Genetic relationship analysis of Dendrobium anosmum Lindl. var. semialba based on the chloroplast matK and rbcL genes
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Abstract
Dendrobium anosmum Lindl. var. semialba has variants of flower shapes. Currently, it has high economic value and is favored on the market. In this study, the genetic relationship of Dendrobium anosmum Lindl. var. semialba species was determined based on the analysis of chloroplast matK, rbcL gene sequences. The matK and rbcL genes of twelve species were amplified and their DNA sequenced. These DNA sequences were compared, calculated genetic distance and constructed phylogenetic tree. The results showed that 100% of samples were amplified and sequenced successfully. The analysis of matK sequences showed that 12 species had very high genetic similarity with the low genetic distance of 0 - 0.001; the nucleotide sequences were almost unchanged except for one variable nucleotide position in TB1 and TB1 was in a separate branch of the phylogenetic tree. The analysis of rbcL sequences showed that all species had a low genetic distance of 0 - 0.012 and had 7 mutant positions in nucleotide sequences of TB1 and TB5. These species were in a separate branch of the phylogenetic tree while the other species were grouped in the other branch of the phylogenetic tree. The study provided a reliable molecular database of the Dendrobium anosmum Lindl. var. semialba for identification, classification, biodiversity assessment and conservation of genetic resources.
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An, J., Moon, J. C., Kim, J. H., Kim, G. S., & Jang, C. S. (2019). Development of DNA-based species-specific real-time PCR markers for four berry fruits and their application in commercial berry fruit foods. Applied Biological Chemistry 62(1), 1-7. https://doi.org/10.1186/s13765-019-0413-9
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
Cabelin, V. L. D., & Alejandro, G. J. D. (2016). Efficiency of matK, rbcL, trnH-psbA, and trnL-F (cpDNA) to molecularly authenticate Philippine ethnomedicinal Apocynaceae through DNA barcoding. Pharmacognosy Magazine 12(46), 384-388. https://doi.org/10.4103/0973-1296.185780
Cao, B. P. (2018). Physiological and biochemical changes of micropropagated Dendrobium anosmum Lindl. in ex vitro acclimatization process. Science and Technology Development Journal-Natural Sciences 2(3), 59-67. https://doi.org/https://doi.org/10.32508/stdjns.v2i3.754
Chattopadhyay, P., Banerjee, G., & Banerjee, N. (2017). Distinguishing orchid species by DNA barcoding: Increasing the resolution of population studies in plant biology. Omics: A Journal of Integrative Biology 21(12), 711-720. https://doi.org/10.1089/omi.2017.0131
Hazlina, N., Wahba, L. E., Fadelah, A., & Wickneswari, R. (2013). Genetic relationships among 81 Dendrobium accessions from Malaysia. Malaysian Applied Biology 42(1), 35-40.
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., Kress, W. J., Schneider, H., van AlphenStahl, J., Barrett, S. C. H., van den Berg, C., Bogarin, D., Burgess, K. S., Cameron, K. M., Carine, M., Chac´on, J., Clark, A., Clarkson, J. J., Conrad, F., Devey, D. S., Ford, C. S., Hedderson, T. A. J., Hollingsworth, M. L., Husband, B. C., Kelly, L. J., Kesanakurti, P. R., Kim, J. S., Kim, Y. D., Lahaye, R., Lee, H. L., Long, D. G., Madrin˜´an, S., Maurin, O., Meusnier, I., Newmaster, S. G., Park, C. W., Percy, D. M., Petersen, G., Richardson, J. E., Salazar, G. A., Savolainen, V., Seberg, O., Wilkinson, M. J., Yi, D. K., & Little, D. P. (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences 106(31), 12794-12797. https://doi.org/10.1073/pnas.0905845106
Ijaz, S., Haq, I. U., & Babar, M. (2019). Jukes-cantor evolutionary model-based phylogenetic relationship of economically important ornamental palms using maximum likelihood approach. Applied Ecology and Environmental Research 17(6), 14859-14865. http://dx.doi.org/10.15666/aeer/1706_1485914865
Ismail, M., Ahmad, A., Nadeem, M., Javed, M. A., Khan, S. H., Khawaish, I., Sthanadar, A. A., Qari, S. H., Alghanem, S. M., Khan, K. A., Khan, M. F., & Qamer, S. (2020). Development of DNA barcodes for selected Acacia species by using rbcL and matK DNA markers. Saudi Journal Biological Science 27(12), 3735-3742. https://doi.org/10.1016/j.sjbs.2020.08.020
Jin, W. T., Schuiteman, A., Chase, M. W., Li, J. W., Chung, S. W., Hsu, T. C., & Jin, X. H. (2017). Phylogenetics of subtribe Orchidinae sl (Orchidaceae; Orchidoideae) based on seven markers (plastid matK, psaB, rbcL, trnL-F, trnH-psba, and nuclear nrITS, Xdh): implications for generic delimitation. BMC Plant Biology 17(1), 222. https://doi.org/10.1186/s12870-017-1160-x
Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33(7), 1870-1874. https://doi.org/10.1093/molbev/msw054
Moudi, M., Go, R., Yien, C. Y. S., & Saleh, M. N. (2013a). A review on molecular systematic of the genus Dendrobium Sw. Acta Biologica Malaysiana 2(2), 71-78. http://dx.doi.org/10.7593/abm/2.2.71
Moudi, M., Yien, C. Y. S., Nazre, M., Abdullah, J. O., & Go, R. (2013b). Phylogenetic analysis among four sections of Genus Dendrobium Sw. (Orchidaceae) in Peninsular Malaysia using rbcL sequence data. International Journal of Bioassays 2(06), 932-937.
Srikulnath, K., Sawasdichai, S., Jantapanon, T. K., Pongtongkam, P., & Peyachoknagul, S. (2015). Phylogenetic relationship of Dendrobium species in Thailand inferred from chloroplast matK gene and nuclear rDNA ITS region. The Horticulture Journal 84(3), 243-252. https://doi.org/10.2503/hortj.MI-028
Steven, G. N., & Subramanyam, R. (2009). Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae). Molecular Ecology Resources 9(1), 172-180. https://doi.org/10.1111/j.1755-0998.2009.02642.x
Thompson, J. D., Gibson, T. J., & Higgins, D. G. (2002). Multiple sequence alignment using ClustalW and ClustalX. Current Protocols in Bioinformatics 1, 2.3.1-2.3.22. https://doi.org/10.1002/0471250953.bi0203s00
Tran, D. D., Khuat, T. H., La, N. T., Nguyen, T. T. T., Pham, H. B., Nguyen, K. T, Tran, D. H., Do, T. M., & Tran, K. D. (2018). Identification of Vietnamese native Dendrobium species based on ribosomal DNA internal transcribed spacer sequence. Advanced Studies in Biology 10(1), 1-12. https://doi.org/10.12988/asb.2018.7823
Vijayan, K., & Tsou, C. H. (2010). DNA barcoding in plants: Taxonomy in a new perspective. Current Science 99(11), 1530-1541.
Wattoo, J. I., Saleem, M. Z., Shahzad, M. S., Arif, A., Hameed, A., & Saleem, M. A. (2016). DNA Barcoding: Amplification and sequence analysis of rbcL and matK genome regions in three divergent plant species. Advancements in Life Sciences 4(1), 3-7.
Xiaohua, J., Singchi, C., & Yibo, L. (2009). Taxonomic revision of Dendrobium moniliforme complex (Orchidaceae). Scientia Horticulturae 120(1),143-145. https://doi.org/10.1016/j.scienta.2008.10.002
Xu, J., Han, Q. B., Li, S. L., Chen, X. J., Wang, X. N., Zhao, Z. Z., & Chen, H. B. (2013) Chemistry, bioactivity and quality control of Dendrobium, a commonly used tonic herb in traditional Chinese medicine. Phytochemistry Reviews 12, 341-367. https://doi.org/10.1007/s11101-013-9310-8
Zhu, S., Niu, Z., Xue, Q., Wang, H., Xie, X., & Ding, X. (2018). Accurate authentication of Dendrobium officinale and its closely related species by comparative analysis of complete plastomes. Acta Pharmaceutica Sinica B 8(6), 969-980. https://doi.org/10.1016/j.apsb.2018.05.009