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

BMC Genomics

Alfredo Ruiz¹  Vera L S Valente²  Alejandra Delprat¹  Victor Hugo Valiati³  Juliana W Gonçalves² 

[1] Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain;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;Programa de Pós-Graduação em Biologia: Diversidade e Manejo de Vida Silvestre, Universidade do Vale do Rio dos Sinos (UNISINOS), CP 275, São Leopoldo, Rio Grande do Sul 93022-000, Brazil

关键词: Target site duplications;    P superfamily;    Terminal inverted repeats;    D. willistoni;    Transposable element;   

Others  :  1139581
DOI  :  10.1186/1471-2164-15-792

 received in 2014-04-26, accepted in 2014-09-09,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Gonçalves et al.; licensee BioMed Central Ltd.

【 图 表 】

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