Evaluation of the discriminatory power of plant dna barcodes rbcl & matk between species of fabaceae
Paper Details
Evaluation of the discriminatory power of plant dna barcodes rbcl & matk between species of fabaceae
Abstract
For species identification, .DNA barcoding is a novel diagnostic technique, the aim of which is to contribute towards wide range of ecological and conservation studies. In this study, we evaluated the capacity of the core DNA barcodes rbcla and matK for identifying 62 plant specimen belonging to 22 species of Fabaceae. All plant specimen were collected from district Dera Ghazi Khan, Punjab, Pakistan. In this research work, highest mean pairwise interspecific distance showed by matK and lowest for rbcl. Based on ‘best match’ and ‘best close match’ analysis function of TaxonDNA , both matK and rbcl was best with almost 73% correct identification, while based on ‘all species barcodes’ analysis, rbcl and matK gave the lowest percentage of correct species identifications 64.51% & 51.11%, respectively. By using MEGA5, for each marker neighbor joining (N/J) trees based on Kimur-2-parameter (K2P) were produced. In tree based analysis, species were considered to be discriminated. that form separate clusters in the tree with a bootstrap support >50%.. In this study both plant DNA barcodes in combination (rbcl +matK) showed best discriminatory power between different species of Fabaceae.
Berry V, Gascuel O. 1996. Interpretation of bootstrap trees, threshold of clade selection and induced gain. Molecular Biology and evolotion 13(7), 999-1011. http://dx.doi.org/10.1093/molbev/13.7.999
CBOL, Plant Working Group. 2009. A DNA barcode for land plants. Proceedings of the National Academy of Sciences USA 106, 12794–12797. http://dx.doi.org/10.1073/pnas.0905845106
De Vere N, Rich TCG, Ford CR. 2012. DNA barcoding the native flowering plants and conifers of Wales. PLoS ONE 7, 37945. http://dx.doi.org/10.1371/journal.pone.0037945
Fazekas AJ, Burgess KS, Kesanakurti PR, Percy DM, Hajibabaei M. 2008. Assessing the utility of coding and non-coding genomic regions for plant DNA barcoding. PLoS ONE 3, 1–12.
Fazekas AJ, Kesanakurti PR, Burgess KS, Percy DM, Graham SW, Barrett SCH, Newmaster SG. 2009. Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? Molecular Ecology Resources 9(1), 130–139. http://dx.doi.org/10.1111/j.1755-0998.2009.02652.x
Fazekas AJ, Steeves R, Newmaster SG. 2010. Improving sequencing quality from PCR products containing long mononucleotide repeats. Biotechniques 48, 277–281. http://dx.doi.org/10..2144/000113369
Felsenstein J. 1985. Confidence limits on phylogenies. An approach using the bootstrap. Evolution 39, 783-791.
Ferguson JWH. 2002. On the use of genetic divergence for identifying species. Biological Journal of Linnaean Society 75, 509–516. http://dx.doi.org/10.1046/j.1095-8312.2002.00042.x
Fu YM, Jiang WM, Fu CX. 2011. Identification of species within Tetrastigma (Miq.) Planch. (Vitaceae) based on DNA barcoding techniques. Journal of Systematics and Evolution 49, 237–245. http://dx.doi.org/10.1111/j.1759-6831.2011.00126.x
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 Medica 77, 92– 94. http://dx.doi.org/10.1055/s-0030-1250050
Gonzalez MA, Baralot C, Engel J, Mori SA, Pétronell P, Riéra B, Roger A, Thébaud C, Chave J. 2009. Identification of Amazonian Trees with DNA Barcodes. PLoS ONE 4(10), 7483. http://dx.doi.org/10.1371/journal.pone.0007483
Hajibabaei M, Janzen DH, Burns JM, Hallwachs Vand, Hebert PDN. 2006. DNA barcodes distinguish species of tropical Lepidoptera. Proceeding of the National Academy of Sciences USA 103, 968–971. http://dx.doi.org/10.1073/pnas.0510466103
Hebert PDN, Cywinska A, Ball SL, De Waard JR. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B. Biological Sciences 270, 313–321. http://dx.doi.org/10.1098/rspb.2002.2218
Ivanova NV, Fazekas AJ, Hebert PDN. 2008. Semi-automated, membrane based protocol for DNA isolation from plants. Plant Molecular Biology Reporter 26, 186–198. http://dx.doi.org/10.1007/s11105-008-0029-4
Jain SK, Rao RR. 1977. A Handbook of Field and Herbarium Methods. Today and Tomorrow’s Printers & Publishers, New Delhi.
Ausubel JH. 2009. A botanical macroscope. Proceeding of the National Academy of Sciences USA 106(31), 1256–1257. http://dx.doi.org/10.1073/pnas.0906757106
Jiang YC, Ding L, Zhang R, Yang Y, Zhou, Tang L. 2011. Identification of the genus Epimedium with DNA barcodes. Journal of Medicinal Plants Research 5, 6413–6417. http://dx.doi.org/10.5897/JMPR11.545
Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of molecular evolution 16, 111-120.
Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. 2005. Use of DNA barcodes to identify flowering plants. Proceeding of the National Academy of Sciences USA. 102, 8369–8374. http://dx.doi.org/10.1073/pnas.0503123102
Kress WJ, Erickson DL. 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), 508. http://dx.doi.org/10.1371/journal.pone.0000508
Kuzmina ML, Johnson K, Barron HR, Hebert PDN. 2012. Identification of the vascular plants of Churchill, Manitoba, using a DNA barcode library. BioMed Central Ecology 12, 25. http://dx.doi.org/10.1186/1472-6785-12-25
Lahaye RM, Van Der Bank, Bogari. 2008. DNA barcoding the floras of biodiversity hotspots. Proceeding of the National Academy of Science USA 105, 2923–2928. http://dx.doi.org/10.1073/pnas.0709936105
Little DP, Stevenson DW. 2007. A comparison of algorithms for the identification of specimens using DNA barcodes, Examples from gymnosperms. Cladistics 23, 1–21. http://dx.doi.org/10.1111/j.1096-0031.2006.00126.x
Levin RA, Wagner W, Hoch PC. 2003. Family-level relationships of Onagraceae based on chloroplast rbcl and ndhF data. American Journal of Botany 90, 107–115. http://dx.doi.org/10.3732/ajb.90.1.107
Maia VH, Mata CS, Franco LO, Cardoso MA, Cardoso SRS. 2012. DNA barcoding Bromeliaceae: achievements and pitfalls. PLoS ONE 7(1), 29877. http://dx.doi.org/10.1371/journal.pone.0029877
Mattio L, Payri C. 2010. Assessment of five markers as potential barcodes for identifying Sargassum subgenus Sargassum species (Phaeophyceae, Fucales). Cryptogamie Algologie 31, 467–485.
Meier R, Shiyang K, Vaidya G, Ng PKL. 2006. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology 55(5), 715–728. http://dx.doi.org/10.1080/10635150600969864
Newmaster SG, Fazekas AJ, Ragupathy S. 2006. DNA barcoding in land plants: Evaluation of rbcl in a multigene tiered approach. Canadian Journal of Botany 84, 335–441. http://dx.doi.org/10.1139/b06-047
Newmaster SG, Fazekas J, Steevea RAD, Janovec J. 2008. Testing candidate plant barcode regions in the Myristicaceae. Molecular Ecology Resources 8, 480–490. http://dx.doi.org/10.1111/j.1471-8286.2007.02002.x
Peter Hollingsworth M, Sean Graham W, Damon Little P. 2011. Choosing and Using a Plant DNA Barcode. PLoS ONE 6(5), 19254. http://dx.doi.org/10.1371/journal.pone.0019254
Pettengill J.B, Neel MC. 2010. An evaluation of candidate plant DNA barcodes and assignment methods in diagnosing 29 species in the genus Agalinis (Orobanchaceae). American Journal of Botany 97, 1391–1406. http://dx.doi.org/10.3732/ajb.0900176
Ren BQ, Xiang XG, Chen ZD. 2010. Species identification of Alnus (Betulaceae) using nrDNA and cpDNA genetic markers. Molecular Ecology Resources 10, 594–605. http://dx.doi.org/10.1111/j.1755-0998.2009.02815.x
Saarela JM, Sokoloff PC, Gillespie LJ, Consaul LL, Bull RD. 2013. DNA barcoding the a Canadian Arctic Flora: core plastid barcodes (rbcl+matK) for 490 Vascular Plant Species. PLoSONE 8, 36. http://dx.doi.org/10.1371/journal.pone.0077982
Tamura K, Peterson D, Peterson N. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28, 2731–2739. http://dx.doi.org/10.1093/molbev/msr121
Xiang XG, Hu H, Wang W, Jin XH. 2011. DNA barcoding of the recently evolved genus Holcoglossum (Orchidaceae: Aeridinae): a test of DNA barcode candidates. Moecular Ecology Resources 11, 1012–1021. http://dx.doi.org/10.1111/j.1755-0998.2011.03044.x
Xu B, Wu N, Gao XF, Zhang LB. 2012. Analysis of DNA sequences of six chloroplast and nuclear genes suggests incongruence, introgression, and incomplete lineage sorting in the evolution of Lespedeza (Fabaceae). Molecular Phylogenetics and Evolution 62, 346–358. http://dx.doi.org/10.1016/j.ympev.2011.10.007
Yang JB, Wang YP, Moller M, Gao LM, Wu D. 2012. Applying plant DNA barcodes to identify species of Parnassia (Parnassiaceae). Moecular Ecology Resources. 12, 267–275. http://dx.doi.org/10.1111/j.1755-0998.2011.03095.x
Zabta Shinwari K. 2010. Medicinal plants research in Pakistan. Journal of Medicinal Plants Research 4(3), 161-176.
Zhang CY, Wang FY, Yan HF, Hao G, Hu CM. 2012. Testing DNA barcoding in closely related groups of Lysimachia L. (Myrsinaceae). Molecular Ecology Resources 12, 98–108. http://dx.doi.org/10.1111/j.1755-0998.2011.03076.x
Saadullah, Zaheer-ud-Din Khan, Muhammad AShfaq, Zaib-u-Nisa, 2016. Evaluation of the discriminatory power of plant dna barcodes rbcl & matk between species of fabaceae. Int. J. Biosci., 8(5), 75-86.
Copyright © 2016 by the Authors. This article is an open access article and distributed under the terms and conditions of the Creative Commons Attribution 4.0 (CC BY 4.0) license.