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

Abstract

BackgroundThe 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 FindingsIn 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/SignificanceAs 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).

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

“…Both of these regions are potential ideal barcodes. In recent years, an increasing number of studies proved that ITS2 is a universal barcode for identifying plants within families Araliaceae, Asteraceae, Rutaceae, Rosaceae, and so on Gao et al, 2010;Liu et al, 2012;Yao et al, 2010). Our results indicate that ITS2 is not the ideal candidate DNA marker for Salvia because it only correctly identified 55.56%.…”

Redescription, new distribution record, DNA sequence and length-weight relationship of the Eel-loach Pangio pangia (Cypriniformes: Cobitidae) in the River Ganges Basin, India

“…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% respectively at the species level (Yao et al, 2010).…”

Use of ITS DNA barcode for identification of Jewels of Opar (Talinum paniculatum) collected in Thanh Hoa, Vietnam

“…The nucleus rADN genes are a multi-gene system coding for rRNA sequences that are both conservative and diverse when it comes to distinguishing close species. In the nucleus of the cell, rADN are arranged as random units, including DNA encoding 18S, 5.8S, 28S ribosomal RNA and alternating between non-encoding sequences ITS1 and ITS2 (internal transcribed spacers) located on either side of the 5.8S gene segment [4][5][6]. The coding sequences of three rADN genes, 18S, 5.8S, 28S, are more conservative than the sequences of ITS1 and ITS2.…”