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Background  Only a few transposable elements are known to exhibit site-specific insertion patterns, including the well-studied R-element retrotransposons that insert into specific sites within the multigene rDNA. The only known rDNA-specific DNA transposon,  Pokey  (superfamily:  piggyBac ) is found in the freshwater microcrustacean,  Daphnia pulex . Here, we present a genome-wide analysis of  Pokey  based on the recently completed whole genome sequencing project for  D. pulex .    Results  Phylogenetic analysis of  Pokey  elements recovered from the genome sequence revealed the presence of four lineages corresponding to two divergent autonomous families and two related lineages of non-autonomous miniature inverted repeat transposable elements (MITEs). The MITEs are also found at the same 28S rRNA gene insertion site as the  Pokey  elements, and appear to have arisen as deletion derivatives of autonomous elements. Several copies of the full-length  Pokey  elements may be capable of producing an active transposase. Surprisingly, both families of  Pokey  possess a series of 200 bp repeats upstream of the transposase that is derived from the rDNA intergenic spacer (IGS). The IGS sequences within the  Pokey  elements appear to be evolving in concert with the rDNA units. Finally, analysis of the insertion sites of  Pokey  elements outside of rDNA showed a target preference for sites similar to the specific sequence that is targeted within rDNA.    Conclusions  Based on the target site preference of  Pokey  elements and the concerted evolution of a segment of the element with the rDNA unit, we propose an evolutionary path by which the ancestors of  Pokey  elements have invaded the rDNA niche. We discuss how specificity for the rDNA unit may have evolved and how this specificity has played a role in the long-term survival of these elements in the subgenus  Daphnia .

In and out of the rRNA genes: characterization of Pokey elements in the sequenced Daphnia genome