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.[1][3] 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 alternative retrotransposon-based markers. In this method, PCR oligonucleotide primers face outwards from terminal retrotransposon regions. Thus, they amplify the fragment between two retrotransposon insertions. As retrotransposon integration patterns vary between genotypes, the number and size of the resulting amplicons can be used for differentiation of genotypes or cultivars, to measure genetic diversity or to reconstruct phylogenies.[9][10][11] SINEs, which are small in size and often integrate within or next to genes represent an optimal source for the generation of effective IRAP markers.[12]


  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 1199538Freely accessible. 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 17876Freely accessible. 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 240696Freely accessible. 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 489989Freely accessible. 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 2910653Freely accessible. 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 1395351Freely accessible. 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. 
  12. ^ Seibt, KM; Wenke, T; Wollrab, C; Junghans, H; Muders, K; Dehmer, KJ; Diekmann, K; Schmidt, T (June 2012). "Development and application of SINE-based markers for genotyping of potato varieties.". TAG. Theoretical and Applied Genetics. Theoretische und angewandte Genetik. 125 (1): 185–96. doi:10.1007/s00122-012-1825-7. PMID 22371142.