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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.

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.

SUBMITTER: Pang X 

PROVIDER: S-EPMC3498263 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Publications

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

Pang Xiaohui X   Liu Chang C   Shi Linchun L   Liu Rui R   Liang Dong D   Li Huan H   Cherny Stacey S SS   Chen Shilin S  

PloS one 20121114 11


<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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  ...[more]

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