Internal transcribed spacer
Internal transcribed spacer (ITS) is the
polycistronic
rRNA precursor transcript.
Across life domains
In
eukaryotes: ITS1 is located between 18S and 5.8S rRNA genes, while ITS2 is between 5.8S and 28S (in opisthokonts, or 25S in plants) rRNA genes. ITS1 corresponds to the ITS in bacteria and archaea, while ITS2 originated as an insertion that interrupted the ancestral 23S rRNA gene.[1][2]
Organization
In
In eukaryotes, genes encoding ribosomal RNA and spacers occur in
intergenic spacer
(IGS) or non-transcribed spacer (NTS).
Each eukaryotic ribosomal cluster contains the 5'
26S or 28S rRNA gene, and finally the 3' ETS.[5]
During rRNA maturation, ETS and ITS pieces are excised. As non-functional by-products of this maturation, they are rapidly degraded.[6]
Use in phylogenetic inference
Sequence comparison of the eukaryotic ITS regions is widely used in
molecular phylogeny because of several favorable properties:[7]
- 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.[8]
- 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-coding spacer sequences.
For example, ITS markers have proven especially useful for elucidating phylogenetic relationships among the following taxa.
| Taxonomic group | Taxonomic level | Year | Authors with references |
|---|---|---|---|
Compositae
|
Species (congeneric) | 1992 | Baldwin et al.[9] |
| Viscaceae: Arceuthobium | Species (congeneric) | 1994 | Nickrent et al.[10] |
| Poaceae: Zea | Species (congeneric) | 1996 | Buckler & Holtsford[11] |
Leguminosae: Medicago
|
Species (congeneric) | 1998 | Bena et al.[5] |
Orchidaceae: Diseae
|
Genera (within tribes) | 1999 | Douzery et al.[12] |
| Odonata: Calopteryx | Species (congeneric) | 2001 | Weekers et al.[13] |
Yeasts of clinical importance
|
Genera | 2001 | Chen et al.[14] |
| Poaceae: Saccharinae | Genera (within tribes) | 2002 | Hodkinson et al.[15] |
| Plantaginaceae: Plantago | Species (congeneric) | 2002 | Rønsted et al.[16] |
| Jungermanniopsida: Herbertus | Species (congeneric) | 2004 | Feldberg et al.[17] |
| Pinaceae: Tsuga | Species (congeneric) | 2008 | Havill et al.[18] |
| Chrysomelidae: Altica | Genera (congeneric) | 2009 | Ruhl et al.[19] |
| Symbiodinium | Clade | 2009 | Stat et al.[20] |
| Brassicaceae | Tribes (within a family) | 2010 | Warwick et al.[21] |
| Ericaceae: Erica | Species (congeneric) | 2011 | Pirie et al.[22] |
| Diptera: Bactrocera | Species (congeneric) | 2014 | Boykin et al.[23] |
| Scrophulariaceae: Scrophularia | Species (congeneric) | 2014 | Scheunert & Heubl[24] |
| Potamogetonaceae: Potamogeton | Species (congeneric) | 2016 | Yang et al.[25] |
ITS2 is known to be more conserved than ITS1 is. All ITS2 sequences share a common core of secondary structure,[26] while ITS1 structures are only conserved in much smaller taxonomic units. Regardless of the scope of conservation, structure-assisted comparison can provide higher resolution and robustness.[27]
Mycological barcoding
The ITS region is the most widely sequenced DNA region in
basidiomycete ITS sequences from mycorrhiza samples).[32] 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.[33][34]
References
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- ISBN 978-1-4398-1995-1. Retrieved 9 March 2015.
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- PMID 11682528.)
{{cite journal}}: CS1 maint: multiple names: authors list (link - S2CID 22971617.
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- .
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- PMID 15769870.
- PMID 24663345.
- S2CID 18363490.
- PMID 22454494.)
{{cite journal}}: CS1 maint: multiple names: authors list (link - ^ White, T.J., Bruns, T., Lee, S., and Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: a Guide to Methods and Applications 18, 315–322.
- ^ The ITS1 primer covers ITS1-5.8S-ITS2 from the 5', and ITS4 covers the same area from the 3'.
- S2CID 24316407.
- PMID 29242834.
- S2CID 53438777.