Abstract
BackgroundWithin 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 FindingsA 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/SignificanceAlthough 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.
Highlights
Species identification is of critical importance in conserving and utilizing biodiversity, but this is often hindered by a lack of professional knowledge of classification [1]
Four plots established by the Xishuangbanna Tropical Rainforest Ecology Station (XSTRES) were selected on basis of vegetation type and different level of ecological surveys (named the 20 ha Xishuangbanna tropical seasonal rainforest dynamics plot (BB), JJYL, GGYL and LSL) (Table 1)
Our results showed higher sequence recovery for matK, compared with only 42% in one case [39] and around 70% in others [40,41,42], Fazekas et al [43] reported a higher level of success (88%) for matK using 10 primer pairs, while sequencing success of 90% was obtained by the CBOL Plant Working Group using two primer pairs [24], which is similar with our results
Summary
Species identification is of critical importance in conserving and utilizing biodiversity, but this is often hindered by a lack of professional knowledge of classification [1]. As one of the most vulnerable floras to the increasing threats from human activities [2], tropical plant species are badly in need of rapid identification methods to aid in the development of reasonable protection strategies [3]. A wide range of molecular methods have been applied to overcome this, but Hebert et al [6] presented an important tool of DNA barcoding which provides a fast and effective means for species assignment without the need for detailed taxonomic expertise. An ideal barcode should meet the need for rapid enough evolution to distinguish between species, combined with conserved regions, which will function as universal primer binding sites for PCR [7]. There are no DNA barcode studies from tropical areas of China, which represents one of the biodiversity hotspots around the world
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