Utility of the trnH-psbA intergenic spacer region and its combinations as plant DNA barcodes: a meta-analysis.

Pang X, Liu C, Shi L, Liu R, Liang D, Li H, Cherny SS, Chen S.

Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.

Abstract

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 DNAbarcodes. 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-psbAexceeded 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-psbAand its combinations for species identification.

PLoS One. 2012;7(11):e48833. doi: 10.1371/journal.pone.0048833. Epub 2012 Nov 14.