Confirmation of Tuntun Angin (Elaeocarpus floribundus) Taxonomic Status Using matK and ITS Sequences

Dewi Indriyani Roslim, Siti Khumairoh, Herman Herman

Abstract


Tuntun angin is one of important floodplain plants in and around Kajuik Lake located in Riau Province, Indonesia. Morphological identification shows that the scientific name of this plant is Elaeocarpus floribundus. The study aimed to confirm the taxonomic status of tuntun angin using matK and nuclear intergenic spacer (ITS) sequences. The methods included fresh leaf DNA isolation, polymerase chain reaction, electrophoresis, sequencing, and data analysis using BLASTn program and MEGA software version 6.06 programs. The results showed that the matK sequence (519 bp) of tuntun angin had highest similarity to E. floribundus matK sequence that was available in GenBank. It was supported by the high max score (937), low E-value (0.0), high identity value (100%), and high query cover (100%). However, the ITS sequence of tuntun angin did not show similarity to E. floribundus ITS sequence because there was no database of the sequence in GenBank. This study was able to confirm the taxonomic status of tuntun angin as E. floribundus using matK sequence and also showed that morphological and molecular identification techniques were complementary to each other. Moreover, this study enriched the DNA sequence database of E. floribundus in GenBank which will be useful for this species molecular identification.

How to Cite

Roslim, D. I., Khumairoh, S. & Herman, H. (2016). Confirmation of Tuntun Angin (Elaeocarpus floribundus) Taxonomic Status Using matK and ITS Sequences. Biosaintifika: Journal of Biology & Biology Education, 8(3), 393-400.


Keywords


Elaeocarpus floribundus; ITS; Kajuik Lake; matK; tuntun angin

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References


Ali, M. A., Gyulai, G., Hidvegi, N., Kerti, B., Al Hemaid, F. M., Pandey, A. K., & Lee, J. (2014). The changing epitome of species identificationDNA barcoding. Saudi journal of biological sciences, 21(3), 204-231.

Altschul, S. F., Madden, T. L., Schffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research, 25(17), 3389-3402.

Bangol, I., Momuata, L. I., & Kumaunang, M. (2014). Barcode DNA tumbuhan pangi (Pangium edule R.) berdasarkan gen matK. Jurnal MIPA Unsrat Online, 3(2), 113-119.

Banner, A. & MacKenzie, W. (1998). Riparian Areas: Providing Landscape Habitat Diversity, Part 5 of 7. Extension Note. Ministry of Forests Research Program, British Columbia.

Bolson, M., Smidt, EdC., Brotto, M. L., & Silva-Pereira, V. (2015). ITS and trnH-psbA as efficient DNA barcodes to identify threatened commercial woody Angiosperms from Southern Brazilian Atlantic rainforests. PLoS ONE, 10(12), e0143049.

Brahma, S., Narzary, H., & Basumatary, S. (2013). Wild edible fruits of Kokrajhar district of Assam, North-East India. Asian Journal of Plant Science and Research, 3(6), 95-100.

Castro, C., Hernandez, A., Alvarado, L., & Flores, D. (2015). DNA Barcodes in Fig Cultivars (Ficus carica L.) Using ITS Regions of Ribosomal DNA, the psbA-trnH Spacer and the matK Coding Sequence. American Journal of Plant Sciences, 6(01), 95.-102.

Cheong, M. L. S. & Ranghoo-Sanmukhiya, V. M. (2013). Phylogeny of Syzygium species using morphological, RAPD and ISSR Markers. International Journal of Agriculture & Biology, 15(3), 511-516.

DeSalle, R. (2006). Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff. Conservation Biology, 20(5), 1545-1547.

Elvyra, R. & Yus, Y. (2012). Ikan Lais dan Sungai Paparan Banjir di Provinsi Riau. Pekanbaru: UR Press Pekanbaru.

Erickson, D. L., Jones, F. A., Swenson, N. G., Pei, N., Bourg, N. A., Chen, W., Davies, S. J., Ge, X. J., Hao, Z., Howe, R. W. & Huang, C. L. (2014). Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach. Frontiers in genetics, 5, 358.

Fern, K. (2014). Elaeocarpus floribundus. Useful tropical plants database. http://tropical. theferns.info/query.php. [7 Nov 2015].

Group, C. P. W., 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. (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences, 106(31), 12794-12797.

Hajibabaei, M., Singer, G. A. C., Hebert, P. D. N., & Hickey, D. A. (2007). DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. TRENDS in Genetics, 23(4), 167-172.

Hebert, P. D., Cywinska, A., & Ball, S. L. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B: Biological Sciences, 270(1512), 313-321.

Hebert, P. D. N. & Gregory, T. R. (2005). The Promise of DNA Barcoding for Taxonomy. Systematic biology, 54(5), 852859.

Khomdram, S., Barthakur, S., & Devi, G. S. (2014). Biochemical and Molecular Analysis of Wild Endemic Fruits of the Manipur Region of India. International Journal of Fruit Science, 14(3), 253-266.

Kolondam, B. J., Lengkong, E., Polii-Mandan, 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.

Kress, W. J., Wurdack, K. J., Zimmer, E. A., Weigt, L. A., & Janzen, D. H. (2005). Use of DNA barcodes to identify flowering plants. PNAS, 102(23), 83698374.

Kress, W. J., & Erickson, D. L. (2007). A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS one, 2(6), e508.

Kurniawaty, N., Hidayat, P., & Rauf, A. (2016). Characterization of Three Species of Thrips on Banyan, Nutmeg, and Marine Seruni Plants Based on COI Gene. Biosaintifika: Journal of Biology & Biology Education, 8(2), 185-192.

Lahaye, R., Bank, M. V., Bogarin, D., Warner, J., & Pupulin, F. (2008). DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences, 105(8), 2923-2928.

Lambowitz, A. M. & Zimmerly, S. (2004). Mobile group II introns. Annu Rev Genet, 38,135.

Madden T. (2013). The NCBI Handbook, 2nd edition. Bethesda (MD): National Center for Biotechnology Information (US).

Nugraha, F., Roslim, D. I., Ardila Y. P., & Herman. (2014). Analisis sebagian sekuen gen ferritin2 pada padi (Oryza sativa L.) Indragiri Hilir Riau. Biosantifika: Journal of Biology and Biology Education, 6(2), 94-103.

Oyen, L. P. A. (2011). Elaeocarpus floribundus Blume. PROTA (Plant Resources of Tropical Africa). Netherlands. http://www.prota4u.org/search.asp. [20 Mar 2016].

Pang, X., Liu, C., Shi, L., Liu, R., Liang, D., Li, H., Cherny, S. S., & Chen, S. (2012). Utility of the trnHpsbA intergenic spacer region and its combinations as plant DNA barcodes: A meta-analysis. PLoS ONE, 7(11), e48833.

Patwardhan, A., Ray, S., Roy, A. (2014). Molecular markers in phylogenetic studies- A Review. Journal of Phylogenetics & Evolutionary Biology, 2, 131.

Pease, A. A., Davis, J. J., Edwards, M. S., & Turner, T. F. (2006). Habitat and resource use by larval and juvenile ?shes in an arid-land river (Rio Grande, New Mexico). Freshwater Biology, 51(3), 475-486.

Porebski, S., Bailey, L. G., & Baum, B. R. (1997). Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant molecular biology reporter, 15(1), 8-15.

Price, P., Lovett, S. (2002). Managing Riparian Land. Fact Sheet 1. Land & Water Australia, Canberra.

Rahman, S. S. & Vacik, H. (2015). Identify appropriate conservation strategies for rural people in Bangladesh. Biodivers Manage Forestry, 4(1)

Raveendar, S., Lee, J., Jae-Wan, P., Gi-An, L., Young-Ah, J., Yun, J. L., Gyu-Taek, C., Kyung-Ho, M., Sok-Young, L., Jong-Wook, C. (2015). Potential use of ITS2 and matK as a Two-Locus DNA Barcode for Identification of Vicia Species. Plant Breed Biotech, 3(1), 58-66.

Rosleine, D & Suzuki, E. (2012). Secondary sucession at abandoned grazing sites, Pangandaran Nature Reserve, West Java, Indonesia. Tropics, 21(3), 91-103.

Roslim, D. I. (2016). Pandan (Pandanus sp), Rotan (Calamus sp), and Rengas (Gluta sp) from Kajuik Lake, Riau Province, Indonesia. Brazilian Archives of Biology and Technology, 59(1), BiolAppl. [in press]

Roslim, D. I., Nurkhairani, P., Herman, & Elvyra, R. (2016a). Identification of Durik-Durik Plant (Syzygium sp) Using the psbA-trnH Intergenic Spacer and ITS Regions. TPGM, 3, 11-16.

Roslim, D. I., Herman, Sofyanti, N., Chaniago, M., Restiani, R., & Novita, L. (2016b). Characteristics of 22 cassavas (Manihot esculenta L., Crantz) from Riau Province, Indonesia. SABRAO J Breed Genet., 48(2), 110-119.

Smith, M. A., Fisher, B. L., & Hebert, P. D. N. (2005). DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: The ants of Madagascar. Philosophical Transactions of the Royal Society of London B: Biological Sciences, 360(1462), 1825-1834.

Snow, N., Young, S. L., Callmander, M. W. (2016). Syzygium dawsoniana (Myrtaceae): A New Species from New Caledonia with Bullate Leaves. Systematic Botany, 41(1), 197-201.

Tjitrosoepomo, G. 2003. Morfologi Tumbuhan. Yogyakarta: Gadjah Mada University Press.

Uddin, S. B. (2014). Medicinal plants of Bangladesh. Cell, 880, 1711065377.

White, T. J., Bruns, T. D., Lee, S. B., & Taylor, J. W. (1990). Amiplification and Direct Sequencing of Fungal Ribosomal RNA Genes for Phylogenetics. In: PCR Protocols and Application: A Guide to Methods and Applications. Academic Press, Inc.

Will, K. W. & Rubinoff, D. (2004). Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics, 20(1), 47-55.

Wojciechowski, M. F., Lavin, M., & Sanderson, M. J. (2004). Phylogeny of legumes (Leguminosae) based on analysis of the plastid Matk gene resolves many well-supported subclades within the family. American Journal of Botany, 91(11), 18461862.

Yu, J., Xue, J. H., & Zhou, S. L. (2011). New universal matK primers for DNA barcoding angiosperms. Journal of Systematics and Evolution, 49(3), 176-181.

Zeug, S. C. & Winemiller, K. O. (2008). Relationships between hydrology, spatial heterogeneity, and fish recruitment dynamics in a temperate floodplain river. River Research and Applications, 24(1), 90-102.

Zoschke, R., Nakamurab, M., Lierea, K., Sugiurab, M., Brnera, T., & Schmitz-Linnewebera, C. (2010). An organellar maturase associates with multiple group II introns. PNAS, 107(7), 3245-3250.




DOI: https://doi.org/10.15294/biosaintifika.v8i3.7406

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