Assessment of the DNA Barcodes Characteristic of Phalaenopsis deliciosa based on matK, rbcL, and ITS
Abstract
Indonesia has high biodiversity for plant species, including orchids with medicinal potential such as Phalaenopsis deliciosa. Generally, morphological characters, especially in flowers are used for orchids identification. However, when the plants are not in the flowering period, the identification becomes difficult. Therefore an alternative method, such as molecular identification (DNA barcoding) needs to be applied for the best solution. This research aims to identify and compare three markers (matK, rbcL, ITS) for their function as potential barcodes for Phalaenopsis deliciosa. This study was conducted by DNA amplification using three different markers set. The data were analyzed using Bioedit, BLAST, and ClustalX. The result found that the identity level of matK, rbcL, and ITS to other orchids species was 99-98%, 98%, and 94-96%, respectively. Furthermore, matK and ITS showed high specificity for Phalaenopsis deliciosa, and are therefore recommended as the best molecular identification marker of genus Phalaenopsis.
References
Azofeifa-Bolaños JB, Gigant LR, Nicolás-García M, Pignal M, Tavares-González F, Hágsater E, Salazar-Chávez GA, Reyes-López D, Archila-Morales FL, García-García JA, da Silva D, Allibert A, Solano-Campos F, Rodríguez-Jimenes G del C, Paniagua-Vásquez A, Besse P, Pérez-Silva A, Grisoni M. 2017. A new vanilla species from Costa Rica closely related to V. planifolia (orchidaceae). European Journal of Taxonomy. vol 284: 1–26. doi: http://dx.doi.org/10.5852/ejt.2017.284.
CBOL Plant Working Group. 2009. A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America. vol 106(31): 12794–12797. doi: https://doi.org/10.1073/pnas.0905845106.
Costion C, Ford A, Cross H, Crayn D, Harrington M, Lowe A. 2011. Plant DNA barcodes can accurately estimate species richness in poorly known floras. PLoS One. vol 6(11): 1–9. doi: https://doi.org/10.1371/journal.pone.0026841.
Dirks-Mulder A, Butôt R, van Schaik P, Wijnands JWPM, van den Berg R, Krol L, Doebar S, van Kooperen K, de Boer H, Kramer EM, Smets EF, Vos RA, Vrijdaghs A, Gravendeel B. 2017. Exploring the evolutionary origin of floral organs of Erycina pusilla, an emerging orchid model system. BMC Evolutionary Biology. vol 17(1): 1–18. doi: https://doi.org/10.1186/s12862-017-0938-7.
Ekor M. 2014. The growing use of herbal medicines: issues relating to adverse reactions and challenges in monitoring safety. Frontiers in Pharmacology. vol 4: 1–10. doi: https://doi.org/10.3389/fphar.2013.00177.
Fay MF. 2018. Orchid conservation: how can we meet the challenges in the twenty-first century?. Botanical Studies. vol 59(1): 1–6. doi: https://doi.org/10.1186/s40529-018-0232-z.
Feng S, Jiang Y, Wang S, Jiang M, Chen Z, Ying Q, Wang H. 2015. Molecular identification of Dendrobium species (Orchidaceae) based on the DNA barcode ITS2 region and ITS application for phylogenetic study. International Journal of Molecular Sciences. vol 16(9): 21975–21988. doi: https://doi.org/10.3390/ijms160921975.
Givnish TJ, Spalink D, Ames M, Lyon SP, Hunter SJ, Zuluaga A, Doucette A, Caro GG, McDaniel J, Clements MA, Arroyo MTK, Endara L, Kriebel R, Williams NH, Cameron KM. 2016. Orchid historical biogeography, diversification, Antarctica and the paradox of orchid dispersal. Journal of Biogeography. vol 43(10): 1905–1916. doi: https://doi.org/10.1111/jbi.12854.
Hani A, Widyaningsih TS, Damayanti RU. 2014. Potensi dan pengembangan jenis-jenis tanaman anggrek dan obat-obatan di jalur wisata Loop-Trail Cikaniki-Citalahab Taman Nasional Gunung Halimun-Salak. Jurnal Ilmu Kehutanan. vol 8(1): 42–49. doi: https://doi.org/10.22146/jik.8574.
Hidayat T, Yukawa T, Ito M. 2005. Molecular phylogenetics of subtribe Aeridinae (Orchidaceae): Insights from plastid matK and nuclear ribosomal ITS sequences. Journal of Plant Research. vol 118: 271–284. doi: https://doi.org/10.1007/s10265-005-0217-3.
Huda MK, Price A, Wilcock CC. 2017. Identification of medicinal orchids of Bangladesh: DNA barcoding vs. traditional taxonomy. The Journal of the Orchid Society of India. vol 31: 33–40.
Jinbo U, Kato T, Ito M. 2011. Current progress in DNA barcoding and future implications for entomology. Entomological Science. vol 14(2): 107–124. doi: https://doi.org/10.1111/j.1479-8298.2011.00449.x.
Kementerian Lingkungan Hidup dan Kehutanan Republik Indonesia. 2007. Peraturan Menteri Kehutanan Nomor: P.35 / Menhut-II/2007. Jakarta: KLKH RI. https://www.menlhk.go.id/.
Kim HM, Oh SH, Bhandari GS, Kim CS, Park CW. 2014. DNA barcoding of Orchidaceae in Korea. Molecular Ecology Resources. vol 14(3): 499–507. doi: https://doi.org/10.1111/1755-0998.12207.
Khew GS-W, Chia TF. 2011. Parentage determination of Vanda Miss Joaquim (Orchidaceae) through two chloroplast genes rbcL and matK. AoB Plants. vol 2011: 1–12. doi: https://doi.org/10.1093/aobpla/plr018.
Li M, Cao H, But PPH, Shaw PC. 2011. Identification of herbal medicinal materials using DNA barcodes. Journal of Systematics and Evolution. vol 49(3): 271–283. doi: https://doi.org/10.1111/j.1759-6831.2011.00132.x.
Martins AC, Scherz MD, Renner SS. 2014. Several origins of floral oil in the Angelonieae, a southern hemisphere disjunct clade of Plantaginaceae. American Journal of Botany. vol 101(12): 2113–2120. doi: https://doi.org/10.3732/ajb.1400470.
Millar A. 1978. Orchids of Papua New Guinea. Canberra: ANU Press.
Ming BSY. 2000. The Catalogue of Medicinal Plants Resources in Taiwan (Chinese Edition). Kuala Lumpur: China Press. p. 120.
Moreira DDL, Teixeira SS, Monteiro MHD, De-Oliveira ACA, Paumgartten FJR. 2014. Traditional use and safety of herbal medicines. Revista Brasileira de Farmacognosia. vol 24(2): 248–257. doi: https://doi.org/10.1016/j.bjp.2014.03.006.
O’Byrne P. 1994. Lowland Orchids of Papua New Guinea. Singapore: National Parks Board Singapore.
Perwitasari DAG, Rohimah S, Ratnasari T, Sugiharto B, Su’udi M. 2020. DNA barcoding anggrek obat Dendrobium discolor Lindl. Tanimbar menggunakan gen rbcL dan ITS. Buletin Penelitian Tanaman Rempah dan Obat. vol 31(1): 8–20. doi: http://dx.doi.org/10.21082/bullittro.v31n1.2020.8-20.
Rohimah S, Mukarramah L, Sindiya V, S VY, K GA, Su’udi M. 2018. Eksplorasi jenis dan potensi DNA barcode Thrixspermum secara in silico. Jurnal Biodjati. vol 3(2): 148–156. doi: https://doi.org/10.15575/biodjati.v3i2.3409.
Saddhe AA, Kumar K. 2018. DNA barcoding of plants: selection of core markers for taxonomic groups. Plant Science Today. vol 5(1): 9–13. doi: https://doi.org/10.14719/pst.2018.5.1.356.
Schuiteman A. 1995. Key to the genera of Orchidaceae of New Guinea. Flora Malesiana Bulletin. vol 11(6): 401–424.
Schuiteman A, Vermeulen JJ, de Vogel EF. 2010. Flora Malesiana: Orchids of New Guinea Vol. VI - Genus Bulbophyllum. Leiden: National Herbarium of the Netherlands.
Semiarti E. 2012. Kebutuhan inovasi dalam pengembangan industri anggrek yang berdaya saing dan berbasis sumber daya lokal. Prosiding Seminar Nasional Anggrek. June 21, 2012. Medan: Puslitbanghorti RI. ISBN: 978-979-8257-50-6. hal 21–28.
Sindiya V, Mukarramah L, Rohimah S, Perwitasari DAG, Su’udi M. 2018. Studi in silico potensi DNA barcode pada anggrek langka Paphiopedilum. Biosfer Jurnal Biologi dan Pendidikan Biologi. vol 3(1): 2549–0486. doi: http://dx.doi.org/10.23969/biosfer.v3i1.1250.
Su CL, Chen WC, Lee AY, Chen CY, Chang YCA, Chao YT, Shih MC. 2013. A modified ABCDE model of flowering in orchids based on gene expression profiling studies of the moth orchid Phalaenopsis aphrodite. PLoS One. vol 8(11): 1–14. doi: https://doi.org/10.1371/journal.pone.0080462.
Sun Y, Skinner DZ, Liang GH, Hulbert SH. 1994. Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA. Theoretical and Applied Genetics. vol 89(1): 26–32. doi: https://doi.org/10.1007/BF00226978.
Taheri JB, Azimi S, Rafieian N, Zanjani HA. 2011. Herbs in dentistry. International Dental Journal. vol 61(6): 287–296. doi: https://doi.org/10.1111/j.1875-595X.2011.00064.x.
Takamiya T, Wongsawad P, Tajima N, Shioda N, Lu JF, Wen CL, Wu JB, Handa T, Ijima H, Kitanaka S, Yukawa T. 2011. Identification of Dendrobium species used for herbal medicines based on ribosomal DNA Internal transcribed spacer sequence. Biological and Pharmaceutical Bulletin. vol 34(5): 779–782. doi: https://doi.org/10.1248/bpb.34.779.
Teoh ES. 2016. Medicinal orchids of Asia. Switzerland: Springer International Publishing. p. 583. doi: https://doi.org/10.1007/978-3-319-24274-3.
Tsiftsis S, Štípková Z, Kindlmann P. 2019. Role of way of life, latitude, elevation and climate on the richness and distribution of orchid species. Biodiversity and Conservation. vol 28(1): 75–96. doi: https://doi.org/10.1007/s10531-018-1637-4.
Utami ESW, Hariyanto S. 2019. In vitro seed germination and seedling development of a rare Indonesian native orchid Phalaenopsis amboinensis J.J.Sm. Scientifica. vol 2019: 1–7. doi: https://doi.org/10.1155/2019/8105138.
Wahyudiningsih TS, Nion YA. 2017. Pemanfaatan anggrek spesies Kalimantan Tengah berbasis kearifan lokal yang berpotensi sebagai bahan obat herbal. Jurnal Biodjati. vol 2(2): 149–158. doi: http://doi.org/10.15575/biodjati.v2i2.1570.
Yao H, Qiao YJ, Zhao YL, Tao XF, Xu LN, Yin LH, Qi Y, Peng JY. 2016. Herbal medicines and nonalcoholic fatty liver disease. World Journal of Gastroenterology. vol 22(30): 6890–6905. doi: https://dx.doi.org/10.3748%2Fwjg.v22.i30.6890.
Zhai JW, Zhang GQ, Chen LJ, Xiao XJ, Liu KW, Tsai WC, Hsiao YY, Tian HZ, Zhu JQ, Wang MN, Wang FG, Xing FW, Liu ZJ. 2013. A new orchid genus, Danxiaorchis, and phylogenetic analysis of the tribe Calypsoeae. PloS One. vol 8(4): 1–10. doi: https://doi.org/10.1371/journal.pone.0060371.
Copyright (c) 2020 Nada Nisrina Maulidya, Siti Rohimah, Zakiyah Ramadany, Tri Ratnasari, Mukhamad Su'udi
This work is licensed under a Creative Commons Attribution 4.0 International License.
COPYRIGHT AND LICENSE STATEMENT
COPYRIGHT
Biogenesis: Jurnal Ilmiah Biologi is published under the terms of the Creative Commons Attribution license. Authors hold the copyright and retain publishing rights without restriction to their work. Users may read, download, copy, distribute, and print the work in any medium, provided the original work is properly cited.
LICENSE TO PUBLISH
1. License
The use of the article will be governed by the Creative Commons Attribution license as currently displayed on http://creativecommons.org/licenses/by/4.0.
2. Author’s Warranties
The author warrants that the article is original, written by stated author/s, has not been published before, contains no unlawful statements, does not infringe the rights of others, is subject to copyright that is vested exclusively in the author and free of any third party rights, and that any necessary written permissions to quote from other sources have been obtained by the author(s).
3. User Rights
Under the Creative Commons Attribution license, the users are free to download, reuse, reprint, modify, distribute and/or copy the content for any purpose, even commercially, as long as the original authors and source are cited. No permission is required from the authors or the publishers.
4. Co-Authorship
If the article was prepared jointly with other authors, the corresponding author warrants that he/she has been authorized by all co-authors, and agrees to inform his/her co-authors of the terms of this statement.
5. Miscellaneous
Biogenesis: Jurnal Ilmiah Biologi may conform the article to a style of punctuation, spelling, capitalization, and usage that it deems appropriate. The author acknowledges that the article may be published so that it will be publicly accessible and such access will be free of charge for the readers.
