Internal transcribed spacer

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rDNA (purple) behind non-transcribed sequences (NTS), rRNA transcripts (orange) with external transcribed sequences (ETS) and internal transcribed sequences (ITS)

An internal transcribed spacer is a nucleotide sequence between the rRNA - genes ( rDNA ) or between the rRNA portions in the from the rDNA during Transcription resulting transcripts .

properties

The RNA of the ribosome (rRNA) consists of different RNA molecules that were generated in eukaryotes from different transcripts of the rRNA genes (rDNA). Within these sequences are the ITS, which as spacers , unlike rRNA, do not occur in the finished ribosome. In contrast to ITS, the external transcribed sequences (ETS) are located outside the ribosomal subunits, but do not occur in the later ribosome either. The ITS and ETS are cut out after transcription and then broken down , sometimes with the participation of snoRNA .

In bacteria and archaea , the ITS are located between the 16 S and 23 S rRNA.

There are two different ITS in eukaryotes: ITS1 lies between 18 S and 5.8 S rRNA and ITS2 between 5.8 S and 26 S (in plants) or 28 S rRNA (in animals). While ITS1 corresponds to the bacterial ITS, ITS2 arose later in the 23 S rRNA through duplication .

use

The 5.8 S rRNA from eukaryotes and the surrounding ITS are used to investigate phylogenetics , since ITS mutate comparatively frequently and the genes of the rRNA occur in many copies in the genome and therefore tend to lead to fewer false negative results, e.g. B. in bacteria, in plants, in mosquitoes and in fungi . Within the ribosomal DNA of the fungi, the ITS are the sequences that are most clearly distinguishable within a species or between species. Standard primer pairs for the polymerase chain reaction to differentiate between fungi are ITS1 with ITS4. Other primer pairs are used to differentiate between Basidiomycetes and Mycorrhiza .

Taxonomic group rich Taxonomic level year reference
Mushrooms Mushrooms Genera 1990 White et al.
Asteraceae : Compositae plants species 1992 Baldwin et al.
Basidiomycetes / Ascomycetes Mushrooms Genera 1993 Gardes et al.
Viscaceae : Arceuthobium plants species 1994 Nickrent et al.
Poaceae : Zea plants species 1996 Buckler & Holtsford
Leguminosae : Medicago plants species 1998 Bena et al.
Orchidaceae : Diseae plants Genera 1999 Douzery, et al.
Odonota : Calopteryx Animals species 2001 Weekers et al.
Yeasts of clinical importance Mushrooms Genera 2001 Chen et al.
Poaceae : Saccharinae plants Genera 2002 Hodkinson et al.
Plantaginaceae : Plantago plants species 2002 Rønsted et al.
Jungermanniopsida : Herbertus plants species 2004 Feldberg et al.
Anophelinae of South America Animals species 2006 Marelli et al.
Pinaceae : Tsuga plants species 2008 Havill et al.
Brassicaceae plants Tribes 2010 Warwick et al.
Ericaceae : Erica plants species 2011 Pirie et al.
Diptera : Bactrocera Animals species 2014 Boykin et al.
Scrophulariaceae : Scrophularia plants species 2014 Scheunert & Heubl
Potamogetonaceae : Potamogeton plants species 2016 Yang et al.

Individual evidence

  1. ^ AW Coleman: Nuclear rRNA transcript processing versus internal transcribed spacer secondary structure. In: Trends in genetics: TIG. Volume 31, number 3, March 2015, pp. 157-163, doi : 10.1016 / j.tig.2015.01.002 , PMID 25648500 .
  2. ↑ Bernard Michot, Jean-Pierre Bachellerie, Francoise Raynal: Structure of mouse rRNA precursors. Complete sequence and potential folding of the spacer regions between 18S and 28S rRNA . In: Nucleic Acids Research . 11, No. 10, May 25, 1983, ISSN  0305-1048 , pp. 3375-3391. doi : 10.1093 / nar / 11.10.3375 .
  3. ^ A b Gilles Bena, Marie-France Jubier, Isabelle Olivieri, Bernard Lejeune: Ribosomal External and Internal Transcribed Spacers: Combined Use in the Phylogenetic Analysis of Medicago (Leguminosae) . In: Journal of Molecular Evolution . 46, No. 3, 1998, ISSN  0022-2844 , pp. 299-306. doi : 10.1007 / PL00006306 .
  4. ↑ Denis LJ Lafontaine, David Tollervey: The function and synthesis of ribosomes. In: Nature Reviews Molecular Cell Biology. 2, 2001, p. 514, doi : 10.1038 / 35080045 .
  5. ↑ J. Trček, F. Barja: Updates on quick identification of acetic acid bacteria with a focus on the 16S-23S rRNA gene internal transcribed spacer and the analysis of cell proteins by MALDI-TOF mass spectrometry. In: International journal of food microbiology. Volume 196, March 2015, pp. 137-144, doi : 10.1016 / j.ijfoodmicro.2014.12.003 , PMID 25589227 .
  6. ↑ a b B. G. Baldwin: Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the compositae. In: Molecular phylogenetics and evolution. Volume 1, Number 1, March 1992, pp. 3-16, PMID 1342921 .
  7. ↑ a b M. T. Marrelli, MA Sallum, O. Marinotti: The second internal transcribed spacer of nuclear ribosomal DNA as a tool for Latin American anopheline taxonomy - a critical review. In: Memorias do Instituto Oswaldo Cruz. Volume 101, Number 8, December 2006, pp. 817-832, PMID 17293975 .
  8. ↑ YC Chen, JD Eisner, MM Kattar, SL Rassoulian-Barrett, K. Lafe, U. Bui, AP Limaye, BT Cookson: Polymorphic internal transcribed spacer region 1 DNA sequences identify medically important yeasts. In: Journal of clinical microbiology. Volume 39, number 11, November 2001, pp. 4042-4051, doi : 10.1128 / JCM.39.11.4042-4051.2001 , PMID 11682528 , PMC 88485 (free full text).
  9. ↑ Kabir G. Peay, Peter G. Kennedy, Thomas D. Bruns: Fungal Community Ecology: A Hybrid Beast with a Molecular Master. In: BioScience. 58, 2008, p. 799, doi : 10.1641 / b580907 .
  10. ↑ CL Schoch, KA Seifert, S. Huhndorf, V. Robert, JL Spouge, CA Levesque, W. Chen: Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. In: Proceedings of the National Academy of Sciences . Volume 109, number 16, April 2012, pp. 6241-6246, doi : 10.1073 / pnas.1117018109 , PMID 22454494 , PMC 3341068 (free full text).
  11. ↑ a b T. J. White, T. Bruns, S. Lee, J. Taylor: Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: a Guide to Methods and Applications (1990), Chapter 18, pp. 315-322.
  12. ↑ a b M. Gardes, TD Bruns: ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. In: Molecular ecology. Volume 2, Number 2, April 1993, pp. 113-118, PMID 8180733 .
  13. ↑ Daniel L. Nickrent, Kevin P. Schuette, Ellen M. Starr: A Molecular Phylogeny of Arceuthobium (Viscaceae) Based on Nuclear Ribosomal DNA Internal Transcribed Spacer Sequences . In: American Journal of Botany . 81, No. 9, Jan. 1, 1994, pp. 1149-1160. doi : 10.2307 / 2445477 .
  14. ↑ ES Buckler, TP Holt Ford: Zea systematics: ribosomal ITS evidence. . In: Molecular Biology and Evolution . 13, No. 4, April 1, 1996, ISSN  0737-4038 , pp. 612-622. PMID 8882504 .
  15. ↑ Emmanuel JP Douzery, Alec M. Pridgeon, Paul Kores, HP Linder, Hubert Kurzweil, Mark W. Chase: Molecular phylogenetics of Diseae (Orchidaceae): a contribution from nuclear ribosomal ITS sequences . In: American Journal of Botany . 86, No. 6, June 1, 1999, ISSN  0002-9122 , pp. 887-899. PMID 10371730 .
  16. ↑ Peter HH Weekers, Johan F. De Jonckheere, Henri J. Dumont: 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 . In: Molecular Phylogenetics and Evolution . 20, No. 1, July 1, 2001, pp. 89-99. doi : 10.1006 / mpev.2001.0947 .
  17. ↑ Chen, YC, JD Eisner, MM Kattar, SL Rassoulian-Barrett, K. Lafe, AP Limaye, and BT Cookson: Polymorphic Internal Transcribed Spacer Region 1 DNA Sequences Identify Medically Important Yeasts . In: J. Clin. Microbiol. . 39, No. 11, 2001, pp. 4042-4051. doi : 10.1128 / JCM.39.11.4042-4051.2001 . PMID 11682528 . PMC 88485 (free full text).
  18. ↑ Trevor R. Hodkinson, Mark W. Chase, Dolores M. Lledó, Nicolas Salamin, Stephen A. Renvoize: 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 . In: Journal of Plant Research . 115, No. 5, August, ISSN  0918-9440 , pp. 381-392. doi : 10.1007 / s10265-002-0049-3 .
  19. ↑ Nina Rønsted, Mark W. Chase, Dirk C. Albach, Maria Angelica Bello: Phylogenetic relationships within Plantago (Plantaginaceae): evidence from nuclear ribosomal ITS and plastid trnL-F sequence data . In: Botanical Journal of the Linnean Society . 139, No. 4, August 1, 2002, ISSN  1095-8339 , pp. 323-338. doi : 10.1046 / j.1095-8339.2002.00070.x .
  20. ↑ K. Feldberg, H. Groth, R. Wilson, A. Schäfer-Verwimp, J. Heinrichs: Cryptic speciation in Herbertus (Herbertaceae, Jungermanniopsida): Range and morphology of Herbertus sendtneri inferred from nrITS sequences . In: Plant Systematics and Evolution . 249, No. 3-4, November 4, 2004, ISSN  0378-2697 , pp. 247-261. doi : 10.1007 / s00606-004-0221-4 .
  21. ↑ Nathan P. Havill, Christopher S. Campbell, Thomas F. Vining, Ben LePage, Randall J. Bayer, Michael J. Donoghue: Phylogeny and Biogeography of Tsuga (Pinaceae) Inferred from Nuclear Ribosomal ITS and Chloroplast DNA Sequence Data . In: Systematic Botany . 33, No. 3, July 1, 2008, pp. 478-489. doi : 10.1600 / 036364408785679770 .
  22. ↑ Suzanne I. Warwick, Klaus Mummenhoff, Connie A. Sauder, Marcus A. Koch, Ihsan A. Al-Shehbaz: Closing the gaps: phylogenetic relationships in the Brassicaceae based on DNA sequence data of nuclear ribosomal ITS region . In: Plant Systematics and Evolution . 285, No. 3-4, April 13, 2010, ISSN  0378-2697 , pp. 209-232. doi : 10.1007 / s00606-010-0271-8 .
  23. ↑ Michael D. Pirie, EGH Oliver, Dirk U. Bellstedt: A densely sampled ITS phylogeny of the Cape flagship genus Erica L. suggests numerous shifts in floral macro-morphology . In: Molecular Phylogenetics and Evolution . 61, No. 2, November 1, 2011, pp. 593-601. doi : 10.1016 / j.ympev.2011.06.007 .
  24. ↑ LM Boykin, MK Schütze, MN Krosch, A. Chomič, TA Chapman, A. Englezou, KF Armstrong, AR Clarke, D. Hailstones: Multi-gene phylogenetic analysis of south-east Asian pest members of the Bactrocera dorsalis species complex ( Diptera: Tephritidae) does not support current taxonomy . In: Journal of Applied Entomology . 138, No. 4, May 1, 2014, ISSN  1439-0418 , pp. 235-253. doi : 10.1111 / jen.12047 .
  25. ^ Agnes Scheunert, Günther Heubl: Diversification of Scrophularia (Scrophulariaceae) in the Western Mediterranean and Macaronesia - Phylogenetic relationships, reticulate evolution and biogeographic patterns . In: Molecular Phylogenetics and Evolution . 70, January 1, 2014, pp. 296-313. doi : 10.1016 / j.ympev.2013.09.023 .
  26. ↑ Tao Yang, Tian-lei Zhang, You-hao Guo, Xing Liu: Identification of Hybrids in Potamogeton : Incongruence between Plastid and ITS Regions Solved by a Novel Barcoding Marker PHYB . In: PLOS ONE . 11, No. 11, November 17, 2016, ISSN  1932-6203 , p. E0166177. doi : 10.1371 / journal.pone.0166177 . PMID 27855191 . PMC 5113904 (free full text).