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

Shilin Chen,Chang Liu,Xiaohui Pang,Ying Li,Xiaocheng Jia,Yulin Lin,Jianping Han,Yingjie Zhu,Christine Leon,Linchun Shi,Xinye Ma,Jingyuan Song,Kun Luo,Hui Yao,Ting Gao,Xiwen Li,M Thomas P Gilbert

doi:10.1371/journal.pone.0008613

Abstract

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.

Highlights

The World Health Organization estimates that 80 percent of the world’s population utilizes traditional medicines for healing and curing diseases
The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species
We propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa

Summary

Introduction

The World Health Organization estimates that 80 percent of the world’s population utilizes traditional medicines for healing and curing diseases (http://www.worldwildlife.org/what/globalmarkets/ wildlifetrade/faqs-medicinalplant.html). Medicinal plants cover a wide range of plant taxa and closely related species. According to surveys in China, medicinal plants belong to 11,146 species from 2,309 genera of 383 families, representing a rich biodiversity. Accurate and rapid authentication of these plants and their adulterants is difficult to achieve at the scale of international trade in medicinal plants. We aim to provide a practical and powerful tool for identifying medicinal plants and their adulterants in trade and for ensuring safety in their use. The 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

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