Molecular taxonomy via DNA barcodes for species identification in selected genera of Fabaceae
Abstract
Fabaceae is an invaluable plant family with considerable ecological and economic importances for example as food sources, bio-fertilizer, and medicinal plants. However, Fabaceae has been overexploited in Indonesia and several species belong to this family are critically endangered. Due to morphological similarity, rapid and accurate identification of Fabaceae species is essential to support its conservation efforts. Nowadays, species identification through DNA barcoding has become an effective taxonomic classification tool. This study was aimed to evaluate the effectiveness of chloroplast markers, matK and rbcL and the combination (matK+rbcL), as DNA barcodes for the identification of seleted genera in Fabaceae. The result showed that matK+rbcL and matK had the highest level of identification (90% and 82.05%) of the investigated genera, respectively. Additionally, matK had the highest mean of interspesific distance (0.134) and intraspecific distance (0.003). The combined barcode matK+rbcL had the highest correct identification rate when comparing the morphological with molecular identification. Furthermore, the best phylogenetic tree was obtained using Neighbor Joining method. Based on the overall performance, matK and matK+rbcL were the best barcodes for the selected genera in this study.
References
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Zheng SH, Ren WG, Wang ZH, Huang LF. 2015. Use of chloroplast DNA barcodes to identify Osmunda japonica and its adulterants. Plant Systematics And Evolution 301(7):1843–1850.
Amandita FY, Reynold K, Vornam B, Rahayu S, Siregar IZ, Kreft H, Finkeldey R. 2019. DNA barcoding of flowering plants in Sumatra, Indonesia. Ecology and Evolution 9(1):1-11.
Barthet MM, Hilu KW. 2007. Evaluating Evolutionary Constraint on the Rapidly Evolving Gene matK Using Protein Composition. J Mol Evol 66:85-97.
Bordewich M, Tokao M. 2016. An algorithm for reconstructing ultametric tree-child networks from inter-taxa distances. Elsevier 213(2016): 47-59.
Christinawati IB, Simamora N, Tampubolon S, Pinem A. 2010. Sequence Alignment Menggunakan Algoritma Smith Waterman. Seminar Nasional Politeknik Batam 2(2): 1-6.ISSN : 2085-3858.
Cumming MP, Nugent JM, Olmstead RG, Palmer JD. 2003. Phylogenetik Analysis Reveals Five Independent Transfer of the Chloroplast Gene rbcL to the Mitochondrial Genome in Angiosperms. Curr Genet 43:131- 138.
Doyle JJ, Chappill JA, Bailey D, Kajita T. 2000. Towards a comprehensive phylogeny of legumes: evidence from rbcL sequences and non-molecular data. Advances in legume systematics 9: 1-20.
Elansary HO, Ashfaq M, Ali HM, Yessoufou K. 2017. The first initiative of DNA barcoding of ornamental plants from Egypt and potential applications in horticulture industry. PloS ONE 12(2).
Gao T, Sun Z, Yao H, Song J, Zhu Y, Ma X, Chen S. 2011. Identification of Fabaceae Plants Using the DNA Barcode matK. Planta Med 77:92-94.
Goba KAE. 2019.Morphological Diversity within Pterocarpus erinaceus Poir (Fabaceae), an Overexploited Species in the Savannahs of Cote d’Ivoire. American Journal of Plant Sciences 10(9): 1675-1688.
Gomes GDS, Silva GS, Silva DLS, Oliveira RRD, Conceicao GM. 2018. Botanical Composition of Fabaceae Family in the Brazilian Northeast, Maranhão, Brazil. Asian Journal of Environment and Ecology 6(4): 1-10.
Hajibabaei M, Singer GAC, Clare EL, Hebert. 2007. Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biology 5(24):1-7.
Hartvig I, Czako M, Kjaer ED, Nielsen LR, Theilade I. 2015. The Use of DNA Barcoding in Identification and Conservation of Rosewood (Dalbergia sp.). PloS ONE 10(9): 1-24.
Hikmah R, Retnoningsih A, Habibah N. 2016. Keragaman durian berdasarkan fragmen Internal Transcibed Spacers (ITS) DNA ribosomal melalui Analisis PCR-RFLP. Jurnal MIPA 39(1): 11-18.
Hollingsworth PM, Graham SW, Little DP. 2011. Choosing and using a plant DNA barcode. J PLoS ONE 6(5): e19254.
Jiang KW, Zhang R, Zhang ZF, Pan B, Tian B. 2020. DNA barcoding and molecular phylogeny of Dumasia (Fabaceae: Phaseoleae) reveals a cryptic lineage. Plant Diversity 42(5): 376-385.
Kolondam BJ, Lengkong E, Mandang JP, Pinaria A, Runtunuwu S. 2012. Barcode DNA berdasarkan Gen rbcL dan matK Anggrek Payus Limondok (Phaius tancarvilleae). Jurnal Bios Logos 2(2): 55-62.
Kumar S, Gadagkar SR. 2001. Efficiency of the Neighbor-Joining Method in Reconstructing Deep and Shallow Evolutionary Relationships in Large Phylogenies. J Mol Evol 2000(51):544–553.
Kress WJ, Prince LM, Williams KJ. 2002. The phylogeny and a new classification of the gingers (Zingiberaceae): evidence from molecular data. Journal Bot. 89: 1682-1696.
Lis JA, Lis B, Ziaja DJ. 2016. In BOLD we trust? A commentary on the reliability of specimen identification for DNA barcoding: a case study on burrower bugs (Hemiptera: Heteroptera: Cydnidae). Zootaxa 4114(1):83-86.
Liu ZF, Ci XQ, Li L. 2017. DNA barcoding evaluation and implications for phylogenetic relationships in Lauraceae from China. PloS ONE 12(4):1-20.
Lompo D, Vinceti B, Gaisberger H, Konrad H, Duminil J, Ouedraogo M, Sina S, Geburek T. 2017. Genetic Conservation In Parkia biglobosa (Fabaceae:Mimosoideae). Silvae Genetica 66(1):1-8
Meyer CP, Paulay G. 2005. DNA barcoding: Error rates based on comprehensive sampling. PloS Biol. 3(12):e422.
Newmaster SG, Fazekas AJ, Steeves AD, Janovec J. 2008. Testing candidate plant barcodes regions in the Myristicaceae. Molecular Ecology Resources 8(3): 480-490.
Ochieng JW, Muigai AWT. 2007. Review: Phylogenetics in plant biotechnology: principles, obstacles and opportunities for resource poor. African Journal of Biotechnology 6(6): 639-649.
Pang X, Song J, Zhu Y, Xu H, Huang L, Chen S. 2010. Applying plant DNA barcodes for Rosaceae species identification. J Cladistics 27(2): 165- 170.
Patwardhan A, Ray S, Roy A. 2014. Molecular Markers in Phylogenetic Studies-A Review. J Phylogen Evolution Biol. 2(2): 1-9.
Rahayu DA, Jannah M. 2019. DNA Barcode: Hewan dan Tumbuhan Indonesia. Jakarta: Yayasan Inspirasi Ide Berdaya.
Ratnasingham S, Hebert PDN. 2007. BOLD: The Barcode of Life Data System. Molecular Ecology Notes 7(3): 355-364.
Romain AS, Pascal AC, Mark AW, Christine AO. 2014. Stability-activity tradeoffs constrain the adaptive evolution of RubisCO. Proceedings of the National Academy of Science of the United States of America 111 (6): 2223-2228
Saadullah Khan ZUD, Ashfaq M, Nisa ZU. 2016. Evaluation of the discriminatory power of plant DNA barcodes rbcL & matK between species of Fabaceae. International Journal of Biosciences 8(5):75-86.
Tabita FR, Hanson TE, Satagopan S, Witte BH, Kreel NE. 2008. Review: Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms. Phil. Trans. R. Soc. B. 363: 2629-2640.
Tallei TE, Rembet RE, Pelealu JJ, Kolondam BJ. 2016. Sequence Variation and Phylogenetic Analysis of Sansevieria trifasciata (Asparagaceae). Bioscience Research 13(1): 01-07.
Tamura K, Stecher G, Kumar S. 2016. MEGA 7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Dataset. Mol Biol Evol 33(7): 1870-1874.
Vaidya G, Lohman DJ, Meier R. 2011. SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Gladistics 27(2011): 171-180.
Wahab MA, Sundari, Suparman. 2014. Kajian Kekerabatan Filogenetik Durian (Durio zibethinus) Varietas Lokal Ternate Berdasarkan Karakter Morfologi. J Bioedukasi 2(1): 230-237.
Wattoo JL, Saleem MZ, Shahzad MS, Arif A, Hameed A, Saleem MA. 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.
Wu Z, Xu X, Zhang J, Wiegleb G, Hou H. 2019. Influence of eanviromental factors on the genetic variation of the aquatic macrophyte Ranunculus subrigidus on the Qinghai-Tibetan Plateau. BMC Evolutionary Biology 19(228): 1-11.
Zheng SH, Ren WG, Wang ZH, Huang LF. 2015. Use of chloroplast DNA barcodes to identify Osmunda japonica and its adulterants. Plant Systematics And Evolution 301(7):1843–1850.
Authors
WardaniI. G. A. K., AmanditaF. Y., Moura C. C. de M., GailingO. and SiregarI. Z. (2022) “Molecular taxonomy via DNA barcodes for species identification in selected genera of Fabaceae”, Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management). Bogor, ID, 12(1), pp. 112-122. doi: 10.29244/jpsl.12.1.112-122.
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