Application of DNA Barcodes in Asian Tropical Trees – A Case Study from Xishuangbanna Nature Reserve, Southwest China

<div><p>Background</p><p>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.</p><p>Methodology and Principal Findings</p><p>A DNA barcoding database of an Asian tropical trees with high diversity was established at Xishuangbanna Nature Reserve, Yunnan, southwest China using <i>rbc</i>L and <i>mat</i>K as standard barcodes, as well as <i>trn</i>H–<i>psb</i>A 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 <i>rbc</i>L and <i>mat</i>K based on Neighbor-Joining tree. The best barcode region for PCR and sequencing was <i>rbc</i>L (97.6%, 90.8%), followed by <i>trn</i>H–<i>psb</i>A (93.6%, 85.6%), while <i>mat</i>K 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 <i>trn</i>H–<i>psb</i>A slightly less effective for species identification. The two standard barcode <i>rbc</i>L and <i>mat</i>K 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.</p><p>Conclusions/Significance</p><p>Although the core barcodes <i>rbc</i>L and <i>mat</i>K 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 <i>trn</i>H–<i>psb</i>A and ITS in combination as the preferred barcodes for tropical tree species identification in China.</p>