Internal transcribed spacer


Internal transcribed spacer is the spacer DNA situated between the small-subunit ribosomal RNA and large-subunit rRNA genes in the chromosome or the corresponding transcribed region in the polycistronic rRNA precursor transcript.

ITS across life domains

In bacteria and archaea, there is a single ITS, located between the 16S and 23S rRNA genes. Contrastingly, there are two ITSs in eukaryotes: ITS1 is located between 18S and 5.8S rRNA genes, while ITS2 is between 5.8S and 28S rRNA genes. ITS1 corresponds to the ITS in bacteria and archaea, while ITS2 originated as an insertion that interrupted the ancestral 23S rRNA gene.

Organization

In bacteria and archaea, the ITS occurs in one to several copies, as do the flanking 16S and 23S genes. When there are multiple copies, these do not occur adjacent to one another. Rather, they occur in discrete locations in the circular chromosome.
In eukaryotes, genes encoding ribosomal RNA and spacers occur in tandem repeats that are thousands of copies long, each separated by regions of non-transcribed DNA termed intergenic spacer or non-transcribed spacer.
Each eukaryotic ribosomal cluster contains the 5' external transcribed spacer, the 18S rRNA gene, the ITS1, the 5.8S rRNA gene, the ITS2, the 26S or 28S rRNA gene, and finally the 3' ETS.
During rRNA maturation, ETS and ITS pieces are excised. As non-functional by-products of this maturation, they are rapidly degraded.

Use in phylogeny

Sequence comparison of the ITS region is widely used in taxonomy and molecular phylogeny because of several favorable properties:
For example, ITS markers have proven especially useful for elucidating phylogenetic relationships among the following taxa.
Taxonomic groupTaxonomic levelYearAuthors with references
Asteraceae: CompositaeSpecies 1992Baldwin et al.
Viscaceae: ArceuthobiumSpecies 1994Nickrent et al.
Poaceae: ZeaSpecies 1996Buckler & Holtsford
Leguminosae: MedicagoSpecies 1998Bena et al.
Orchidaceae: DiseaeGenera 1999Douzery et al.
Odonota: CalopteryxSpecies 2001Weekers et al.
Yeasts of clinical importanceGenera2001Chen et al.
Poaceae: SaccharinaeGenera 2002Hodkinson et al.
Plantaginaceae: PlantagoSpecies 2002Rønsted et al.
Jungermanniopsida: HerbertusSpecies 2004Feldberg et al.
Pinaceae: TsugaSpecies 2008Havill et al.
Chrysomelidae: AlticaGenera 2009Ruhl et al.
SymbiodiniumClade2009Stat et al.
BrassicaceaeTribes 2010Warwick et al.
Ericaceae: EricaSpecies 2011Pirie et al.
Diptera: BactroceraSpecies 2014Boykin et al.
Scrophulariaceae: ScrophulariaSpecies 2014Scheunert & Heubl
Potamogetonaceae: PotamogetonSpecies 2016Yang et al.

Mycological barcoding

The ITS region is the most widely sequenced DNA region in molecular ecology of fungi and has been recommended as the universal fungal barcode sequence. It has typically been most useful for molecular systematics at the species to genus level, and even within species. Because of its higher degree of variation than other genic regions of rDNA, variation among individual rDNA repeats can sometimes be observed within both the ITS and IGS regions. In addition to the universal ITS1+ITS4 primers used by many labs, several taxon-specific primers have been described that allow selective amplification of fungal sequences. Despite shotgun sequencing methods becoming increasingly utilized in microbial sequencing, the low biomass of fungi in clinical samples make the ITS region amplification an area of ongoing research.