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Identification of the grass family (Poaceae) by using the plant dna barcodes rbcl and matK

Saadullah, Zaheer-ud-din Khan, Muhammad Ashfaq, Zaib-u-Nisa

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J. Bio. Env. Sci.8(5), 175-186, May 2016


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Due to phenotypic plasticity, with few distinguishable and many overlapping characters, grasses are very difficult to identify by morphological characters, The current research evaluated how standard plant barcode rbcl and matK can help in floristic evaluation of. grasses belonging to a not well studied flora in district Dera Ghazi Khan, Punjab, Pakistan. In this study, 54 specimen belonging to 24 species of Poaceae were examined. Species wise sequencing success for rbcl and matK was 100% and 66.67% respectively. The determination of intra and inter-specific divergence and phylogentic analysis by reconstruction of neighbor joining trees were carried out. The results demonstrated that individually both rbcl and matK totally failed in discrimination of congeneric species. In neighbor joining phylogenetic analysis both rbcl and matK provided well resolved monophyletic tree with weak bootstrap threshold value. While in combination (rbcl+matK) both marker provided well resolved monophyletic tree with strong bootstrap threshold value.


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Identification of the grass family (Poaceae) by using the plant dna barcodes rbcl and matK

Berry V, Gascuel O. 1996. Interpretation of bootstrap trees, threshold of clade selection, and induced gain. Molecular Biology and evolution 13, 999-1011.

Burgess KS, Fazekas AJ, Kesanakurti PR, Graham SW, Husband BC, Newmaster SG, Percy DM, Hajibabaei M, Barrett SCH. 2011. Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode. Method in Ecology and Evolution, 2,333–340.

CBOL Plant Working Group. 2009. A DNA barcode for land plants. Proceeding of National Academy of Sciences USA 106, 12794–12797.

Chase MW, Fay MF. 2009. Barcoding of plants and fungi. Science 325, 682–683

Chase MW, Soltis DE, Olmstead RG, Morgan D, Les DH, Mishler BD, Duvall MR, Price RA, Hills HG QIUYL, Kron KA, Rettig JH, Conti E, Palmer JD, Manhart JR, Sytsma KJ, Michaels HJ, Kress WJ, Karol KG, Clark WD, Hedren M, Gaut BS, Jansen RK, Kim KJ, Wimpee CF, Smith JF, Furnier GR, Strauss SH, Xiang QY, Plunkett GM, Soltis PS. 1993. Phylogenetics of seed plants, an analysis of nucleotide sequences from the plastid gene rebel. Annals of the Missouri Botanical Garden. 80, 528–580.

Chen SL, Sun B, Leu L, Wu Z, Lu S, Li D, Wang Z, Zhu Z, Xia N, Wu PH, Raven, Young DY. 2006. Flora of China (Poaceae) 22. Science press, Beijing China and Missouri Botanical Garden, Missouri USA.

Cope TA, Nasir E, Ali SI. 1982. Poaceae. In Flora of Pakistan. (Eds.) Karachi, Islamabad 143, 40-678.

de Vere N, Rich TCG, Ford CR. 2012. DNA barcoding the native flowering plants and conifers of Wales. PLoS ONE 7, 37945.

Edgar RC. 2004. MUSCLE, multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32, 1792–1797.

Fazekas AJ, Steeves R, Newmaster SG. 2010. Improving  sequencing  quality  from  PCR  products containing long mononucleotide repeats. Biotechniques 48, 277–281.

Fazekas AJ, Kuzmina ML, Newmaster SG, Hollingsworth PM. 2012. DNA barcoding methods for land plants. Methods in Molecular Biology: In DNA barcodes, methods and protocols 858.

Felsenstein J. 1985. Confidence limits on phylogenies. An approach using the bootstrap. Evolution 39, 783-791.

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.

Gao T, Sun Z, Yao H, Song J, Zhu Y. 2011. Identification of Fabaceae plants using the DNA barcode matK. Planta Medica 77, 92–94.

Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proceeding of Royal Society of London, Biological Sciences 270, 313–321.

Ivanova NV, DeWaard JR, Hajibabaei M, Hebert PDN. 2005. Protocols for high volume DNA barcoding. http://www.dnabarcoding.ca/

Ivanova NV, Fazekas AJ, Hebert PDN. 2008, Semi-automated, membrane-based protocol for DNA isolation from plants. Plant Molecular Biology Reporter 26,186–198.

Jain SK, Rao RR, 1977. A Handbook of Field and Herbarium Methods. Today and Tomorrow’s Printers & Publishers, New Delhi.

Ivanova N, Kuzmina M, Fazekas A. 2011. CCDB Protocols. Manual Protocol Employing Centrifugation. Glass  Fiber Plate  DNA Extraction Protocol For Plants, Fungi, Echinoderms and Mollusks. http://www.ccdb.ca/CCDB_DOCS/CCDB_DNA_Extraction-Plants.pdf

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.

Kelly LJ, Ameka GK, Chase MW. 2010. DNA barcoding of African Podostemaceae (river-weeds), a test of proposed barcode regions. Taxon 59, 251–260.

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.

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, 508.

Kress WJ, Erickson DL, Swenson NG. 2010. Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican Forest Dynamics Plot. PLoS ONE 5,15409.

Kuzmina M, Ivanova N. 2011 PCR Amplification for Plants and Fungi. http://www.ccdb.ca/CCDB_DOCS/CCDB_Amplificat ion-Plants.pdf

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.

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.

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.

Liu J, Moller M, Gao LM, Zhang DQ, Li DZ. 2011. DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species. Molecular Ecology Resources 11, 89–100.

Maia VH, Mata CS, Franco LO, Cardoso MA, Cardoso SRS. 2012. DNA barcoding Bromeliaceae: achievements and pitfalls. PLoS ONE 7(1), 29877.

Meier R, Shiyang K, Vaidya G, Peter KLN. 2006. DNA Barcoding and taxonomy in Diptera, a tale of high intraspecific variability and low identification success. Syst Biol 55, 715–728.

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.

Newmaster SG, Ragupathy S. 2009. Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae).Molecular Ecology Resource 9, 172–180.

Peter Hollingsworth M, Sean Graham W, Damon Little P. 2011. Choosing and Using a Plant DNA Barcode. PLoS ONE 6(5), 19254.

Pettengill JB, 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.

Ratnasingham S, Hebert PDN. 2007. BOLD, The Barcode of Life Data System (www.barcodinglife.org). Mol. Ecol. Notes 7, 355–364.

Roy S, Tyagi A, Shukla V, Kumar A, Singh UM. 2010. Universal plant DNA barcode loci may not work in complex groups: A case study with Indian Berberis Species. PLoS ONE 5(10), 13674.

Ren BQ, Xiang XG, Chen ZD. 2010. Species identification of Alnus (Betulaceae) using nrDNA and cpDNA genetic markers. Molecular Ecology Resources 10, 594–605.

Rinovize SA. 1986. A survey of leaf blade Anatomy in Grasses VIII. Kew Bull 41, 323-338.

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. PLoS ONE 8, 36.

Spooner DM. 2009. DNA barcoding will frequently fail in complicated groups: an example in wild potatoes. American Journal of Botany 96, 1177–1189.

Starr JR, Naczi RFC, Chouinard BN. 2009. Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae). Moecular Ecology Resources 9, 151–163.

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6, Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution 30, 2725-2729

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.

Roy S, Tyagi A, Shukla V, Kumar A, Singh UM. 2010. Universal plant DNA barcode loci may not work in complex groups: A case study with Indian Berberis Species. PLoS ONE 5(10), 13674.

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.

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.


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