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Background   Galileo  is one of three members of the  P superfamily  of DNA transposons. It was originally discovered in  Drosophila buzzatii , in which three segregating chromosomal inversions were shown to have been generated by ectopic recombination between  Galileo  copies. Subsequently,  Galileo  was identified in six of 12 sequenced  Drosophila  genomes, indicating its widespread distribution within this genus.  Galileo  is strikingly abundant in  Drosophila willistoni , a neotropical species that is highly polymorphic for chromosomal inversions, suggesting a role for this transposon in the evolution of its genome.    Results  We carried out a detailed characterization of all  Galileo  copies present in the  D. willistoni  genome. A total of 191 copies, including 133 with two terminal inverted repeats (TIRs), were classified according to structure in six groups. The TIRs exhibited remarkable variation in their length and structure compared to the most complete copy. Three copies showed extended TIRs due to internal tandem repeats, the insertion of other transposable elements (TEs), or the incorporation of non-TIR sequences into the TIRs. Phylogenetic analyses of the transposase (TPase)-encoding and TIR segments yielded two divergent clades, which we termed  Galileo  subfamilies V and W. Target-site duplications (TSDs) in  D. willistoni Galileo  copies were 7- or 8-bp in length, with the consensus sequence GTATTAC. Analysis of the region around the TSDs revealed a target site motif (TSM) with a 15-bp palindrome that may give rise to a stem-loop secondary structure.    Conclusions  There is a remarkable abundance and diversity of  Galileo  copies in the  D. willistoni  genome, although no functional copies were found. The TIRs in particular have a dynamic structure and extend in different ways, but their ends (required for transposition) are more conserved than the rest of the element. The  D. willistoni  genome harbors two  Galileo  subfamilies (V and W) that diverged ~9 million years ago and may have descended from an ancestral element in the genome.  Galileo  shows a significant insertion preference for a 15-bp palindromic TSM.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-792) contains supplementary material, which is available to authorized users.

Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome