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Licensed Unlicensed Requires Authentication Published by De Gruyter August 27, 2018

Applicability of chloroplast DNA barcodes for wood identification between Santalum album and its adulterants

  • Lichao Jiao , Tuo He , Eleanor E. Dormontt , Yonggang Zhang , Andrew J. Lowe and Yafang Yin EMAIL logo
From the journal Holzforschung

Abstract

The East Indian sandalwood, Santalum album L., is known for its fragrant heartwood and extractive oils. The increasing demand for the valuable sandalwood products has led to illegal and excessive logging, and there are other Santalum species in the commercial market as substitutes (adulterants). Improved tools for the identification of Santalum species are needed to control this situation. In this study, four chloroplast DNA (cpDNA) regions were screened (matK, psbA-trnH, trnK and trnL) on 35 vouchered specimens covering five Santalum species, i.e. Santalum acuminatum, S. album, Santalum lanceolatum, Santalum murrayanum and Santalum spicatum. The goal of this study was to test the species discrimination ability by means of both the TaxonDNA and neighbor-joining (NJ) methods. The results indicate that the combination of psbA-trnH+trnK gave the best performance for discrimination (100%) of the studied Santalum species concerning the discrimination ability and recovery rate. Meanwhile, six unvouchered wood specimens were retrieved and accurately identified at the species level based on the recommended DNA barcodes. The DNA barcode method is now ready for application in the monitoring of the trade of this valuable resource, and provides an effective approach for wood species identification and product authentication.

Award Identifier / Grant number: 31600451

Funding statement: This work was supported financially by National Natural Science Foundation of China (Funder Id: 10.13039/501100001809; Grant No. 31600451), Fundamental Research Funds of CAF (Grant No. CAFYBB2017ZE003) and National High-level Talents Special Support Plan (Ten-Thousand Talents Program) of China (No. W02020331).

Acknowledgments

We would like to express our gratitude to Mrs. Helen Vonow and Mr. Martin O’Leary at the State Herbarium of South Australia, Dr. Bianca Dunker and Dr. Rainbo Dixon at School of Biological Sciences, University of Adelaide, and Dr. Xiaojin Liu at Research Institute of Tropical Forestry, Chinese Academy of Forestry for their help in collecting specimens and conducting the experiment.

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Employment or leadership: None declared.

  3. Honorarium: None declared.

References

Bolson, M., Smidt, E.C., Brotto, M.L., Silva-Pereira, V. (2015) ITS and trnH-psbA as efficient DNA barcodes to identify threatened commercial woody angiosperms from Southern Brazilian Atlantic rainforests. PLoS One 10:e0143049.10.1371/journal.pone.0143049Search in Google Scholar PubMed PubMed Central

Butaud, J.-F., Raharivelomanana, P., Bianchini, J.-P., Gaydou, E.M. (2008) Santalum insulare acetylenic fatty acid seed oils: comparison within the Santalum genus. J. Am. Oil Chem. Soc. 85:353–356.10.1007/s11746-008-1196-zSearch in Google Scholar

Chen, S.L., Yao, H., Han, J.P., Liu, C., Song, J.Y., Shi, L.C., Zhu, Y.J., Ma, X.Y., Gao, T., Pang, X.H. (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

Chen, S., Pang, X., Song, J., Shi, L., Yao, H., Han, J., Leon, C. (2014) A renaissance in herbal medicine identification: from morphology to DNA. Biotechnol. Adv. 32:1237.10.1016/j.biotechadv.2014.07.004Search in Google Scholar PubMed

Collins, R.A., Cruickshank, R.H. (2013) The seven deadly sins of DNA barcoding. Mol. Ecol. Resour. 13:969–975.10.1111/1755-0998.12046Search in Google Scholar PubMed

Deguilloux, M.F., Pemonge, M.H., Petit, R.J. (2002) Novel perspectives in wood certification and forensics: dry wood as a source of DNA. Proc. R. Soc. Lond. B 269:1039–1046.10.1098/rspb.2002.1982Search in Google Scholar PubMed PubMed Central

Dev, S.A., Muralidharan, E.M., Sujanapal, P., Balasundaran, M. (2014) Identification of market adulterants in East Indian sandalwood using DNA barcoding. Ann. For. Sci. 71:517–522.10.1007/s13595-013-0354-0Search in Google Scholar

Dormontt, E.E., Boner, M., Braun, B., Breulmann, G., Degen, B., Espinoza, E., Gardner, S., Guillery, P., Hermanson, J.C., Koch, G., Lee, S.L., Kanashiro, M., Rimbawanto, A., Thomas, D., Wiedenhoeft, A.C., Yin, Y., Zahnen, J., Lowe, A.J. (2015) Forensic timber identification: it’s time to integrate disciplines to combat illegal logging. Biol. Conserv. 191:790–798.10.1016/j.biocon.2015.06.038Search in Google Scholar

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

Harbaugh, D.T., Baldwin, B.G. (2007) Phylogeny and biogeography of the sandalwoods (Santalum, Santalaceae): repeated dispersals throughout the Pacific. Am. J. Bot. 94:1028.10.3732/ajb.94.6.1028Search in Google Scholar PubMed

Hartvig, I., Czako, M., Kjær, E.D., Nielsen, L.R., Theilade, I. (2015) The use of DNA barcoding in identification and conservation of rosewood (Dalbergia spp.). PLoS One 10:e0138231.10.1371/journal.pone.0138231Search in Google Scholar PubMed PubMed Central

Hassold, S., Bauert, M.R., Razafintsalama, A., Ramamonjisoa, L., Widmer, A. (2016) DNA barcoding of malagasy rosewoods: towards a molecular identification of CITES-listed Dalbergia species. PLoS One 11:e0157881.10.1371/journal.pone.0157881Search in Google Scholar PubMed PubMed Central

Höltken, A.M., Schröder, H., Wischnewski, N., Degen, B., Magel, E., Fladung, M. (2012) Development of DNA-based methods to identify CITES-protected timber species: a case study in the Meliaceae family. Holzforschung 66:97–104.Search in Google Scholar

Howes, M.J., Simmonds, M.S., Kite, G.C. (2004) Evaluation of the quality of sandalwood essential oils by gas chromatography-mass spectrometry. J. Chromatogr. A 1028:307–312.10.1016/j.chroma.2003.11.093Search in Google Scholar PubMed

IAWA Committee. (1989) IAWA list of microscopic features for hardwood identification. IAWA Bull. 10:219–332.Search 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

Jiao, L., Liu, X., Jiang, X., Yin, Y. (2015) Extraction and amplification of DNA from aged and archaeological Populus euphratica wood for species identification. Holzforschung 69:925–931.10.1515/hf-2014-0224Search in Google Scholar

Jiao, L., Yu, M., Wiedenhoeft, A.C., He, T., Li, J., Liu, B., Jiang, X., Yin, Y. (2018) DNA barcode authentication and library development for the wood of six commercial Pterocarpus species: the critical role of xylarium specimens. Sci. Rep. 8:1945.10.1038/s41598-018-20381-6Search in Google Scholar PubMed PubMed Central

Li, Q., Wu, J., Wang, Y., Lian, X., Wu, F., Zhou, L., Huang, Z., Zhu, S. (2017) The phylogenetic analysis of Dalbergia (Fabaceae: Papilionaceae) based on different DNA barcodes. Holzforschung 71:939–949.10.1515/hf-2017-0052Search in Google Scholar

Liu, J., Provan, J., Gao, L.M., Li, D.Z. (2012) Sampling strategy and potential utility of indels for DNA barcoding of closely related plant species: a case study in Taxus. Int. J. Mol. Sci. 13: 8740–8751.10.3390/ijms13078740Search in Google Scholar PubMed PubMed Central

Lowe, A.J., Dormontt, E.E., Bowie, M.J., Degen, B., Gardner, S., Thomas, D., Clarke, C., Rimbawanto, A., Wiedenhoeft, A., Yin, Y., Sasaki, N. (2016) Opportunities for improved transparency in the timber trade through scientific verification. BioScience 66:990–998.10.1093/biosci/biw129Search 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

Meyer, C.P., Paulay, G. (2005) DNA barcoding: error rates based on comprehensive sampling. PLoS Biol. 3:e422.10.1371/journal.pbio.0030422Search in Google Scholar PubMed PubMed Central

Moniodis, J., Jones, C.G., Liz Barbour, E., Plummer, J.A., Ghisalberti, E.L., Bohlmann, J. (2015) The transcriptome of sesquiterpenoid biosynthesis in heartwood xylem of Western Australian sandalwood (Santalum spicatum). Phytochemistry 113:79–86.10.1016/j.phytochem.2014.12.009Search in Google Scholar PubMed

Nuroniah, H.S., Gailing, O., Finkeldey, R. (2017) Development of a diagnostic DNA marker for the geographic origin of Shorea leprosula. Holzforschung 71:1–10.10.1515/hf-2016-0086Search in Google Scholar

Srinivasa Rao, M., Ravikumar, G., Triveni, P.R., Soundara Rajan, V., Nautiyal, S. (2016) Analysis of policies in sustaining sandalwood resources in India. In: Climate Change Challenge (3C) and Social-Economic-Ecological Interface-Building. Eds. Nautiyal, S., Schaldach, R., Raju, K., Kaechele, H., Pritchard, B., Rao, K. Environmental Science and Engineering. Springer, Cham.10.1007/978-3-319-31014-5_19Search in Google Scholar

Srivathsan, A., Meier, R. (2012) On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature. Cladistics 28:190–194.10.1111/j.1096-0031.2011.00370.xSearch in Google Scholar PubMed

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 PubMed PubMed Central

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 PubMed

Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876–4882.10.1093/nar/25.24.4876Search in Google Scholar PubMed PubMed Central

Valder, C., Neugebauer, M., Meier, M., Kohlenberg, B., Hammerschmidt, F., Braun, N.A. (2003) Western Australian sandalwood oil – new constituents of Santalum spicatum (R. Br.) A. DC. (Santalaceae). J. Essent. Oil Res. 15:178–186.10.1080/10412905.2003.9712106Search in Google Scholar

Yan, L.J., Liu, J., Möller, M., Zhang, L., Zhang, X.M., Li, D.Z., Gao, L.M. (2015) DNA barcoding of Rhododendron (Ericaceae), the largest Chinese plant genus in biodiversity hotspots of the Himalaya-Hengduan Mountains. Mol. Ecol. Resour. 15:932–944.10.1111/1755-0998.12353Search in Google Scholar PubMed

Yao, H., Song, J., Liu, C., Luo, K., Han, J., Li, Y., Pang, X., Xu, H., Zhu, Y., Xiao, P. (2010) Use of ITS2 region as the universal DNA barcode for plants and animals. PLoS One 5:e13102.10.1371/journal.pone.0013102Search in Google Scholar PubMed PubMed Central

Yu, M., Liu, K., Zhou, L., Zhao, L., Liu, S. (2016) Testing three proposed DNA barcodes for the wood identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain. Holzforschung 70:127–136.10.1515/hf-2014-0234Search in Google Scholar

Yu, M., Jiao, L., Guo, J., Wiedenhoeft, A.C., He, T., Jiang, X., Yin, Y. (2017) DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species. Planta 246:1165–1176.10.1007/s00425-017-2758-9Search in Google Scholar PubMed

Zhang, X., Silva, J.A.T.D., Niu, M., Li, M., He, C., Zhao, J., Zeng, S., Duan, J., Ma, G. (2017) Physiological and transcriptomic analyses reveal a response mechanism to cold stress in Santalum album L. leaves. Sci. Rep. 7:42165.10.1038/srep42165Search in Google Scholar PubMed PubMed Central


Supplementary Material

The online version of this article offers supplementary material (https://doi.org/10.1515/hf-2018-0047).


Received: 2018-03-12
Accepted: 2018-07-24
Published Online: 2018-08-27
Published in Print: 2019-02-25

©2019 Walter de Gruyter GmbH, Berlin/Boston

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