Retrotransposon marker

Retrotransposon marker

Retrotransposon markersare 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 (Shedlock and Okada, 2000). 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). 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 (Hamdi "et al." 1999; Shedlock and Okada 2000). The “presence” of a given retrotransposon in related taxa suggests their orthologues 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 (Nikaido et al., 1999), hominoid relationships (Salem et al. 2003), the Strepsirrhine tree (Roos et al., 2004) and the placental mammalian evolution (Kriegs et al., 2006).

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 (see Flavell et al. 1999; Kalendar et al. 1999; Kumar & Hirochika 2001).


* Flavell AJ, Knox MR, Pearce SR and Ellis THN. (1999) Retrotransposon-based insertion polymorphisms (RBIP) for high-throughput marker analysis. Plant J. 16: 643-650
* Hamdi H, Nishio H, Zielinski R, Dugaiczyk A (1999) Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates. J Mol Biol 289: 861–871. [ GS]
* Kalendar R, Grob T, Regina M, Suomeni A, Schulman A. 1999. IRAP and RE

* Kumar A, Hirochika H. 2001. Applications of retrotransposons as genetic tools in plant biology. Trends in Plant Sciences 6: 127–134
* Shedlock AM, Okada N (2000) SINE insertions: Powerful tools for molecular systematics. Bioessays 22: 148–160. [ GS]
* van de Lagemaat LN, Gagnier L, Medstrand P, Mager DL (2005) Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. Genome Res 15: 1243–1249. [ GS]
* Nikaido M, Rooney AP, Okada N (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: 10261–10266. [ GS]
* Salem AH, Ray DA, Xing J, Callinan PA, Myers JS, Hedges DJ, Garber RK, Witherspoon DJ, Jorde LB, Batzer MA (2003) Alu elements and hominid phylogenetics. Proc Natl Acad Sci U S A 100: 12787–12791. [ GS]
* Roos C, Schmitz J, Zischler H (2004) Primate jumping genes elucidate strepsirrhine phylogeny. Proc Natl Acad Sci U S A 101: 10650–10654. [ GS]
* Kriegs JO, Churakov G, Kiefmann M, Jordan U, Brosius J, Schmitz J. (2006) Retroposed Elements as Archives for the Evolutionary History of Placental Mammals. PLoS Biol 4(4): e91. []

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