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DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species

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Abstract

Main conclusion

ITS2+ trnH - psbA was the best combination of DNA barcode to resolve the Dalbergia wood species studied. We demonstrate the feasibility of building a DNA barcode reference database using xylarium wood specimens.

The increase in illegal logging and timber trade of CITES-listed tropical species necessitates the development of unambiguous identification methods at the species level. For these methods to be fully functional and deployable for law enforcement, they must work using wood or wood products. DNA barcoding of wood has been promoted as a promising tool for species identification; however, the main barrier to extensive application of DNA barcoding to wood is the lack of a comprehensive and reliable DNA reference library of barcodes from wood. In this study, xylarium wood specimens of nine Dalbergia species were selected from the Wood Collection of the Chinese Academy of Forestry and DNA was then extracted from them for further PCR amplification of eight potential DNA barcode sequences (ITS2, matK, trnL, trnH-psbA, trnV-trnM1, trnV-trnM2, trnC-petN, and trnS-trnG). The barcodes were tested singly and in combination for species-level discrimination ability by tree-based [neighbor-joining (NJ)] and distance-based (TaxonDNA) methods. We found that the discrimination ability of DNA barcodes in combination was higher than any single DNA marker among the Dalbergia species studied, with the best two-marker combination of ITS2+trnH-psbA analyzed with NJ trees performing the best (100% accuracy). These barcodes are relatively short regions (<350 bp) and amplification reactions were performed with high success (≥90%) using wood as the source material, a necessary factor to apply DNA barcoding to timber trade. The present results demonstrate the feasibility of using vouchered xylarium specimens to build DNA barcoding reference databases.

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Acknowledgements

This work was supported by the China Postdoctoral Science Foundation (Grant no. 2016M590152), the National Natural Science Foundation of China (Grant no. 31600451), the Fundamental Research Funds of Chinese Academy of Forestry (Grant no. CAFYBB2017ZE003), the China Scholarship Council (Grant no. 2016-3035), and U.S. State Department Interagency Agreement (19318814Y0010-140001-0001/P00001).We thank Sarah Friedrich, Department of Botany, University of Wisconsin-Madison for her technical assistance with the phylogram figure.

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    1. Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China

      Min Yu, Lichao Jiao, Juan Guo, Tuo He, Xiaomei Jiang & Yafang Yin

    2. Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China

      Min Yu, Lichao Jiao, Juan Guo, Tuo He, Xiaomei Jiang & Yafang Yin

    3. Center for Wood Anatomy Research, USDA Forest Service, Forest Products Laboratory, Madison, WI, 53726, USA

      Alex C. Wiedenhoeft

    4. Department of Botany, University of Wisconsin, Madison, WI, 53706, USA

      Alex C. Wiedenhoeft

    5. Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA

      Alex C. Wiedenhoeft

    6. Ciências Biológicas (Botânica), Univesidade Estadual Paulista, Botucatu, São Paulo, Brazil

      Alex C. Wiedenhoeft

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    Min Yu and Lichao Jiao contributed to the work equally and should be regarded as co-first authors.

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    Supplementary material 1 (PDF 2918 kb) Fig. S1 Relative distributions of interspecific and intraspecific Kimura two-parameter (K2P) distances for the eight DNA markers and their combinations

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    Supplementary material 2 (PDF 1372 kb) Fig. S2 Taxon identification trees constructed using neighbor-joining analysis of Kimura 2-parameter (K2P) distances showing patterns of the eight DNA markers and their combinations

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    Yu, M., Jiao, L., Guo, J. et al. DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species. Planta 246, 1165–1176 (2017). https://doi.org/10.1007/s00425-017-2758-9

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