TY - JOUR
T1 - Utility of the trnH-psbA Intergenic Spacer Region and Its Combinations as Plant DNA Barcodes
T2 - A Meta-Analysis
AU - Pang, Xiaohui
AU - Liu, Chang
AU - Shi, Linchun
AU - Liu, Rui
AU - Liang, Dong
AU - Li, Huan
AU - Cherny, Stacey S.
AU - Chen, Shilin
PY - 2012/11/14
Y1 - 2012/11/14
N2 - Background: The trnH-psbA intergenic spacer region has been used in many DNA barcoding studies. However, a comprehensive evaluation with rigorous sequence preprocessing and statistical testing on the utility of trnH-psbA and its combinations as DNA barcodes is lacking. Methodology/Principal Findings: Sequences were searched from GenBank for a meta-analysis on the usefulness of trnH-psbA and its combinations as DNA barcodes. After preprocessing, we constructed full and matching data sets that contained 17 983 trnH-psbA sequences and 2190 sets of trnH-psbA, matK, rbcL, and ITS2 sequences from the same sample, repectively. These datasets were used to analyze the ability of trnH-psbA and its combinations to discriminate species by the BLAST and BLAST+P methods. The Fisher's exact test was used to evaluate the significance of performance differences. For the full data set, the identification success rates of trnH-psbA exceeded 70% in 18 families and 12 genera, respectively. For the matching data set, the identification rates of trnH-psbA were significantly higher than those of the other loci in two families and four genera. Similarly, the identification rates of trnH-psbA+ITS2 were significantly higher than those of matK+rbcL in 18 families and 21 genera. Conclusion/Significane: This study provides valuable information on the higher utility of trnH-psbA and its combinations. We found that trnH-psbA+ITS2 combination performs better or equally well compared with other combinations in most taxonomic groups investigated. This information will guide the optimal usage of trnH-psbA and its combinations for species identification.
AB - Background: The trnH-psbA intergenic spacer region has been used in many DNA barcoding studies. However, a comprehensive evaluation with rigorous sequence preprocessing and statistical testing on the utility of trnH-psbA and its combinations as DNA barcodes is lacking. Methodology/Principal Findings: Sequences were searched from GenBank for a meta-analysis on the usefulness of trnH-psbA and its combinations as DNA barcodes. After preprocessing, we constructed full and matching data sets that contained 17 983 trnH-psbA sequences and 2190 sets of trnH-psbA, matK, rbcL, and ITS2 sequences from the same sample, repectively. These datasets were used to analyze the ability of trnH-psbA and its combinations to discriminate species by the BLAST and BLAST+P methods. The Fisher's exact test was used to evaluate the significance of performance differences. For the full data set, the identification success rates of trnH-psbA exceeded 70% in 18 families and 12 genera, respectively. For the matching data set, the identification rates of trnH-psbA were significantly higher than those of the other loci in two families and four genera. Similarly, the identification rates of trnH-psbA+ITS2 were significantly higher than those of matK+rbcL in 18 families and 21 genera. Conclusion/Significane: This study provides valuable information on the higher utility of trnH-psbA and its combinations. We found that trnH-psbA+ITS2 combination performs better or equally well compared with other combinations in most taxonomic groups investigated. This information will guide the optimal usage of trnH-psbA and its combinations for species identification.
UR - http://www.scopus.com/inward/record.url?scp=84869136099&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0048833
DO - 10.1371/journal.pone.0048833
M3 - ???researchoutput.researchoutputtypes.contributiontojournal.article???
C2 - 23155412
AN - SCOPUS:84869136099
SN - 1932-6203
VL - 7
JO - PLoS ONE
JF - PLoS ONE
IS - 11
M1 - e48833
ER -