title: Utility of the trnH-psbA intergenic spacer region and its combinations as plant DNA barcodes: a meta-analysis.
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.
  
  
  RESULTS
  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.
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Pang
authors.forename: Chang
authors.initials: C
authors.lastname: Liu
authors.forename: Linchun
authors.initials: L
authors.lastname: Shi
authors.forename: Rui
authors.initials: R
authors.lastname: Liu
authors.forename: Dong
authors.initials: D
authors.lastname: Liang
authors.forename: Huan
authors.initials: H
authors.lastname: Li
authors.forename: Stacey S
authors.initials: SS
authors.lastname: Cherny
authors.forename: Shilin
authors.initials: S
authors.lastname: Chen
mesh_terms: D058893:DNA Barcoding, Taxonomic; D021901:DNA, Intergenic; D018744:DNA, Plant / Q000235:genetics*; D030541:Databases, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D021901:DNA, Intergenic; D018744:DNA, Plant