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

Huang XC, Ci XQ, Conran JG, Li J - PLoS ONE (2015)

Bottom Line: 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%).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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China; Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People's Republic of China; Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People's Republic of China; University of Chinese Academy of Sciences, Beijing, People's Republic of China.

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.

No MeSH data available.


Related in: MedlinePlus

Species resolution success at the family, genus and species levels for single regions and combinations, based on Neighbor-Joining Tree analysis of all the species (samples ≥ 2), collected from the four plots (BB, JJYL, GGYL and LSL) of Xishuangbanna Nature Reserve in southwest China.(R, M, T, S represent rbcL, matK, trnH–psbA and ITS respectively.)
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pone.0129295.g001: Species resolution success at the family, genus and species levels for single regions and combinations, based on Neighbor-Joining Tree analysis of all the species (samples ≥ 2), collected from the four plots (BB, JJYL, GGYL and LSL) of Xishuangbanna Nature Reserve in southwest China.(R, M, T, S represent rbcL, matK, trnH–psbA and ITS respectively.)

Mentions: The highest success of species discrimination based on two tree building methods (NJ and ML) with single barcode were obtained with ITS (44.6% and 47.8%), followed by matK (34.1% and 35.3%) and then rbcL (28.5% and 27.8%). At the genus level, the results also performed best with ITS (72.8% and 77.2%), followed by matK (66.7% and 63.1%) and rbcL (64.3% and 59.1%) (see Figs 1 and 2).


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

Huang XC, Ci XQ, Conran JG, Li J - PLoS ONE (2015)

Species resolution success at the family, genus and species levels for single regions and combinations, based on Neighbor-Joining Tree analysis of all the species (samples ≥ 2), collected from the four plots (BB, JJYL, GGYL and LSL) of Xishuangbanna Nature Reserve in southwest China.(R, M, T, S represent rbcL, matK, trnH–psbA and ITS respectively.)
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4509572&req=5

pone.0129295.g001: Species resolution success at the family, genus and species levels for single regions and combinations, based on Neighbor-Joining Tree analysis of all the species (samples ≥ 2), collected from the four plots (BB, JJYL, GGYL and LSL) of Xishuangbanna Nature Reserve in southwest China.(R, M, T, S represent rbcL, matK, trnH–psbA and ITS respectively.)
Mentions: The highest success of species discrimination based on two tree building methods (NJ and ML) with single barcode were obtained with ITS (44.6% and 47.8%), followed by matK (34.1% and 35.3%) and then rbcL (28.5% and 27.8%). At the genus level, the results also performed best with ITS (72.8% and 77.2%), followed by matK (66.7% and 63.1%) and rbcL (64.3% and 59.1%) (see Figs 1 and 2).

Bottom Line: 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%).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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China; Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People's Republic of China; Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People's Republic of China; University of Chinese Academy of Sciences, Beijing, People's Republic of China.

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.

No MeSH data available.


Related in: MedlinePlus