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

Authors

  • Dinh Thi Phong
  • DÆ°Æ¡ng Van Tang
  • Vu Thi Thu Hien
  • Nguyen Dang Ton
  • Nong Van Hai

Keywords:

Dalbergia, nucleotide regions, phylogeny, rare, woody trees

Abstract

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.

 

References

I. Alvarez, J. F. Wendel, “Ribosomal ITS sequences and plant phylogenetic inferenceâ€. 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 NWFPâ€, 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)â€, 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 Forestâ€, Gen Mol Bio, vol. 35, no. 4, pp. 838-846, 2012.

CBOL Plant Working Group, “A DNA barcode for land plantsâ€, 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 goalsâ€, 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 plantsâ€, 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 wellâ€, 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 markersâ€, 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 Protocolsâ€, 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 gymnospermsâ€, 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 sequencesâ€, 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 plantsâ€, Proc Natl Acad Sci USA, vol. 106, pp. 12794-12797, 2009.

http://data.gbif.org/tutorial/datauseagreement/ 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)â€, 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)â€, 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 regionâ€, 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 plantsâ€, 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 hotspotsâ€, 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 otherwiseâ€, Syst Bot, vol. 25, pp. 449-467, 2000.

Y. Liu, H. F. Yan, X. J. Ge, “Evaluation of 10 plant barcordes in Bryophyta (Mosses)â€, 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 approachâ€, 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)â€, 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 sequenceâ€, J Mol Evol, vol. 28, pp. 87-97, 1988.

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

M. H. Peter, L. F. Laura, L. S. John, “A DNA barcode for land plantsâ€, 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 systematicsâ€, 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 componentâ€, 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 Dataâ€, 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 Forestâ€, Heredity, vol. 106, pp. 46-47, 2011.

N. Saitou, M. Nei “The neighbor-joining method: A new method for reconstructing phylogenetic treesâ€, 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)â€, 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 techniqueâ€, 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)â€, 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)â€, 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 dataâ€, 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 barcodingâ€, 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 4.0â€, 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 methodâ€, 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 speciesâ€, 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 applicationsâ€, Academic Press, San Diego, California, USA, pp. 315-322, 1990.

Downloads

Published

2014-04-03

How to Cite

Phong, D. T., Tang, D. V., Hien, V. T. T., Ton, N. D., & Hai, N. V. (2014). Nucleotide Diversity of a Nuclear and Four Chloroplast DNA Regions in Rare Tropical Wood Species of Dalbergia in Vietnam: A DNA Barcode Identifying Utility. Asian Journal of Applied Sciences, 2(2). Retrieved from https://www.ajouronline.com/index.php/AJAS/article/view/1004

Issue

Vol. 2 No. 2 (2014): April 2014

Section

Articles

License

  • Papers must be submitted on the understanding that they have not been published elsewhere (except in the form of an abstract or as part of a published lecture, review, or thesis) and are not currently under consideration by another journal published by any other publisher.
  • It is also the authors responsibility to ensure that the articles emanating from a particular source are submitted with the necessary approval.
  • The authors warrant that the paper is original and that he/she is the author of the paper, except for material that is clearly identified as to its original source, with permission notices from the copyright owners where required.
  • The authors ensure that all the references carefully and they are accurate in the text as well as in the list of references (and vice versa).
  • Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Attribution-NonCommercial 4.0 International that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
  • Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
  • Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
  • The journal/publisher is not responsible for subsequent uses of the work. It is the author's responsibility to bring an infringement action if so desired by the author.