Skip to content
Licensed Unlicensed Requires Authentication Published by De Gruyter March 28, 2015

Testing three proposed DNA barcodes for the wood identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain

  • Min Yu , Kai Liu , Liang Zhou , Lei Zhao and Shengquan Liu EMAIL logo
From the journal Holzforschung


Dalbergia odorifera T. Chen is a first-grade state protected plant in China. However, it is difficult to distinguish it from the closely related species Dalbergia tonkinensis Prain, which is less important in economic value, by wood anatomical features. In this study, three potential DNA barcode sequences, namely rpoC1, trnH-psbA and internal transcribed spacer (ITS), were used to differentiate wood of D. odorifera from D. tonkinensis. The average quantities of DNA extracts from twigs, sapwood and heartwood were 16.3, 11.5 and 6.0 ng mg-1, respectively. The success rates for polymerase chain reaction (PCR) amplification for three loci, namely ITS, trnH-psbA and rpoC1, were 62.5, 100 and 81.25%, respectively. The success rate for bidirectional sequencing of amplified products was 100% for all the three loci. The identification power of the three proposed DNA barcodes has been calculated by the BLAST, tree-based method and the TAXONDNA method. The interspecific differences of the trnH-psbA region were greater than intraspecific variations. Moreover, the identification power of trnH-psbA was higher than that of ITS and rpoC1 regions at the species level. Finally, the trnH-psbA region is proposed as a DNA barcode for wood identification between D. odorifera and D. tonkinensis.

Corresponding author: Shengquan Liu, School of Forestry & Landscape Architecture, Anhui Agricultural University, Hefei 230036, Anhui Province, P.R. China, Tel: +86 551 65786261, Fax: +86 551 65786518, e-mail:


This work is supported by a grant from the National Natural Science Foundation of China (No. 31070636) and a project of the Chinese State Forestry Administration (No. 201304508). We are grateful to vice director Dazhou Li (Hainan Provincial Forestry Science Institute, Hainan, P.R. China) and Professor Feng Xu (Guangxi University, Guangxi, P.R. China) for providing the heartwood samples of D. odorifera. Our special thanks also go to Professor Vu Huy Dai (Vietnam Forestry University, Hanoi, Vietnam) for courtesy in helping collect D. tonkinensis samples in Vietnam.


Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215:403–410.10.1016/S0022-2836(05)80360-2Search in Google Scholar

Asif, M.J., Cannon, C.H. (2005) DNA extraction from processed wood: a case study for the identification of an endangered timber species (Gonystylus bancanus). Plant Mol. Biol. Rep. 23:185–192.10.1007/BF02772709Search in Google Scholar

Bamber, R.K. (1976) Heartwood, its function and formation. Wood Sci. Technol. 10:1–8.10.1007/BF00376379Search in Google Scholar

Beldjoudi, N., Mambu, L., Labaïed, M., Grellier, P., Ramanitrahasimbola, D., Rasoanaivo, P., Martin, M. T., Frappier, F. (2003) Flavonoids from Dalbergia louvelii and their antiplasmodial activity. J. Nat. Prod. 66:1447–1450.10.1021/np030008xSearch in Google Scholar

Burland, T. G. Bioinformatics Methods and Protocols. Springer, Berlin, 1999.Search in Google Scholar

Cano, R.J. (1996) Analysing ancient DNA. Endeavour. 20:162–167.10.1016/S0160-9327(96)10031-4Search in Google Scholar

CBOL Plant Working Group. (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA. 106:12794–12797.10.1073/pnas.0905845106Search in Google Scholar

Chan, S.C., Chang, Y.S., Kuo, S.C. (1997) Neoflavonoids from Dalbergia odorifera. Phytochem. 46:947–949.10.1016/S0031-9422(97)00365-8Search in Google Scholar

Chan, S.C., Chang, Y.S., Wang, J.P., Chen, S.C., Kuo, S.C. (1998) Three new flavonoids and antiallergic, anti-inflammatory constituents from the heartwood of Dalbergia odorifera. Planta Med. 64:153–158.10.1055/s-2006-957394Search in Google Scholar PubMed

Chen, S., Yao, H., Han, J., Liu, C., Song, J., Shi, L., Zhu, Y., Ma, X., Gao, T., Pang, X. (2010) Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PloS One. 5:e8613.10.1371/journal.pone.0008613Search in Google Scholar PubMed PubMed Central

Choi, C.W., Choi, Y.H., Cha, M.R., Kim, Y.S., Gyu, h.Y., Kim, Y.K., Choi, S.U., Kim, Y.H., Ryu, S.Y. (2009) Antitumor components isolated from the heartwood extract of Dalbergia odorifera. J. Korean Soc. Appl. Bi. 52:375–379.10.3839/jksabc.2009.067Search in Google Scholar

Fukuda, H. (2000) Programmed cell death of tracheary elements as a paradigm in plants. Plant Mol. Biol. 44:245–253.10.1023/A:1026532223173Search in Google Scholar

Goda, Y., Kiuchi, F., Shibuya, M., Sankawa, U. (1992) Inhibitors of prostaglandin biosynthesis from Dalbergia odorifera. Chem. Pharm. Bull. 40:2452–2457.10.1248/cpb.40.2452Search in Google Scholar

Gonzalez, M.A., Baraloto, C., Engel, J., Mori, S.A., Pétronelli, P., Riéra, B., Roger, A., Thébaud, C., Chave, J. (2009) Identification of Amazonian trees with DNA barcodes. PLoS one. 4:e7483.10.1371/journal.pone.0007483Search in Google Scholar PubMed PubMed Central

Gu, J., Su, J., Lin, R., Li, R., Xiao, P. (2011) Testing four proposed barcoding markers for the identification of species within Ligustrum L. (Oleaceae). J. Syst. Evol. 49:213–224.10.1111/j.1759-6831.2011.00136.xSearch in Google Scholar

Gugerli, F., Parducci, L., Petit, R.J. (2005) Ancient plant DNA: review and prospects. New Phytol. 166:409–418.10.1111/j.1469-8137.2005.01360.xSearch in Google Scholar PubMed

Hajibabaei, M., Singer, G.A., Hebert, P.D., Hickey, D.A. (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet. 23:167–172.10.1016/j.tig.2007.02.001Search in Google Scholar PubMed

Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95–98.Search in Google Scholar

Hanssen, F., Wischnewski, N., Moreth, U., Magel, E.A. (2011) Molecular identification of Fitzroya cupressoides, Sequoia sempervirens, and Thuja plicata wood using taxon-specific rDNA-ITS primers. IAWA J. 32:273–284.10.1163/22941932-90000057Search in Google Scholar

Hebert, P.D., Cywinska, A., Ball, S.L. (2003a) Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B. Bio. 270:313–321.10.1098/rspb.2002.2218Search in Google Scholar

Hebert, P.D., Ratnasingham, S., de Waard, J.R. (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. Lond. B. Bio. 270:S96–S99.10.1098/rsbl.2003.0025Search in Google Scholar

Jiao, L., Yin, Y., Cheng, Y., Jiang, X. (2014) DNA barcoding for identification of the endangered species Aquilaria sinensis: comparison of data from heated or aged wood samples. Holzforschung. 68:487–494.10.1515/hf-2013-0129Search in Google Scholar

Kelman, L.M., Kelman, Z. (1999) The use of ancient DNA in paleontological studies. J. Vertebr. Paleontol. 19:8–20.10.1080/02724634.1999.10011118Search in Google Scholar

Kim, N.Y., Pae, H.O., Oh, G.S., Kang, T.H., Kim, Y.C., Rhew, H.Y., Chung, H.T. (2001) Butein, a plant polyphenol, induces apoptosis concomitant with increased caspase-3 activity, decreased Bcl-2 expression and increased Bax expression in HL-60 Cells. Pharmacol. Toxicol. 88:261–266.10.1034/j.1600-0773.2001.d01-114.xSearch in Google Scholar

Koski, L.B., Golding, G.B. (2001) The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52:540–542.10.1007/s002390010184Search in Google Scholar

Kress, W.J., Erickson, D.L. (2007) A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PloS One. 2:1–10.10.1371/journal.pone.0000508Search in Google Scholar

Kumar, S., Nei, M., Dudley, J., Tamura, K. (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinform. 9:299–306.10.1093/bib/bbn017Search in Google Scholar

Lahaye, R., Van der Bank, M., Bogarin, D., Warner, J., Pupulin, F., Gigot, G., Maurin, O., Duthoit, S., Barraclough, T.G., Savolainen, V. (2008) DNA barcoding the floras of biodiversity hotspots. Proc. Natl. Acad. Sci. USA. 105:2923–2928.10.1073/pnas.0709936105Search in Google Scholar

Li, G., Xu, F., Luo, J., Li, Y., Lan, F. (2008) Comparative anatomical research on the wood structure between Dalbergia odorifera T. Chen and D. rimosa Roxb. J. Guangxi Agric. Biol. Sci. 27:154–157.Search in Google Scholar

Liu, R., Ye, M., Guo, H., Bi, K., Guo, D. (2005) Liquid chromatography/electrospray ionization mass spectrometry for the characterization of twenty-three flavonoids in the extract of Dalbergia odorifera. Rapid Commun. Mass Spectr. 19:1557–1565.10.1002/rcm.1936Search in Google Scholar

Luo, Z., Zhang, X., Pan, B., Lu, B., Ruan, Z.,Wu, B. (2012) Anatomy structure and physical and mechanical properties of Dalbergia tonkinensis. J. Anhui Agric. Univ. 39:493–496.Search in Google Scholar

Miller, D., Sadowski, S., Han, G.Q., Joshua, H. (1989) Identification and isolation of medicarpin and a substituted benzofuran as potent leukotriene inhibitors in an anti-inflammatory Chinese herb. Prostaglandins, Leukotrienes Essent. Fatty Acids. 38:137–143.10.1016/0952-3278(89)90098-7Search in Google Scholar

Meier, R., Shiyang, K., Vaidya, G., Ng, P.K. (2006) DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst. Biol. 55:715–728.10.1080/10635150600969864Search in Google Scholar PubMed

Newmaster, S., Fazekas, A., Steeves, R., Janovec, J. (2008) Testing candidate plant barcode regions in the Myristicaceae. Mol. Ecol. Resour. 8:480–490.10.1111/j.1471-8286.2007.02002.xSearch in Google Scholar

Nitta, J.H. (2008) Exploring the utility of three plastid loci for biocoding the filmy ferns (Hymenophyllaceae) of Moorea. Taxon. 57:725–736.10.1002/tax.573006Search in Google Scholar

Ogata, T., Yahara, S., Hisatsune, R., Konishi, R., Nohara, T. (1990) Isoflavan and related compounds from Dalbergia odorifera. Chem. Pharma. Bull. 38:2750–2755.10.1248/cpb.38.2750Search in Google Scholar

Ohyama, M., Baba, K., Itoh, T. (2001) Wood identification of Japanese Cyclobalanopsis species (Fagaceae) based on DNA polymorphism of the intergenic spacer between trn T and trn L 5′ exon. J. Wood Sci. 47:81–86.10.1007/BF00780554Search in Google Scholar

Pang, X., Song, J., Zhu, Y., Xu, H., Huang, L., Chen, S. (2011) Applying plant DNA barcodes for Rosaceae species identification. Cladistics. 27:165–170.10.1111/j.1096-0031.2010.00328.xSearch in Google Scholar

Pang, X., Liu, C., Shi, L., Liu, R., Liang, D., Li, H., Cherny, S.S., Chen, S. (2012) Utility of the trnHpsbA intergenic spacer region and its combinations as plant DNA barcodes: A meta-analysis. PloS One. 7:e48833.10.1371/journal.pone.0048833Search in Google Scholar

Panshin, A.J., Zeeuw, C.D. Textbook of Wood Technology. McGraw-Hill, New York, 1980.Search in Google Scholar

Rachmayanti, Y., Leinemann, L., Gailing, O., Finkeldey, R. (2006) Extraction, amplification and characterization of wood DNA from Dipterocarpaceae. Plant Mol. Biol. Rep. 24:45–55.10.1007/BF02914045Search in Google Scholar

Rachmayanti, Y., Leinemann, L., Gailing, O., Finkeldey, R. (2009) DNA from processed and unprocessed wood: factors influencing the isolation success. Forensic Sci. Int. Genet. 3:185–192.10.1016/j.fsigen.2009.01.002Search in Google Scholar

Ross, H.A., Murugan, S., Li, W.L.S. (2008) Testing the reliability of genetic methods of species identification via simulation. Syst. Biol. 57:216–230.10.1080/10635150802032990Search in Google Scholar

Santos, G.U., Callado, C.H., da Costa Souza, M., Costa, C.G. (2013) Wood anatomy of Myrciaria, Neomitranthes, Plinia and Siphoneugena species (Myrteae, Myrtaceae). IAWA J. 34:313–323.10.1163/22941932-00000026Search in Google Scholar

Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731–2739.10.1093/molbev/msr121Search in Google Scholar

Tang, X., Zhao, G., Ping, L. (2011) Wood identification with PCR targeting noncoding chloroplast DNA. Plant Mol. Biol. 77:609–617.10.1007/s11103-011-9837-2Search in Google Scholar

Tnah, L.H., Lee, S.L., Ng, K.K.S., Bhassu, S., Othman, R.Y. (2012) DNA extraction from dry wood of Neobalanocarpus heimii (Dipterocarpaceae) for forensic DNA profiling and timber tracking. Wood Sci. Technol. 46:813–825.10.1007/s00226-011-0447-6Search in Google Scholar

Xu, L., Shi, H., Liang, T., Feng, J., Jin, Y., Ke, Y., Liang, X. (2011) Selective separation of flavonoid glycosides in Dalbergia odorifera by matrix solid-phase dispersion using titania. J. Sep. Sci. 34:1347–1354.10.1002/jssc.201100024Search in Google Scholar

Wang, W., Weng, X., Cheng, D. (2000) Antioxidant activities of natural phenolic components from Dalbergia odorifera T. Chen. Food Chem. 71:45–49.10.1016/S0308-8146(00)00123-0Search in Google Scholar

Yang, E.B., Zhang, K., Cheng, L.Y., Mack, P. (1998) Butein, a specific protein tyrosine kinase inhibitor. Biochem. Bioph. Res. Co. 245:435–438.10.1006/bbrc.1998.8452Search in Google Scholar

Yu, M., Zhang, H., Zhou, L., Liu, S., Qian, L., Jin, Q., Li, D. (2013) Isolating genomic DNA from wood tissue of Dalbergia odorifera T. Chen. J. Anhui Agric. Univ. 40:603–607.Search in Google Scholar

Yu, M., Zhang, H., Liu, S., Jin, Q., Li, D. (2014) DNA extraction and ribosomal DNA-ITS sequence molecule barcode identification from wood tissue of Dalbergia odorifera T. Chen. Chem. Industry Forest Prod. 34:103–108.Search in Google Scholar

Zhang, Y.M., Rock, C.O. (2004) Evaluation of epigallocatechin gallate and related plant polyphenols as inhibitors of the FabG and FabI reductases of bacterial type II fatty-acid synthase. J. Biol. Chem. 279:30994–31001.10.1074/jbc.M403697200Search in Google Scholar

Supplemental Material:

The online version of this article (DOI: 10.1515/hf-2014-0234) offers supplementary material, available to authorized users

Received: 2014-8-27
Accepted: 2015-2-25
Published Online: 2015-3-28
Published in Print: 2016-2-1

©2016 by De Gruyter

Downloaded on 1.12.2023 from
Scroll to top button