Abstract
BackgroundThe 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 FindingsSequences 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/SignificaneThis 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.
Highlights
Accurate species identification is a prerequisite for conducting numerous basic and applied studies on monitoring and conserving natural resources, blocking the traffic of endangered and invasive species, as well as controlling the quality of pharmaceutical and food products
The usefulness of the ITS region as a DNA barcode has been further assessed by the China Plant BOL Group, who proposed that ITS should be used as the core plant barcode [23]
Intraspecific inversions and rps19 insertions, which are both well known to be present in the trnH–psbA region, are not explicitly examined and processed, which may negatively affect the species identification success rate
Summary
Accurate species identification is a prerequisite for conducting numerous basic and applied studies on monitoring and conserving natural resources, blocking the traffic of endangered and invasive species, as well as controlling the quality of pharmaceutical and food products. DNA barcoding is based on sequence diversity within a short and standardized gene region for species discrimination. This method can identify known species and discover novel ones [2,3]. Further evaluation of other noncoding markers, trnH–psbA and the internal transcribed spacers of nuclear ribosomal DNA (nrITS/nrITS2), is necessary before a universal plant barcode can be designated [22]. Intraspecific inversions and rps insertions, which are both well known to be present in the trnH–psbA region, are not explicitly examined and processed, which may negatively affect the species identification success rate. A comprehensive evaluation with rigorous sequence preprocessing and statistical testing on the utility of trnH–psbA and its combinations as DNA barcodes is lacking
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