In Silico Approach for DNA Barcoding using Phylogenetic Analysis of Coelogyne spp. based on the matK, rpoC1, rbcL and nrDNA Markers

https://doi.org/10.22146/jtbb.73130

Apriliana Pratiwi(1), Anggiresti Kinasih(2), Maura Indria Meidianing(3), Febri Yuda Kurniawan(4), Endang Semiarti(5*)

(1) Biology Orchid Study Club (BiOSC); Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, 55281 Yogyakarta, Indonesia
(2) Biology Orchid Study Club (BiOSC); Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, 55281 Yogyakarta, Indonesia
(3) Biology Orchid Study Club (BiOSC); Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, 55281 Yogyakarta, Indonesia
(4) Biology Orchid Study Club (BiOSC); Study Program of Biotechnology, Graduate School, Universitas Gadjah Mada, 55281 Yogyakarta, Indonesia
(5) Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, 55281 Yogyakarta, Indonesia
(*) Corresponding Author

Abstract


In silico biology is considered as an effective and applicable approach to initiate various research, such as biodiversity taxonomical conservation. Phylogenetic analysis using in silico taxonomy method for orchid species can provide data on genetic diversity and evolutionary relationships. One particular method that can be used to evaluate specific targets of gene loci in the taxonomic study is DNA barcoding. This research was conducted to determine the specific target locus gene using matK, rbcL, rpoC1, and nrDNA markers for DNA barcoding of the Coelogyne genus with in silico approach using phylogenetic analysis. All marker sequences were collected from the NCBI website and analysed using several softwares and methods, namely Clustal X for sample sequence alignment and MEGA 11 for phylogenetic tree construction and analysis. The results showed that the gene locus in Coelogyne recommended was the nrDNA gene locus. Phylogenetic analysis revealed that the use of the nrDNA gene locus was able to separate 17 Coelogyne species with two outgroup species, namely Cymbidium and Vanilla, then followed with ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) while the other gene loci, namely maturase K (matK) and polymerase beta' subunit (rpoC1) provided a visual phylogenetic tree in which the two outgroup species entered into the same clade as the Coelogyne species. Thus, the results of this study can be used as a reference to support the Coelogyne breeding and conservation program.

 


Keywords


DNA barcoding, conservation, in silico, Coelogyne, phylogenetic analysis

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References

Bafeel, S.O. et al., 2011. Comparative evaluation of PCR success with universal primers of maturase K (matK) and ribulose-1, 5-bisphosphate carboxylase oxygenase large subunit (rbcL) for barcoding of some arid plants. Plant Omics, 4, pp.195-198.

CBOL Plant Working Group, 2009. A DNA barcode for land plants. In Proceedings of the National Academy of Sciences, 106. pp. 12794–12797.

Chase, M.W. et al., 2015. An updated classification of Orchidaceae. Botanical Journal of the Linnean Society, 177(2), pp.151–174. doi: 10.1111/boj.12234.

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), pp.711–720. doi: 10.1089/omi.2017.0131.

Duan, H. et al., 2019. The screening and identification of DNA barcode sequences for Rehmannia. Scientific Reports, 9(1), p.17295. doi: 10.1038/s41598-019-53752-8.

El-Sherif, N. & Ibrahim, M., 2020. Implications of rbcL and rpoC1 DNA Barcoding in Phylogenetic Relationships of some Egyptian Medicago sativa L. Cultivars. Egyptian Journal of Botany, 0(0), pp.0–0. doi: 10.21608/ejbo.2020.20028.1399.

Haider, N., 2018. A Brief Review on Plant Taxonomy and its Components. Jour Pl Sci Res, 34(2), pp.275–290.

Hall, B.G., 2013. Building Phylogenetic Trees from Molecular Data with MEGA. Molecular Biology and Evolution, 30(5), pp.1229–1235. doi: 10.1093/molbev/mst012.

Hartati, S. et al., 2019. Morphological characterization of Coelogyne spp for germplasm conservation of orchids. Revista Ceres, 66(4), pp.265–270. doi: 10.1590/0034-737x201966040004.

Hartati, S. & Muliawati, E.S., 2020. Short Communication: Genetic variation of Coelogyne pandurate, C. rumphii and their hybrids based on RAPD markers. Biodiversitas Journal of Biological Diversity, 21(10). doi: 10.13057/biodiv/d211033.

Ho, V.T. et al., 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), p.93. doi: 10.1186/s43141-021-00188-1.

Ho, V.T. & Nguyen, M.P., 2020. An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family. Biodiversitas Journal of Biological Diversity, 21(8). doi: 10.13057/biodiv/d210858.

Hollingsworth, P.M., Graham, S.W. & Little, D.P., 2011. Choosing and Using a Plant DNA Barcode. PLoS ONE, 6(5), e19254. doi: 10.1371/journal.pone.0019254.

Hosein, F.N. et al., 2017. Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad. Ecology and Evolution. Ecology and Evolution, 7(18), pp.7311–7333. doi: 10.1002/ece3.3220.

Dharmayanti, N.L.P.I., 2011. Molecular phylogenetic: organism taxonomy method based on evolution history. Wartazoa, 21(1), pp.1–5.

Jiang, K. et al., 2020. Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification. Plants, 9(10), 1332. doi: 10.3390/plants9101332.

Kim, H.M. et al., 2014. DNA barcoding of Orchidaceae in Korea. Molecular Ecology Resources, 14(3), pp.499–507. doi: 10.1111/1755-0998.12207.

Kim, Y.-K. et al., 2020. Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences. Frontiers in Plant Science, 11. doi: 10.3389/fpls.2020.00022.

Li, J. et al., 2018. Prioritizing the orchids of a biodiversity hotspot for conservation based on phylogenetic history and extinction risk. Botanical Journal of the Linnean Society, 186(4), pp.473–497. doi: 10.1093/botlinnean/box084.

Maloukh, L. et al., 2017. Discriminatory power of rbcL barcode locus for authentication of some of United Arab Emirates (UAE) native plants. 3 Biotech, 7(2), p.144. doi: 10.1007/s13205-017-0746-1.

Mishra, P. et al., 2016. DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. Plant Biotechnology Journal, 14(1), pp.8–21. doi: 10.1111/pbi.12419.

Nauheimer, L. et al., 2018. Australasian orchid biogeography at continental scale: Molecular phylogenetic insights from the Sun Orchids (Thelymitra, Orchidaceae). Molecular Phylogenetics and Evolution, 127, pp.304–319. doi: 10.1016/j.ympev.2018.05.031.

Parveen, I. et al., 2016. DNA Barcoding for the Identification of Botanicals in Herbal Medicine and Dietary Supplements: Strengths and Limitations. Planta Medica, 82(14), pp.1225–1235. doi: 10.1055/s-0042-111208.

Parveen, I. et al., 2017. Evaluating five different loci (rbcL, rpoB, rpoC1, matK, and ITS) for DNA barcoding of Indian orchids. Genome, 60(8), pp.665–671. doi: 10.1139/gen-2016-0215.

Rajaram, M.C. et al., 2019. DNA Barcoding of Endangered Paphiopedilum species (Orchidaceae) of Peninsular Malaysia. Phytotaxa, 387(2), pp.94–104. doi: 10.11646/phytotaxa.387.2.2.

Ramudu, J. & Khasim, S.M., 2016. DNA Barcoding of some Indian Coelogyne (Epidendroideae, Orchidaceae). J. Orchid Soc. India, 30, pp.65–73.

Raskoti, B.B. & Ale, R., 2021. DNA barcoding of medicinal orchids in Asia. Scientific Reports, 11(1), p.23651. doi: 10.1038/s41598-021-03025-0.

Rivero, D.G., 2016. Darwinian Archaeology and Cultural Phylogenetics. In Cultural Phylogenetics Springer, pp.43–72. doi: 10.1007/978-3-319-25928-4_3.

Singh, N. & Kumaria, S., 2020. A Combinational Phytomolecular-Mediated Assessment in Micropropagated Plantlets of Coelogyne ovalis Lindl.: A Horticultural and Medicinal Orchid. Proceedings of the National Academy of Sciences, India Section B: Biological Sciences, 90(2), pp.455–466. doi: 10.1007/s40011-019-01118-5.

Srivastava, D. & Manjunath, K., 2020. DNA barcoding of endemic and endangered orchids of India: A molecular method of species identification. Pharmacognosy Magazine, 16(70), p.290. doi: 10.4103/pm.pm_574_19.

Vu, H.-T. et al., 2018. In Silico Study on Molecular Sequences for Identification of Paphiopedilum Species. Evolutionary Bioinformatics, 14, p.117693431877454. doi: 10.1177/1176934318774542.

Wang, X. et al., 2018. DNA barcoding a taxonomically complex hemiparasitic genus reveals deep divergence between ploidy levels but lack of species-level resolution. AoB PLANTS, 10(3). doi: 10.1093/aobpla/ply026.

Wu, Q.-P. et al., 2020. Characterization of the complete chloroplast genome of Coelogyne fimbriata (Orchidaceae). Mitochondrial DNA Part B, 5(3), pp.3507–3509. doi: 10.1080/23802359.2020.1827058.

Yun, S.A. et al., 2020. Genetic diversity and population structure of the endangered orchid Pelatantheria scolopendrifolia (Orchidaceae) in Korea. PLOS ONE, 15(8), p.e0237546. doi: 10.1371/journal.pone.0237546.

Zhang, G.-Q. et al., 2021. Phylogenetic incongruence in Cymbidium orchids. Plant Diversity, 43(6), pp.452–461. doi: 10.1016/j.pld.2021.08.002.



DOI: https://doi.org/10.22146/jtbb.73130

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