Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species

BackgroundThe plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL + matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over.
Methodology/Principal FindingsHere, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level.
ConclusionsThe ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.

**背景** 国际生命条形码联盟（Consortium for the Barcode of Life）植物工作组推荐将rbcL与matK双位点组合作为植物DNA条形码（DNA barcode），但该组合在对550个物种的907份样本进行物种水平鉴定时，成功率仅为72%。该工作组同时承认，由于鉴定准确率偏低，这一双位点条形码远非完善，相关研究仍未终止。

**方法与主要结果** 本研究针对药用植物的7个候选DNA条形码区域（psbA-trnH、matK、rbcL、rpoC1、ycf5、ITS2及ITS）开展对比分析。我们选用的评价指标包括PCR扩增效率、种内与种间遗传差异的区分度，以及DNA条形码间隙（DNA barcoding gap）。研究数据表明，细胞核核糖体DNA的第二内部转录间隔区（ITS2）是最适用于DNA条形码应用的候选区域。进一步地，我们对隶属于753个不同属、4800个物种的6600余份植物样本，测试了ITS2的物种鉴定能力，结果显示ITS2在物种水平上的鉴定成功率可达92.7%。

**结论** 本研究认为，ITS2区域可作为标准DNA条形码，用于药用植物及其近缘物种的鉴定。我们同时提出，ITS2可作为一种新型通用条形码，用于更广泛类群的植物物种鉴定。