Internal transcribed spacer

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Internal transcribed spacer (ITS) refers to a piece of non-functional RNA situated between structural ribosomal RNAs (rRNA) on a common precursor transcript. Read from 5' to 3', this polycistronic rRNA precursor transcript contains the 5' external transcribed sequence (5' ETS), 18S rRNA, ITS1, 5.8S rRNA, ITS2, 28S rRNA and finally the 3' ETS. During rRNA maturation, ETS and ITS pieces are excised and as non-functional maturation by-products rapidly degraded. 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.[citation needed]

For example, ITS has proven especially useful for elucidating relationships among congeneric species and closely related genera in Asteraceae[1] as well as clinically important yeast species.[2]

The ITS region is the most widely sequenced DNA region in molecular ecology of fungi[3] and has been recommended as the universal fungal barcode sequence.[4] 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[5] 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).[6]

ITS and organismal life history[edit]

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,[7] in which ITS sequence data was 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.


  1. ^ 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. 
  2. ^ 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 88485. PMID 11682528. 
  3. ^ 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. 
  4. ^ 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.
  5. ^ 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.
  6. ^ Gardes, M., and 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. 
  7. ^ 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. 
  • Jeeva, M. L. Sharma, K. Mishra, A. K. and Misra, R. S. (2008) Rapid Extraction of Genomic DNA from Sclerotium rolfsii Causing Collar Rot of Amorphophallus. Genes, Genomes and Genomics. 2 (1), 60-62.
  • White, T. J, Bruns, T, Lee, S. and Taylor, J. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In ‘PCR protocols: a guide to methods and applications’. pp. 315–322.

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