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

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.

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

“…This was not the case for the rbcL barcode as the tree topology was poorly resolved due to very low variation among the sequences of the reference sequence database. Others have used different barcodes such as ITS2 in similar ethno‐pharmacology‐based identifications with success (Chen et al., 2010; Gao et al., 2010). DNA barcoding also involves massive sample sets with often industrial‐scale laboratory practices and bioinformatics pipelines (Hollingsworth et al., 2016).…”

Finding the pond through the weeds: eDNA reveals underestimated diversity of pondweeds

“…The data sets included a ~740–770‐bp region for atpB ‐ rbcL (Appendix S1, A: primers 1–2; Manen et al., 1994) and a ~360–490‐bp region for ITS2 (Appendix S1, A: primers 3–5; White et al., 1990; Chen et al., 2010). Sequences were aligned with MAFFT (Katoh et al., 2002) and used to manually design primers with a high specificity for Potamogetonaceae.…”

Potential use of DNA barcoding for the identification of Salvia based on cpDNA and nrDNA sequences

“…ITS2 is a widely used marker for identifying medicinal materials and it often achieves high efficiency rates. Chen et al (2010) correctly recognized S. miltiorrhiza from more than 4000 species. However, ITS2 was unsuitable for the accessions we tested.…”