Puneet Varma (Editor)

Internal transcribed spacer

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

Contents

ITS across life domains

In bacteria and archaea, ITS is located between the 16S and 23S rRNA genes. On the other hand, there are two ITS's in eukaryotes; ITS1 is located between 18S and 5.8S rRNA genes, while ITS2 is between 5.8S and 26S (in plants, or 28S in animals) 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

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 (IGS) or non-transcribed spacer (NTS).

Each eukaryotic ribosomal cluster contains the 5' external transcribed sequence (5' ETS), the 18S rRNA gene, the ITS1, the 5.8S rRNA gene, the ITS2, the 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:

  • it is routinely amplified thanks to its small size associated to the availability of highly conserved flanking sequences ;
  • it is easy to detect even from small quantities of DNA due to the high copy number of the rRNA clusters ;
  • it undergoes rapid concerted evolution via unequal crossing-over and gene conversion. This promotes intra-genomic homogeneity of the repeat units, although high-throughput sequencing showed the occurrence of frequent variations within plant species.
  • it has a high degree of variation even between closely related species. This can be explained by the relatively low evolutionary pressure acting on such non-functional spacer sequences.
  • For example, ITS markers have proven especially useful for elucidating phylogenetic relationships among the following taxa.

    Fungal 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 level, and even within species (e.g., to identify geographic races). Because of its higher degree of variation than other genic regions of rDNA (for small- and large-subunit rRNA), variation among individual rDNA repeats can sometimes be observed within both the ITS and IGS regions. In addition to the standard ITS1+ITS4 primers used by most labs, several taxon-specific primers have been described that allow selective amplification of fungal sequences (e.g., see Gardes & Bruns 1993 paper describing amplification of basidiomycete ITS sequences from mycorrhiza samples).

    ITS and organismal life history

    There are some indications suggesting that ITS sequences are conserved irrespective of the life history evolution in plants. First confirmation was reported on marine green algae, Monostroma latissimum, in which ITS sequence data were identical between sexual (heteromorphic alternation) and asexual (no alternation) strains. In other words, this study reported that the "two different life cycles in the eukaryote belong to the same species" with identical ITS sequences.

    References

    Internal transcribed spacer Wikipedia