A strategy for developing high-resolution DNA barcodes for species discrimination of wood specimens using the complete chloroplast genome of three Pterocarpus species
- 238 Downloads
A method for extraction of wood DNA and a strategy for designing high-resolution barcodes for wood were developed. Ycf1b was the prioritized barcode to resolve the Pterocarpus wood species studied.
DNA barcoding, an effective tool for wood species identification, mainly focuses on universal barcodes and often lacks high resolution to differentiate species, especially for closely related taxa within the same genus. Therefore, more highly informative DNA barcodes need to be identified. This study is the first to report a strategy for developing specific DNA barcodes of wood tissues. The complete chloroplast genomes of leaf samples of three Pterocarpus species, i.e., P. indicus, P. santalinus, and P. tinctorius, were sequenced, and thereafter, the most variable DNA regions were identified on the scale of the complete chloroplast genomes. Finally, wood DNA was extracted from 30 wood specimens of the three Pterocarpus species, and DNA recovery rates of the selected regions were tested for applicability to verification on the wood specimens studied. The seven regions with the most variation (rpl32-ccsA, rpl20-clpP, trnC-rpoB, ycf1b, accD-ycf4, ycf1a, and psbK-accD) were identified from the chloroplast genome by quantifying nucleotide diversity (Pi > 0.02), which was remarkably higher than that of the plant universal barcodes (rbcL, matK, and trnH-psbA) and the previously reported barcodes (ndhF-rpl32 and trnL-F) used for phylogenetic analysis in Pterocarpus. After comprehensive evaluation of species discrimination ability and applicability, the ycf1b region performed well in terms of the recovery success rate (76.7%) and species identification (100%) for wood specimens of the three Pterocarpus species, and was identified as the preferred high-resolution chloroplast barcode for selected Pterocarpus species. It will offer technical support for curbing illegal timber harvesting activities and for conserving endangered and valuable wood species.
KeywordsComparative genomics DNA extraction Specific barcode Timber identification Wood anatomy Ycf1b
Large single copy
Small single copy
This work was supported financially by the Fundamental Research Funds of CAF (Grant No. CAFYBB2017MA013), the National Natural Science Foundation of China (Grant No. 31600451), and the National High-level Talents Special Support Plan (Ten-Thousand Talents Program) of China (No. W02020331). We would like to express our gratitude to Professor Shiliang Zhou, Dr. Chao Xu, and Dr. Wenpan Dong of the Institute of Botany, Chinese Academy of Science for technical support with chloroplast genome sequencing, and Mr. Changyu Xu and postgraduate student Qiongqiong Li for assistance with collecting samples.
- Dormontt EE, Boner M, Braun B, Breulmann G, Degen B, Espinoza E, Gardner S, Guillery P, Hermanson JC, Koch G, Lee SL, Kanashiro M, Rimbawanto A, Thomas D, Wiedenhoeft AC, Yin Y, Zahnen J, Lowe AJ (2015) Forensic timber identification: it’s time to integrate disciplines to combat illegal logging. Biol Conserv 191:790–798CrossRefGoogle Scholar
- Hall TA (1999) A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acid Symp Ser 41:95–98Google Scholar
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C et al (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649CrossRefPubMedPubMedCentralGoogle Scholar
- 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 71:939–949Google Scholar
- Martin GE, Rousseau-Gueutin M, Cordonnier S, Lima O, Michoncoudouel S, Naquin D et al (2014) The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family. Ann Bot 113(7):1197–1210CrossRefPubMedPubMedCentralGoogle Scholar
- Saslis-Lagoudakis CH, Klitgaard BB, Forest F, Francis L, Savolainen V, Williamson EM et al (2011) The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae). PLoS One 6(7):e22275CrossRefPubMedPubMedCentralGoogle Scholar