Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals

By Hui Yao, Jingyuan Song, Chang Liu, K. Luo, Jianping Han, Ying Li, Xiaohui Pang, Hongxi Xu, Yingjie Zhu, Peigen Xiao and 1 more. PLoS ONE, 2010

940 citations recorded by the source corpus.

Background The internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA is regarded as one of the candidate DNA barcodes because it possesses a number of valuable characteristics, such as the availability of conserved regions for designing universal primers, the ease of its amplification, and sufficient variability to distinguish even closely related species. However, a general analysis of its ability to discriminate species in a comprehensive sample set is lacking. Methodology/Principal Findings In the current study, 50,790 plant and 12,221 animal ITS2 sequences downloaded from GenBank were evaluated according to sequence length, GC content, intra- and inter-specific divergence, and efficiency of identification. The results show that the inter-specific divergence of congeneric species in plants and animals was greater than its corresponding intra-specific variations. The success rates for using the ITS2 region to identify dicotyledons, monocotyledons, gymnosperms, ferns, mosses, and animals were 76.1%, 74.2%, 67.1%, 88.1%, 77.4%, and 91.7% at the species level, respectively. The ITS2 region unveiled a different ability to identify closely related species within different families and genera. The secondary structure of the ITS2 region could provide useful information for species identification and could be considered as a molecular morphological characteristic. Conclusions/Significance As one of the most popular phylogenetic markers for eukaryota, we propose that the ITS2 locus should be used as a universal DNA barcode for identifying plant species and as a complementary locus for CO1 to identify animal species. We have also developed a web application to facilitate ITS2-based cross-kingdom species identification (http://its2-plantidit.dnsalias.org).

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9f041c97c5a3ee5b6b2844eee96808b2268e6b0f

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Citations in the corpus

Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring (2012, background): “Other barcode genes are proposed for plants, protists, andmeiofauna (Hollingsworth et al. 2009; Creer et al. 2010; Medinger et al. 2010; Yao et al. 2010).”
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences (2012, background): “Commons Attribution License (http://creativec reproduction in any medium, provided the or provide important insights into the mechanism of molecular phylogeny and RNA editing, as well as the divergence of species [6-8].”
Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants (2011, background): “Furthermore, in cases where ITS is difficult to amplify and performs unsatisfactorily, ITS2 represents a useful alternative for gymnosperms, or even for other seed plants (13), because of the relative ease of amplification with a single set of universal primers in all green plants (21).”
Choosing and Using a Plant DNA Barcode (2011, neutral): “8SITS2 is to use just a portion of the region as a barcode, namely nrITS2 [54,55].”
Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates (2017, methodology): “The ITS2 region was selected as it has been shown to be a good marker to separate and identify species 30,32,33 .”