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

By Shilin Chen, Hui Yao, Jianping Han, Chang Liu, Jingyuan Song, Linchun Shi, Yingjie Zhu, Xinye Ma, T. Gao, Xiaohui Pang and 6 more. PLoS ONE, 2010

1,617 citations recorded by the source corpus.

Background 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. Methodology/Principal Findings Here, 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. Conclusions The 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.

Subfields: Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/9b474e1f0ea6d2f9c5edd6d44946c2b21b48b8e5

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Citations in the corpus

Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals (2010, positive): “Although the rate of fungal contamination is very low, we should pay more attention to the data from the public database [11].”
Plant DNA barcodes: Applications today and in the future (2017, background): “…for plant DNA barcode markers (e.g., Kress et al., 2005) for the botanical community to reach some consensus on the regions that showed the highest promise of success (Lahaye et al, 2008; CBOL Plant Working Group, 2009; Chen et al., 2010; China Plant BOL Group, 2011; Hollingsworth, 2011).”
The sooty moulds (2014, background): “There have been limited investigations for other gene markers (Seifert et al. 2007; Chen et al. 2010), but so far none share the same widespread usage as the ITS.”
Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants (2011, background): “This ITS region, or a portion of it (ITS2), has already been suggested as a potential DNA barcode for plants (9, 13, 14, 19).”
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences (2012, methodology): “Background Regions on chloroplast genomes have been widely used as phylogenetic [1,2] and DNA barcoding markers [3-5] to determine the phylogenetic relationships of organisms and the identity of particular DNA samples.”
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, result): “Other kits appear to yield similar results as the DNeasy kit (Chen et al. 2010a).”
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities (2017, background): “…cytochrome c oxidase subunit I (COI or cox1), for taxonomical identification of animals (Hebert, Ratnasingham, & de Waard, 2003), and a two-loci combination of rbcL and matK as the plant barcode (Hollingsworth et al., 2009) with ITS2 also suggested as valid plant barcode marker (Chen et al., 2010).”
The Application of Biotechnology to Orchids (2013, background): “…1997; Cameron et al., 1999; Kores et al., 1997, 2000, 2001; Hedren et al., 2001; Been et al., 2002; Carlsward et al., 2006; Kishor et al., 2008; Bateman et al., 2009; Wang et al., 2009b; Ding et al., 2009; Hopper, 2009; Chen et al., 2010; Khew et al., 2011; Lu et al., 2011; Parveen et al., 2012).”
Choosing and Using a Plant DNA Barcode (2011, background): “[56–58]) and it has been argued that focusing on the nrITS2 region reduces amplification and sequencing problems associated with the entire nrITS assemblage [54].”
Conservation and sustainable use of medicinal plants: problems, progress, and prospects (2016, background): “Background Medicinal plants are globally valuable sources of new drugs [1–4].”