Abstract
Although the retrotransposon copia has been studied in the melanogaster group of Drosophila species, very little is known about copia dynamism and evolution in other groups. We analyzed the occurrence and heterogeneity of the copia 5'LTR-ULR partial sequence and their phylogenetic relationships in 24 species of the repleta group of Drosophila. PCR showed that copia occurs in 18 out of the 24 species evaluated. Sequencing was possible in only eight species. The sequences showed a low nucleotide diversity, which suggests selective constraints maintaining this regulatory region over evolutionary time. On the contrary, the low nucleotide divergence and the phylogenetic relationships between the D. willistoni/Zaprionus tuberculatus/melanogaster species subgroup suggest horizontal transfer. Sixteen transcription factor binding sites were identified in the LTR-ULR repleta and melanogaster consensus sequences. However, these motifs are not homologous, neither according to their position in the LTR-ULR sequences, nor according to their sequences. Taken together, the low motif homologies, the phylogenetic relationship and the great nucleotide divergence between the melanogaster and repleta copia sequences reinforce the hypothesis that there are two copia families.
Highlights
Ty1-copia is present as a highly heterogeneous group of retrotransposons within all higher eukaryotes [10, 21]
The retrotransposon copia is harbored by the genome of these 52 species, nucleotide sequences have been described only for eight species of the melanogaster group, two species of the repleta group, D. willistoni and Zaprionus tuberculatus
Strong amplification was observed in species belonging to the buzzatii (D. koepferae, D. buzzatii, D. serido, D. gouveai, D. antonietae and D. seriema), mulleri (D. aldrichi, D. mulleri and D. wheeleri) and longicornis (D. pachuca, D. propachuca, D. hexastigma and D. spenceri) clusters
Summary
Ty1-copia is present as a highly heterogeneous group of retrotransposons within all higher eukaryotes [10, 21]. The Drosophila retrotransposon copia, which is structurally similar to retroviral proviruses, is 5.4 kb in length and flanked by 276-bp direct long terminal repeats (LTR). Twentytwo species out of this total belong to the melanogaster group, seven to the willistoni group, seven to the obscura group, six to the saltans group, two to the immigrans group, one to the mesophragmatica group, and one to the pinicola group. The retrotransposon copia is harbored by the genome of these 52 species, nucleotide sequences have been described only for eight species of the melanogaster group, two species of the repleta group, D. willistoni and Zaprionus tuberculatus. Drosophila copia phylogeny studies are difficult to carry out, because of the low number of copia sequences in the group, and because these sequences are partial, most of them concerning 5’ long terminal repeats (LTR) and untranslated leader regions (ULR)
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