Nucleotide Diversity of a Nuclear and Four Chloroplast DNA Regions in Rare Tropical Wood Species of Dalbergia in Vietnam: A DNA Barcode Identifying Utility

Dinh Thi Phong, Dương Van Tang, Vu Thi Thu Hien, Nguyen Dang Ton, Nong Van Hai


Five nucleotide regions (a nuclear ribosomal DNA internal transcribed sequence (ITS) and four chloroplast DNA fragments (trnL intron, matK-designed, matK-barcode and psbA-trnH spacer) were used for the assesment nucleotide diversity for the eight woody tree species in genus Dalbergia (Dalbergia oliveri Gamble ex Prain, Dalbergia cochinchinensis Pierre, Dalbergia nigrescens Kurz, Dalbergia tonkinensis Prain, Dalbergia assamica Bentham, Dalbergia entadoides Pierre ex Prain, Dalbergia hancei Bentham and Dalbergia dialoides Pierre Niyomdham) of Vietnam. The number of variable sites for individual loci ranged from 13 (psbA-trnH spacer) to 111 (ITS). The highest divergence region was ITS (7.4  %), followed by psbA-trnH spacer (2.2 %), trnL intron (1.5 %), matK-designed (1.2 %) and matK-barcode (1.3 %). Analyses based on threshold genetic distances, Phylogenetic trees-based and nucleotide character differences methods showed that only nuclear ITS region is the best nucleotide diversity of rare woody tree species in Dalbergia genus. Therefore, it can be used as an identification of eight Dalbergia species.



Dalbergia, nucleotide regions, phylogeny, rare, woody trees

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I. Alvarez, J. F. Wendel, “Ribosomal ITS sequences and plant phylogenetic inference”. Mol. Phylogenet Evol., vol. 29, pp. 417-434, 2003.

M. Ashraf, A. B. Mumtaz, R. Riasat, S. Tabassum, “A molecular study of genetic diversity in Shisham (Dalbegia sisso) plantation of NWFP”, Pakistan. Pak J Bot, vol. 42, no. 1, pp. 79-88, 2010.

F. T. Barrer, A. Culham, C. E. Pkhurst, M. Gibby, “Mitochondrial and chloroplast DNA-based phylogeny of pelargonium (Geraniaceae)”, Amer J Bot, vol. 87, pp. 727-734, 2000.

O. R. S. Buzatti, R. A. Ribeiro, J. P. L. Filho, M. B. lovato, “Fine-scale spatial gebetic structure of Dalbergia nigra (Fabaceae), a threatened and endemic tree of the Brazilian Atlantic Forest”, Gen Mol Bio, vol. 35, no. 4, pp. 838-846, 2012.

CBOL Plant Working Group, “A DNA barcode for land plants”, Proc Natl Acad Sci USA, vol. 106, pp. 12794-12797, 2009.

M. W. Chase, N. Salamin, M. Wilkinson,J. M. Dunwell, R. P. Kesanakurthi, N. Haidar, V. Savolainen, “Land plants and DNA barcodes: short-term and long-term goals”, Biol Sci, vol. 360, no. 1889-1895, 2005.

R. S. Cowan, M. W. Chase, W. J. Kress, V. Savolainen, “300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants”, Taxon, vol. 55, no. 611-616, 2006.

N. T. Dang, T. B. Nguyen, Vietnam Red List, Publishing House for Science and Technology Hanoi, 2007.

A. J. Fazekas, K. S. Burgess, P. R. Kesanakurti, S. W. Graham, S. G. Newmaster, B. C. Husband, D. M. Percy, M. Hajibabaei, S. C. H. Barrett, “Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well”, PloS ONE, vol. 3, pp. 2802 – 2901, 2008.

A. J. Fazekas, P. R. Kesanakurti, K. S. Burgess, D. M. Percy, S. W. Graham, S. C. H. Barrett, S. G. Newmaster, M. Hajibabaei, B. C. Husband, “Are plant species inherently harder to discriminate than animal species using DNA barcoding markers”, Mol Ecol Res, vol. 9, pp. 130-139, 2009.

A. J. Fazekas, L. Kuzmina, S. G. Newmaster, P. M. Hollingsworth, “DNA Barcoding methords for land plants. In: Kress WJ, Erickson DL (ed) DNA Barcodes: Methods and Protocols”, Meth Mol Biol, vol. 858, pp. 223-252, 2012.

D. C. Hao, S. L. Chen, P. G. Xiao, “Sequence characteristics and divergent evolution of the chloroplast psbA-trnH noncoding region in gymnosperms”, J App Genet, vol. 51, pp. 259-273, 2010.

D. C. Hao, P. G. Xiao, B. Huang, G. B. Ge, L. Yang, “Interspecific relationships and origins of Taxaceae and Cephalotaxaceae revealed by partitioned Bayesian analyses of chloroplast and nuclear DNA sequences”, Pl Syst Evol, vol. 276, pp. 89-104, 2008.

P. M. Hollingsworth, L. L. Forrest, J. L. Spouge, M. Hajibabaei, S. Ratnasingham, V. D. M. Bank, “A DNA barcode for land plants”, Proc Natl Acad Sci USA, vol. 106, pp. 12794-12797, 2009. GBIF Data Sharing Agreement/dalbergia

IUCN (1998) The World List of Threatened Trees. World Conservation Press, UK

B. P. James, M. C. Neel, “An evaluation of candidate plant DNA barcodes and assignment methods in diagnosing 29 species in the genus Agalinis (Orobanchaceae)”, Amer J Bot, vol. 97, pp. 1391-1406, 2010.

R. S. Julian, F. C. N. Robert, N. C. Btianna, “Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae)”, Mol Ecol Res, vol. 9, pp. 151-163, 2009.

W. J. Kress, D. L. Erickson, “A two-locus global DNA barcode for land plants: The coding rbcL gene complements the non-coding trnH-psbA spacer region”, PloS ONE, vol. 2, pp. 508-610, 2007.

W. J. Kress, K. J. Wurdack, E. A. Zimmer, L. A. Weigt, D. H. Janzen, “Use of DNA barcodes to identify flowering plants”, Proc Natl Acad Sci USA, vol. 102, pp. 8369-8374, 2005.

R. Lahaye, M. van der Bank, D. Bogarin, J. Warner, F. Pupulin, G. Gigot, O. Maurin, S. Duthoit, T. G. Barraclough, V. Savolainen, “DNA barcoding the floras of biodiversity hotspots”, Proc Natl Acad Sci USA, vol. 105, pp. 2923-2928, 2008.

M. Lavin, M. Thulin, J. N. Labat, R. T. Pennington, “Africa, the odd man out: molecular biogeography of dalbergioid legumes (Fabaceae) suggests otherwise”, Syst Bot, vol. 25, pp. 449-467, 2000.

Y. Liu, H. F. Yan, X. J. Ge, “Evaluation of 10 plant barcordes in Bryophyta (Mosses)”, J Syst Evol, vol. 48, pp. 36-46, 2010.

S. G. Newmaster, A. J. Fazekas, S. Ragupathy, “DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach”, Can J Bot, vol. 84, pp. 335-341, 2006.

Newmaster SG, Fazekas AJ, Steeves AD, Janovec J (2008) Testing candidate plant barcode regions in the Myristicaceae. Mol Ecol Res 8: 480-490

S. G. Newmaster, S. Ragupathy, “Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae)”, Mol Ecol Res, vol. 9, pp. 172-180, 2009.

J. D. Palmer, L. A. Herbon, “Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence”, J Mol Evol, vol. 28, pp. 87-97, 1988.

E. Pennisi, “Taxonomy. Wanted: a barcode for plants”, Sciences, vol. 318, pp. 190-191, 2007.

M. H. Peter, L. F. Laura, L. S. John, “A DNA barcode for land plants”, Proc Natl Acad Sci USA, vol. 106, pp. 12794-12797, 2009.

M. D. Pirie, M. P. B. Vargas, M. Botermans, F. T. Bakker, L. W. Chatrou, “Ancient paralogy in the cpDNA trnL-F region in Annonaceace: implications for plant molecular systematics”, Amer J Bot, vol. 94, pp. 1003-1016, 2007.

S. Porebski, L. G. Bailey, B. R. Baum, “Modification of a CTAB DNA extraction protocol for plants containing high polysaccharides and polyphenol component”, Pl Mol Biol Rep, vol. 15, pp. 8-15, 1997.

R. A. Ribeiro, M. Lavin, J. P. Lemos-Filho, F. C. V. Mendonca, F. R. Santos, M. B. Lovato, “The Genus Machaerium (Leguminosae) is More Closely Related to Aeschynomene Sect. Ochopodium than to Dalbergia: Inferences from Combined Sequence Data”, Syst Bot, vol. 32, pp. 762-771, 2007.

R. A. Ribeiro, J. P. Lemoos-Filho, A. C. S. Ramos, M. B. Lavato, “Phylogeography of the endangered rosewood Dalbergia nigna (Fabaceae): insight into the evolutionary history and conservation of the Brazilia Atlantic Forest”, Heredity, vol. 106, pp. 46-47, 2011.

N. Saitou, M. Nei “The neighbor-joining method: A new method for reconstructing phylogenetic trees”, Mol Ecol Res, vol. 4, pp. 406-425, 1987.

T. Sang, D. J. Crawford, T. Stuessy “Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae)”, Amer J Bot, vol. 84, pp. 1120-1136, 2009.

J. Song, H. Yao, Y. Li, X. Li, Y. Lin, C. Liu, J. Han, C. Xie, S. Chen, “Authentication of the family Polygonaceae in Chinese pharmacopoeia by DNA barcoding technique”, J Ethnop, vol. 124, pp. 434-439, 2009.

J. R. Starr, F. C. N. Robert, C. Briannan, “Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae)”, Mol Ecol Res, vol. 9, pp. 151-163, 2009.

G. N. Steven, S. Ragupathy, “Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae)”, Mol Ecol Res, vol. 9, pp. 172-180, 2009.

G. R. Sylvain, B. Bremer, “Phylogeny and classification of Naucleeae S.l (Rubiaceae) inferred from molecular (ITS, rBCL and trnT-F) and morphological data”, Amer J Bot, vol. 86, pp. 1027-1047, 2002.

P. Taberlet, C. Eric, P. Francois, G. Ludovic, M. Christian, V. Alice, V. Thierry, G. Cortthier, B. Christian, W. Eske, “Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding”, Nucleic Acids Res, vol. 35, pp. 14 – 20, 2006.

K. Tamura, J. Dudley, M. Nei, S. Kumar, “MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0”, Mol Biol Evol, vol. 24, pp. 1596-1599, 2007.

K. Tamura, M. Nei, S. Kumar, “Prospects for inferring very large phylogenies by using the neighbor-joining method”, Proc Natl Acad Sci USA, vol. 101, pp. 11030-11035, 2004.

J. A. Tate, B. B. Simpson BB, “Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid species”, Syst Bot, vol. 28, pp. 723-737, 2003.

T. J. White, T. Bruns, S. Lee, D. J. Taylor DJ, “Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Gelfand D, Sminsky J, White T (ed) PCR protocols: a guide to methods and applications”, Academic Press, San Diego, California, USA, pp. 315-322, 1990.


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