USING SHORT SEQUENCE matK GENE AS BARCODE DNA FOR IDENTIFICATION OF DURIO Sp IN TERNATE ISLAND
Keywords:
Identification, Local Durian, matK Gene, Ternate Island
Abstract
The Barcode of Life Consortium (CBOL) recommended a standard method for the identification of plant species using matK and rbcL barcoding gene. This study was aimed to evaluate the efficiency of matK DNA barcoding for identification of local durian (Durio sp.) from Ternate Island. Total 15 local durian has been used in this study. Whole genom DNA was isolated by Geneid plant DNA kit and then successfully amplified by the Polymerase Chain Reaction (PCR) technique using specific primer. MatK successfully amplified with 245 bp in length. MatK has sequencing success (71.3%) and relative high of Quality value 20+ (86%). BLAST analysis of the sequence showed that local durian in Ternate are identifies as Durio zibethinus and Neesia malayana with query cover 97%-99%. It could be concluded that matK with short sequence is not efficience for durian identification. The recommended in this studies for using of molecular markers with sequence lengths above 500 bp would be more effective for the identification of cryptic species Durio sp. and other.
References
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Dick, C.W., & Kress, W.J. (2009). Dissecting tropical plant diversity with forest plots and a molecular toolkit. BioScience, 59(9), 745-755.
Group, C.P.W., Hollingsworth, P.M., Forrest, L.L., Spouge, J.L., Hajibabaei, M., Ratnasingham, S., & Fazekas, A.J. (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences, 106(31), 12794-12797.
Hollingsworth, M.L., Andra C., Forrest, L.L., Richardson, J., Pennington, R.T., Long, D.G., & Hollingsworth, P.M. (2009). Selecting barcoding loci for plants: evaluation of seven candidate loci with species‐level sampling in three divergent groups of land plants. Molecular ecology resources, 9(2), 439-457.
Hollingsworth, P.M., Graham, S.W., & Little, D.P. (2011). Choosing and using a plant DNA barcode. PloS one, 6(5), e19254.
Kolondam, B. J., Lengkong, E., Polii M.J., Pinaria, A., & Runtunuwu, S. (2012). DNA barcode of payus limondok orchid (Phaius tancarvilleae) based on the rbcL and matK genes. Jurnal Bioslogos, 2(2), 55-62.
Kuzmina ML, Johnson KL, Barron HR, Herbert PDN. 2012. Identification of vascular plants of Churchill, Manitoba, using a DNA barcode library. BMC Ecology 12:1-11. http:// dx.doi.org/10.1186/1472-6785-12-25
Ministry of Agriculture. (2014). Outlook Durian Commodity, Jakarta; Agricultural Data and Information System Center of the Secretariat General of Agriculture. pp 38-42
Morgulis, A., Coulouris, G., Raytselis, Y., Madden, T.L., Agarwala, R., & Schäffer, A.A. (2008). Database indexing for production MegaBLAST searches. Bioinformatics, 24(16), 1757-1764.
Muller, K.F., Borsch, T., & Hilu, K.W. (2006). Phylogenetic utility of rapidly evolving DNA at high taxonomical levels: contrasting matK, trnT-F, and rbcL in basal angiosperms. Molecular phylogenetics and evolution, 41(1), 99-117.
Newsmaster SG, Ragupathy S. (2009). Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae). Molecular Ecology Resources, 9:172-180. http:// doi: 10.1111/j.1755-0998.2009.02642.x
Santoso, P.J. (2010). Lai durian Colorful Attractive Flesh; Export Potential. Tropical Fruit Plant Research Center. pp 36-41.
Shen, Y.Y., Chen, X., & Murphy, R.W. (2013). Assessing DNA barcoding as a tool for species identification and data quality control. PLoS One, 8(2), e57125.
Siew, G.Y., Ng, W.L., Salleh, M.F., Tan, S.W., Ky, H., Alitheen, N.B. M., & Yeap, S.K. (2018). Assessment of the Genetic Variation of Malaysian Durian Varieties using Inter-Simple Sequence Repeat Markers and Chloroplast DNA Sequences. Pertanika Journal of Tropical Agricultural Science, 41(1), 321-332.
Siregar, M. (2006). Species diversity of local fruit trees in Kalimantan: problems of conservation and its development. Biodiversitas Journal of Biological Diversity, 7(1), 94-99.
Soltis, P.S., Soltis, D.E., & Doyle, J.J. (1992). Molecular systematics of plants. Chapman & Hall: New York & London, 434, 1-13.
Sundari & Tolangara A.R. (2014). The study of taxonometric and philogenetic of local durian variety of Ternate and Jailolo in North Moluccas Province, Indonesia. International Journal of Engineering Research and Development, 10 (8), 52-57.
Sundari, Arumingtyas, E.L., Hakim, L., Azrianingsih, R. (2015). Morphological variation of local durian (Durio zibethinus Murr.) on the Ternate Island, Proceedings of International Biology and Life Science Conference (ICOLIB), 10 (2), 52-57.
Sundari, Arumingtyas, E.L., Hakim, L., Azrianingsih, R., Wahyudi, D. (2017). Genetic variability of local durian (durio zibethinus murr.) In Ternate island based on RAPD markers. Plant Cell Biotechnology and Molecular Biology Journa,l 18 (1&2), 68-75.
Xue, C.Y., & li, D.Z. (2011). Use of DNA barcode sensu lato to identify traditional Tibetan medicinal plant Gentianopsis paludosa (Gentianaceae). Journal of Systematics and Evolution, 49(3), 267-270.
Zang, H., Jue, J. P., & Mukherjee, B. (2000). A review of routing and wavelength assignment approaches for wavelength-routed optical WDM networks. Optical networks magazine, 1(1), 47-60.
