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Type: Journal article
Title: Application of DNA barcodes in Asian tropical trees - a case study from Xishuangbanna nature reserve, Southwest China
Author: Huang, X.C.
Ci, X.Q.
Conran, J.G.
Li, J.
Citation: PLoS One, 2015; 10(6):e0129295-1-e0129295-17
Publisher: Public Library of Science
Issue Date: 2015
ISSN: 1932-6203
Statement of
Xiao-cui Huang, Xiu-qin Ci, John G. Conran, Jie Li
Abstract: BACKGROUND: Within a regional floristic context, DNA barcoding is more useful to manage plant diversity inventories on a large scale and develop valuable conservation strategies. However, there are no DNA barcode studies from tropical areas of China, which represents one of the biodiversity hotspots around the world. METHODOLOGY AND PRINCIPAL FINDINGS: A DNA barcoding database of an Asian tropical trees with high diversity was established at Xishuangbanna Nature Reserve, Yunnan, southwest China using rbcL and matK as standard barcodes, as well as trnH-psbA and ITS as supplementary barcodes. The performance of tree species identification success was assessed using 2,052 accessions from four plots belonging to two vegetation types in the region by three methods: Neighbor-Joining, Maximum-Likelihood and BLAST. We corrected morphological field identification errors (9.6%) for the three plots using rbcL and matK based on Neighbor-Joining tree. The best barcode region for PCR and sequencing was rbcL (97.6%, 90.8%), followed by trnH-psbA (93.6%, 85.6%), while matK and ITS obtained relative low PCR and sequencing success rates. However, ITS performed best for both species (44.6-58.1%) and genus (72.8-76.2%) identification. With trnH-psbA slightly less effective for species identification. The two standard barcode rbcL and matK gave poor results for species identification (24.7-28.5% and 31.6-35.3%). Compared with other studies from comparable tropical forests (e.g. Cameroon, the Amazon and India), the overall performance of the four barcodes for species identification was lower for the Xishuangbanna Nature Reserve, possibly because of species/genus ratios and species composition between these tropical areas. CONCLUSIONS/SIGNIFICANCE: Although the core barcodes rbcL and matK were not suitable for species identification of tropical trees from Xishuangbanna Nature Reserve, they could still help with identification at the family and genus level. Considering the relative sequence recovery and the species identification performance, we recommend the use of trnH-psbA and ITS in combination as the preferred barcodes for tropical tree species identification in China.
Keywords: Trees; Likelihood Functions; Polymerase Chain Reaction; Sequence Analysis, DNA; Conservation of Natural Resources; Tropical Climate; Species Specificity; Molecular Sequence Data; China; DNA Barcoding, Taxonomic
Rights: © 2015 Huang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
RMID: 0030031677
DOI: 10.1371/journal.pone.0129295
Appears in Collections:Ecology, Evolution and Landscape Science publications

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