Internal transcribed spacer

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. 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 25S (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.[1][2]

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). Sequence comparison of the ITS region is widely used in taxonomy and molecular phylogeny because it a) is easy to amplify even from small quantities of DNA (due to the high copy number of rRNA genes), and b) 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 sequences.

For example, ITS has proven especially useful for elucidating relationships among congeneric species and closely related genera in Asteraceae[3] as well as clinically important yeast species.[4]

The ITS region is the most widely sequenced DNA region in molecular ecology of fungi[5] and has been recommended as the universal fungal barcode sequence.[6] 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[7] 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).[8]

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,[9] 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

  1. ↑ Lafontaine, D. L. J.; Tollervey, D. (2001). "The function and synthesis of ribosomes". Nature Reviews Molecular Cell Biology. 2 (7): 514. doi:10.1038/35080045.
  2. ↑ Scott Orland Rogers (27 July 2011). Integrated Molecular Evolution. CRC Press. pp. 65–66. ISBN 978-1-4398-1995-1. Retrieved 9 March 2015.
  3. ↑ Baldwin, B.G. (1992). "Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: An example from the Compositae". Molecular Phylogenetics and Evolution. 1 (1): 3–16. doi:10.1016/1055-7903(92)90030-K. PMID 1342921.
  4. ↑ Chen,Y-C, J. D. Eisner, M. M. Kattar, S. L. Rassoulian-Barrett, K. Lafe, A. P. Limaye, and B. T. Cookson (2001). "Polymorphic Internal Transcribed Spacer Region 1 DNA Sequences Identify Medically Important Yeasts". J. Clin. Microbiol. 39 (11): 4042–4051. doi:10.1128/JCM.39.11.4042-4051.2001. PMC 88485Freely accessible. PMID 11682528.
  5. ↑ Peay K.G.; Kennedy P.G.; Bruns T.D. (2008). "Fungal community ecology: a hybrid beast with a molecular master". BioScience. 58: 799–810. doi:10.1641/b580907.
  6. ↑ Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V., Spouge, J.L., Levesque, C.A., Chen, W., Bolchacova, E., Voigt, K., Crous, P.W.; et al. (2012). "Nuclear Ribosomal Internal Transcribed Spacer (ITS) Region as a Universal DNA Barcode Marker for Fungi". PNAS. 109 (16): 6241–6246. doi:10.1073/pnas.1117018109.
  7. ↑ 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.
  8. ↑ Gardes, M.; Bruns, T.D. (1993). "ITS primers with enhanced specificity for basidiomycetes: application to the identification of mycorrhiza and rusts". Molecular Ecology. 2 (2): 113–118. doi:10.1111/j.1365-294X.1993.tb00005.x. PMID 8180733.
  9. ↑ Bast, Felix (2009). "Bast, F., Shimada, S., Hiraoka, M., & Okuda, K. (2009). Asexual life history by biflagellate zoids in Monostroma latissimum (Ulotrichales)". Aquatic Botany. 91 (3): 213–218. doi:10.1016/j.aquabot.2009.06.006.

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