title: Structural and sequence diversity of the transposon Galileo in the Drosophila willistoni genome.
abstract: 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.
authors.forename: Juliana W
authors.initials: JW
authors.lastname: Gonçalves
authors.forename: Victor Hugo
authors.initials: VH
authors.lastname: Valiati
authors.forename: Alejandra
authors.initials: A
authors.lastname: Delprat
authors.affiliation: Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), CP 15053, Porto Alegre, Rio Grande do Sul 91501-970, Brazil. vera.valente@pq.cnpq.br.
authors.forename: Vera L S
authors.initials: VL
authors.lastname: Valente
authors.forename: Alfredo
authors.initials: A
authors.lastname: Ruiz
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D004251:DNA Transposable Elements; D004330:Drosophila / Q000145:classification / Q000235:genetics*; D018628:Gene Dosage; D023061:Gene Order; D014644:Genetic Variation; D016678:Genome; D023281:Genomics; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs; D010802:Phylogeny; D056510:Position-Specific Scoring Matrices; D011995:Recombination, Genetic; D016415:Sequence Alignment; D020079:Terminal Repeat Sequences
chemical_list: D004251:DNA Transposable Elements