservation and Agribusiness of Orchids in Indonesia. IOP Conference Series: Earth and Environmental Science, 207(1). https://doi.org/10.1088/1755-1315/207/1/012006
Kim, H. M., Oh, S. H., Bhandari, G. S., Kim, C. S., & Park, C. W. (2014). DNA barcoding of orchidaceae in Korea. Molecular Ecology Resources, 14(3), 499–507. https://doi.org/10.1111/1755-0998.12207
Kress, W. J., Prince, L. M., & Williams, K. J. (2002). The phylogeny and a new classification of the gingers (Zingiberaceae): Evidence from molecular data. American Journal of Botany, 89(10), 1682–1696. https://doi.org/10.3732/ajb.89.10.1682
Mailund, T., Brodal, G. S., Fagerberg, R., Pedersen, C. N. S., & Phillips, D. (2006). Recrafting the neighbor-joining method. BMC Bioinformatics, 7, 1–8. https://doi.org/10.1186/1471-2105-7-29
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), 327–337. https://doi.org/10.1007/s12298-018-0610-8
Millar, A. (1978). Orchids of Papua New Guinea. In HortTechnology (pp. 1–101). Australian National University.
Perwitasari, D. A. G., Rohimah, S., Ratnasari, T., Sugiharto, B., & Su’udi, M. (2020). DNA Barcoding of Medicinal Orchid Dendrobium discolor Lindl. Tanimbar Using rbcL and ITS genes. Buletin Penelitian Tanaman Rempah Dan Obat, 31(1), 8. https://doi.org/10.21082/bullittro.v31n1.2020.8-20
Ramesh, T., Koperuncholan, M., Praveena, R., Ganeshkumari, K., Vanithamani, J., Muruganantham, P., & Renganathan, P. (2019). Medicinal properties of some Dendrobium orchids – A review. Journal of Applied and Advanced Research, August, 119–128. https://doi.org/10.21839/jaar.2019.v4i4.72
Schuiteman, A. (1995). Key To The Genera of Orchidaceae of New Guinea. Flora Malesiana Bulletin, 11(6), 401–423.
Schuiteman, A., Vermeulen, J. J., & de Vogel, E. F. (2010). Flora Malesiana: orchids of New Guinea vol. I-VI. CD-ROM.: Vol. VI. Margraf Publisher.
Silalahi, M., & Nisyawati. (2015). Pemanfaatan Anggrek Sebagai Obat Tradisional Pada Etnis Batak Sumatera Utara. Berita Biologi, 14(2), 187–193.
Su’udi, M., Ulum, F. B., Ardiyansah, M., & Fitri, N. E. (2024). Evaluasi Lokus Potensial matK dan ITS2 Untuk DNA Barcoding Anggrek Bulbophyllum lobbii Lindl. Al-Kauniyah: Jurnal Biologi, 17(2), 406–418. https://doi.org/10.15408/kauniyah.v17i2.33897
Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38(7), 3022–3027. https://doi.org/10.1093/molbev/msab120
Wahyudiningsih, T. S., Nion, Y. A., & . P. (2017). Pemanfaatan Anggrek Spesies Kalimantan Tengah Berbasis Kearifan Lokal yang Berpotensi sebagai Bahan Obat Herbal. Jurnal Biodjati, 2(2), 149–158. https://doi.org/10.15575/biodjati.v2i2.1570
Zhang, J., Onakpoya, I. J., Posadzki, P., & Eddouks, M. (2015). The safety of herbal medicine: From prejudice to evidence. Evidence-Based Complementary and Alternative Medicine, 2015. https://doi.org/10.1155/2015/316706
Ziyaroh, P. L., Rosida, W., Dwinianti, E. F., & Su, M. (2024). Propagation of Dendrobium crumenatum Sw . through In Vitro Seed Culture Using Organic Complex Media. 2(2), 64–68.
License
Copyright (c) 2025 Edia Fitri Dwinianti, Durotun Ainiyah, Yusfi Afidah, Mukhamad Su'udi
This work is licensed under a Creative Commons Attribution 4.0 International License.
Jurnal Biologi Tropis is licensed under a Creative Commons Attribution 4.0 International License.
The copyright of the received article shall be assigned to the author as the owner of the paper. The intended copyright includes the right to publish the article in various forms (including reprints). The journal maintains the publishing rights to the published articles.
Authors are permitted to disseminate published articles by sharing the link/DOI of the article at the journal. Authors are allowed to use their articles for any legal purposes deemed necessary without written permission from the journal with an acknowledgment of initial publication to this journal.
