ITS2

Internal Transcribed Spacer 2 (ITS2) is a noncoding segment of the eukaryotic ribosomal DNA (rDNA) repeat unit. It lies between the 5.8S and 28S rRNA genes (with ITS1 between the 18S and 5.8S) and is transcribed as part of the same precursor rRNA transcript by RNA polymerase I. During ribosome biogenesis, ITS regions, including ITS2, are excised and do not appear in mature rRNA. ITS2 thus functions as a spacer sequence rather than a coding element.

ITS2 is notable for high sequence variability among species, while flanking 5.8S and 28S rRNA genes provide some conserved context. This combination makes ITS2 useful for distinguishing closely related species in many groups. In practice, ITS2 is widely employed in molecular taxonomy and phylogenetics as a DNA barcode, especially for fungi, where the ITS region (often including ITS1 and ITS2) is a primary identification marker. It is also used in plants and some invertebrates, sometimes as a supplementary barcode or for resolving species-level questions. Because of its relatively short length, ITS2 is amenable to amplification from degraded DNA and to high-throughput sequencing techniques. There are specialized resources, such as curated ITS2 databases, that assist in annotation and alignment by incorporating secondary structure information.

Analytical considerations include intragenomic variation, potential paralogs, and alignment challenges arising from length and sequence diversity. In some taxa, secondary structure models of ITS2 improve alignment and homology assessment, aiding comparisons across diverse species. Overall, ITS2 remains a core tool for species identification and evolutionary studies in many eukaryotes, with strengths and limitations that depend on the taxonomic group and the research question.