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.

ITS across life domains[edit]

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]

Organization[edit]

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.[3]

During rRNA maturation, ETS and ITS pieces are excised. As non-functional by-products of this maturation, they are rapidly degraded.[4]

Use in phylogeny[edit]

Sequence comparison of the ITS region is widely used in taxonomy and molecular phylogeny because of several favorable properties:[5]

  • 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.[6]
  • 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.

Taxonomic group Taxonomic level Year Authors with references
Asteraceae: Compositae Species (congeneric) 1992 Baldwin et al.[7]
Viscaceae: Arceuthobium Species (congeneric) 1994 Nickrent et al.[8]
Poaceae: Zea Species (congeneric) 1996 Buckler & Holtsford[9]
Leguminosae: Medicago Species (congeneric) 1998 Bena et al.[3]
Orchidaceae: Diseae Genera (within tribes) 1999 Douzery et al.[10]
Odonota: Calopteryx Species (congeneric) 2001 Weekers et al.[11]
Yeasts of clinical importance Genera 2001 Chen et al.[12]
Poaceae: Saccharinae Genera (within tribes) 2002 Hodkinson et al.[13]
Plantaginaceae: Plantago Species (congeneric) 2002 Rønsted et al.[14]
Jungermanniopsida: Herbertus Species (congeneric) 2004 Feldberg et al.[15]
Pinaceae: Tsuga Species (congeneric) 2008 Havill et al.[16]
Brassicaceae Tribes (within a family) 2010 Warwick et al.[17]
Ericaceae: Erica Species (congeneric) 2011 Pirie et al.[18]
Diptera: Bactrocera Species (congeneric) 2014 Boykin et al.[19]
Scrophulariaceae: Scrophularia Species (congeneric) 2014 Scheunert & Heubl[20]
Potamogetonaceae: Potamogeton Species (congeneric) 2016 Yang et al.[21]

Fungal barcoding[edit]

The ITS region is the most widely sequenced DNA region in molecular ecology of fungi[22] and has been recommended as the universal fungal barcode sequence.[23] 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[24] 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).[25]

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,[26] 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[edit]

  1. ^ Lafontaine, D. L. J.; Tollervey, D. (2001). "The function and synthesis of ribosomes". Nature Reviews Molecular Cell Biology. 2 (7): 514–520. 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. ^ a b Bena, Gilles; Jubier, Marie-France; Olivieri, Isabelle; Lejeune, Bernard (1998). "Ribosomal External and Internal Transcribed Spacers: Combined Use in the Phylogenetic Analysis of Medicago (Leguminosae)". Journal of Molecular Evolution. 46 (3): 299–306. doi:10.1007/PL00006306. ISSN 0022-2844. 
  4. ^ Michot, Bernard; Bachellerie, Jean-Pierre; Raynal, Francoise (1983-05-25). "Structure of mouse rRNA precursors. Complete sequence and potential folding of the spacer regions between 18S and 28S rRNA". Nucleic Acids Research. 11 (10): 3375–3391. doi:10.1093/nar/11.10.3375. ISSN 0305-1048. 
  5. ^ Baldwin, Bruce G.; Sanderson, Michael J.; Porter, J. Mark; Wojciechowski, Martin F.; Campbell, Christopher S.; Donoghue, Michael J. (1995-01-01). "The ITS Region of Nuclear Ribosomal DNA: A Valuable Source of Evidence on Angiosperm Phylogeny". Annals of the Missouri Botanical Garden. 82 (2): 247–277. doi:10.2307/2399880. 
  6. ^ Song, Jingyuan; Shi, Linchun; Li, Dezhu; Sun, Yongzhen; Niu, Yunyun; Chen, Zhiduan; Luo, Hongmei; Pang, Xiaohui; Sun, Zhiying (2012-08-30). "Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA". PLOS ONE. 7 (8): e43971. doi:10.1371/journal.pone.0043971. ISSN 1932-6203. PMC 3431384Freely accessible. PMID 22952830. 
  7. ^ 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. 
  8. ^ Nickrent, Daniel L.; Schuette, Kevin P.; Starr, Ellen M. (1994-01-01). "A Molecular Phylogeny of Arceuthobium (Viscaceae) Based on Nuclear Ribosomal DNA Internal Transcribed Spacer Sequences". American Journal of Botany. 81 (9): 1149–1160. doi:10.2307/2445477. 
  9. ^ Buckler, E. S.; Holtsford, T. P. (1996-04-01). "Zea systematics: ribosomal ITS evidence.". Molecular Biology and Evolution. 13 (4): 612–622. ISSN 0737-4038. PMID 8882504. 
  10. ^ Douzery, Emmanuel J. P.; Pridgeon, Alec M.; Kores, Paul; Linder, H. P.; Kurzweil, Hubert; Chase, Mark W. (1999-06-01). "Molecular phylogenetics of Diseae (Orchidaceae): a contribution from nuclear ribosomal ITS sequences". American Journal of Botany. 86 (6): 887–899. ISSN 0002-9122. PMID 10371730. 
  11. ^ Weekers, Peter H. H.; De Jonckheere, Johan F.; Dumont, Henri J. (2001-07-01). "Phylogenetic Relationships Inferred from Ribosomal ITS Sequences and Biogeographic Patterns in Representatives of the Genus Calopteryx (Insecta: Odonata) of the West Mediterranean and Adjacent West European Zone". Molecular Phylogenetics and Evolution. 20 (1): 89–99. doi:10.1006/mpev.2001.0947. 
  12. ^ 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. 
  13. ^ Hodkinson, Trevor R.; Chase, Mark W.; Lledó, Dolores M.; Salamin, Nicolas; Renvoize, Stephen A. "Phylogenetics of Miscanthus, Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnL intron and trnL-F intergenic spacers". Journal of Plant Research. 115 (5): 381–392. doi:10.1007/s10265-002-0049-3. ISSN 0918-9440. 
  14. ^ Rønsted, Nina; Chase, Mark W.; Albach, Dirk C.; Bello, Maria Angelica (2002-08-01). "Phylogenetic relationships within Plantago (Plantaginaceae): evidence from nuclear ribosomal ITS and plastid trnL-F sequence data". Botanical Journal of the Linnean Society. 139 (4): 323–338. doi:10.1046/j.1095-8339.2002.00070.x. ISSN 1095-8339. 
  15. ^ Feldberg, K.; Groth, H.; Wilson, R.; Schäfer-Verwimp, A.; Heinrichs, J. (2004-11-04). "Cryptic speciation in Herbertus (Herbertaceae, Jungermanniopsida): Range and morphology of Herbertus sendtneri inferred from nrITS sequences". Plant Systematics and Evolution. 249 (3-4): 247–261. doi:10.1007/s00606-004-0221-4. ISSN 0378-2697. 
  16. ^ Havill, Nathan P.; Campbell, Christopher S.; Vining, Thomas F.; LePage, Ben; Bayer, Randall J.; Donoghue, Michael J. (2008-07-01). "Phylogeny and Biogeography of Tsuga (Pinaceae) Inferred from Nuclear Ribosomal ITS and Chloroplast DNA Sequence Data". Systematic Botany. 33 (3): 478–489. doi:10.1600/036364408785679770. 
  17. ^ Warwick, Suzanne I.; Mummenhoff, Klaus; Sauder, Connie A.; Koch, Marcus A.; Al-Shehbaz, Ihsan A. (2010-04-13). "Closing the gaps: phylogenetic relationships in the Brassicaceae based on DNA sequence data of nuclear ribosomal ITS region". Plant Systematics and Evolution. 285 (3-4): 209–232. doi:10.1007/s00606-010-0271-8. ISSN 0378-2697. 
  18. ^ Pirie, Michael D.; Oliver, E. G. H.; Bellstedt, Dirk U. (2011-11-01). "A densely sampled ITS phylogeny of the Cape flagship genus Erica L. suggests numerous shifts in floral macro-morphology". Molecular Phylogenetics and Evolution. 61 (2): 593–601. doi:10.1016/j.ympev.2011.06.007. 
  19. ^ Boykin, L. M.; Schutze, M. K.; Krosch, M. N.; Chomič, A.; Chapman, T. A.; Englezou, A.; Armstrong, K. F.; Clarke, A. R.; Hailstones, D. (2014-05-01). "Multi-gene phylogenetic analysis of south-east Asian pest members of the Bactrocera dorsalis species complex (Diptera: Tephritidae) does not support current taxonomy". Journal of Applied Entomology. 138 (4): 235–253. doi:10.1111/jen.12047. ISSN 1439-0418. 
  20. ^ Scheunert, Agnes; Heubl, Günther (2014-01-01). "Diversification of Scrophularia (Scrophulariaceae) in the Western Mediterranean and Macaronesia – Phylogenetic relationships, reticulate evolution and biogeographic patterns". Molecular Phylogenetics and Evolution. 70: 296–313. doi:10.1016/j.ympev.2013.09.023. 
  21. ^ Yang, Tao; Zhang, Tian-lei; Guo, You-hao; Liu, Xing (2016-11-17). "Identification of Hybrids in Potamogeton: Incongruence between Plastid and ITS Regions Solved by a Novel Barcoding Marker PHYB". PLOS ONE. 11 (11): e0166177. doi:10.1371/journal.pone.0166177. ISSN 1932-6203. PMC 5113904Freely accessible. PMID 27855191. 
  22. ^ 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. 
  23. ^ 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. PMC 3341068Freely accessible. PMID 22454494. 
  24. ^ 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.
  25. ^ 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. 
  26. ^ 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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