@article {20408, title = {Application of DNA barcodes in Asian tropical trees {\textendash} a case study from Xishuangbanna Nature Reserve, Southwest China}, journal = {PLoS ONE}, volume = {10}, year = {2015}, month = {06/2015}, pages = {1-17}, chapter = {1}, 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.

}, doi = {10.1371/journal.pone.0129295}, author = {Huang, Xiao-cui and Ci, Xiu-Qin and Conran, J. G. and Li, Jie} } @article {20351, title = {DNA barcoding evaluation and implications for phylogenetic relationships in Lauraceae from China}, journal = {PLoS ONE}, volume = {12}, year = {2017}, month = {04/2017}, abstract = {

Lauraceae are an important component of tropical and subtropical forests and have major ecological and economic significance. Owing to lack of clear-cut morphological differences between genera and species, this family is an ideal case for testing the efficacy of DNA barcoding in the identification and discrimination of species and genera. In this study, we evaluated five widely recommended plant DNA barcode loci matK, rbcL, trnH-psbA, ITS2 and the entire ITS region for 409 individuals representing 133 species, 12 genera from China. We tested the ability of DNA barcoding to distinguish species and as an alternative tool for correcting species misidentification. We also used the rbcL+matK+trnH-psbA+ITS loci to investigate the phylogenetic relationships of the species examined. Among the gene regions and their combinations, ITS was the most efficient for identifying species (57.5\%) and genera (70\%). DNA barcoding also had a positive role for correcting species misidentification (10.8\%). Furthermore, based on the results of the phylogenetic analyses, Chinese Lauraceae species formed three supported monophyletic clades, with the Cryptocarya group strongly supported (PP = 1.00, BS = 100\%) and the clade including the Persea group, Laureae and Cinnamomum also receiving strong support (PP = 1.00, BS = 98\%), whereas the Caryodaphnopsis-Neocinnamomum received only moderate support (PP = 1.00 and BS = 85\%). This study indicates that molecular barcoding can assist in screening difficult to identify families like Lauraceae, detecting errors of species identification, as well as helping to reconstruct phylogenetic relationships. DNA barcoding can thus help with large-scale biodiversity inventories and rare species conservation by improving accuracy, as well as reducing time and costs associated with species identification.

}, doi = {https://doi.org/10.1371/journal.pone.0175788}, author = {Liu, Zhi-Fang and Ci, Xiu-Qin and Li, Lang and Li, Hsi-Wen and Conran, J. G. and Li, Jie} }