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<p>Abstract</p> <p>Background</p> <p><it>Roo </it>is the most abundant retrotransposon in the fruit fly <it>Drosophila melanogaster</it>. Its evolutionary origins and dynamics are thus of special interest for understanding the evolutionary history of <it>Drosophila </it>genome organization. We here study the phylogenetic distribution and evolution of <it>roo</it>, and its highly diverged relative <it>rooA </it>in 12 completely sequenced genomes of the genus <it>Drosophila</it>.</p> <p>Results</p> <p>We identify a total of 164 <it>roo </it>copies, 57 of which were previously unidentified copies that occur in 9 of the 12 genomes. Additionally we find 66 <it>rooA </it>copies in four genomes and remnants of this element in two additional genomes. We further increased the number of elements by searching for individual <it>roo</it>/<it>rooA </it>sequence domains. Most of our <it>roo </it>and <it>rooA </it>elements have been recently inserted. Most elements within a genome are highly similar. A comparison of the phylogenetic tree of our <it>roo </it>and <it>rooA </it>elements shows that the split between <it>roo </it>and <it>rooA </it>took place early in <it>Drosophila </it>evolution. Furthermore there is one incongruency between the species tree and the phylogenetic tree of the <it>roo </it>element. This incongruency regards the placement of elements from <it>D. mojavensis</it>, which are more closely related to <it>D. melanogaster </it>than elements from <it>D. willistoni</it>.</p> <p>Conclusion</p> <p>Within genomes, the evolutionary dynamics of <it>roo </it>and <it>rooA </it>range from recent transpositional activity to slow decay and extinction. Among genomes, the balance of phylogenetic evidence, sequence divergence distribution, and the occurrence of solo-LTR elements suggests an origin of <it>roo/rooA </it>within the <it>Drosophila </it>clade. We discuss the possibility of a horizontal gene transfer of <it>roo </it>within this clade.</p>