Retrotransposon marker

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Retrotransposon markers are retrotransposons that are used as cladistic markers.

The analysis of SINEs – Short INterspersed Elements – LINEs – Long INterspersed Elements – or truncated LTRs – Long Terminal Repeats – as molecular cladistic markers represents a particularly interesting complement to DNA sequence and morphological data.

The reason for this is that retrotransposons are assumed to represent powerful noise-poor synapomorphies.[1] The target sites are relatively unspecific so that the chance of an independent integration of exactly the same element into one specific site in different taxa is not large and may even be negligible over evolutionary time scales. Retrotransposon integrations are currently assumed to be irreversible events; this might change since no eminent biological mechanisms have yet been described for the precise re-excision of class I transposons, but see van de Lagemaat et al. (2005).[2] A clear differentiation between ancestral and derived character state at the respective locus thus becomes possible as the absence of the introduced sequence can be with high confidence considered ancestral.

In combination, the low incidence of homoplasy together with a clear character polarity make retrotransposon integration markers ideal tools for determining the common ancestry of taxa by a shared derived transpositional event.[3][1] The “presence” of a given retrotransposon in related taxa suggests their orthologous integration, a derived condition acquired via a common ancestry, while the “absence” of particular elements indicates the plesiomorphic condition prior to integration in more distant taxa. The use of presence/absence analyses to reconstruct the systematic biology of mammals depends on the availability of retrotransposons that were actively integrating before the divergence of a particular species.

Examples for phylogenetic studies based on retrotransposon presence/absence data are the definition of whales as members of the order Cetartiodactyla with hippos being their closest living relatives,[4] hominoid relationships,[5] the strepsirrhine tree,[6] the marsupial radiation from South America to Australia,[7] and the placental mammalian evolution.[8]

Inter-Retrotransposons Amplified Polymorphisms (IRAPs) are an alternative valuable retrotransposon-based markers. In this method, PCR oligonucleotide primers facing outwards from the LTR or other regions of retrotransposons are made and amplify between two retroelements inserted into the genome. As discussed above, the insertion of elements into the genome mean that the number of sites amplified and sizes of inter-retroelement fragments differ between different lines, and can be used as markers to detect genotypes, measure diversity or reconstruct phylogeny.[9][10][11]

References[edit]

  1. ^ a b Shedlock AM, Okada N (February 2000). <148::AID-BIES6>3.0.CO;2-Z "SINE insertions: powerful tools for molecular systematics". Bioessays 22 (2): 148–60. doi:10.1002/(SICI)1521-1878(200002)22:2<148::AID-BIES6>3.0.CO;2-Z. PMID 10655034. 
  2. ^ van de Lagemaat LN, Gagnier L, Medstrand P, Mager DL (September 2005). "Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates". Genome Res. 15 (9): 1243–9. doi:10.1101/gr.3910705. PMC 1199538. PMID 16140992. 
  3. ^ Hamdi H, Nishio H, Zielinski R, Dugaiczyk A (June 1999). "Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates". J. Mol. Biol. 289 (4): 861–71. doi:10.1006/jmbi.1999.2797. PMID 10369767. 
  4. ^ Nikaido M, Rooney AP, Okada N (August 1999). "Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales". Proc. Natl. Acad. Sci. U.S.A. 96 (18): 10261–6. doi:10.1073/pnas.96.18.10261. PMC 17876. PMID 10468596. 
  5. ^ Salem AH, Ray DA, Xing J et al. (October 2003). "Alu elements and hominid phylogenetics". Proc. Natl. Acad. Sci. U.S.A. 100 (22): 12787–91. doi:10.1073/pnas.2133766100. PMC 240696. PMID 14561894. 
  6. ^ Roos C, Schmitz J, Zischler H (July 2004). "Primate jumping genes elucidate strepsirrhine phylogeny". Proc. Natl. Acad. Sci. U.S.A. 101 (29): 10650–4. doi:10.1073/pnas.0403852101. PMC 489989. PMID 15249661. 
  7. ^ Nilsson, M. A.; Churakov, G.; Sommer, M.; Van Tran, N.; Zemann, A.; Brosius, J.; Schmitz, J. (2010-07-27). Penny, David, ed. "Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions". PLoS Biology (Public Library of Science) 8 (7): e1000436. doi:10.1371/journal.pbio.1000436. PMC 2910653. PMID 20668664. 
  8. ^ Kriegs JO, Churakov G, Kiefmann M, Jordan U, Brosius J, Schmitz J (April 2006). "Retroposed elements as archives for the evolutionary history of placental mammals". PLoS Biol. 4 (4): e91. doi:10.1371/journal.pbio.0040091. PMC 1395351. PMID 16515367. 
  9. ^ Kalendar R, Grob T, Regina M, Suomeni A, Schulman A (April 1999). "IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques". Theoretical and Applied Genetics 98 (5): 704–711. doi:10.1007/s001220051124. 
  10. ^ Flavell AJ, Knox MR, Pearce SR, Ellis TH (December 1998). "Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis". Plant J. 16 (5): 643–50. doi:10.1046/j.1365-313x.1998.00334.x. PMID 10036780. 
  11. ^ Kumar A, Hirochika H (March 2001). "Applications of retrotransposons as genetic tools in plant biology". Trends Plant Sci. 6 (3): 127–34. doi:10.1016/s1360-1385(00)01860-4. PMID 11239612.