Internal transcribed spacer

ITS (for internal transcribed spacer) 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 (due to the high copy number of rRNA genes) easy to amplify even from small quantities of DNA, 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 [1](Baldwin, 1992; Baldwin et al., 1995; Kim et al., 1996) as well as clinically important yeast species.[2]

The ITS region is now perhaps the most widely sequenced DNA region in fungi (Peay et al., 2008).[3] 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).[4]

References

  1. ^ Baldwin, B.G. (1992). "Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: An example from the Compositaogy". 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=88485. 
  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. 
  4. ^ 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. 

5) 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.

6) 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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