Abstract
Transposable elements (TEs) are not randomly distributed in the genome. A genome-wide analysis of the D. melanogaster genome found that differences in TE density across 50 kb genomic regions was due both to transposition and duplication. At smaller genomic scales, promoter regions of hsp genes and the promoter region of CG18446 have been shown to accumulate TE insertions. In this work, we have further analyzed the promoter region of CG18446. We screened 218 strains collected in 15 natural populations, and we found that the CG18446 promoter region contains 20 independent roo insertions. Based on phylogenetic analysis, we suggest that the presence of multiple roo insertions in this region is likely to be the result of several bursts of transposition. Moreover, we found that the roo insertional cluster in the CG18446 promoter region is unique: no other promoter region in the genome contains a similar number of roo insertions. We found that, similar to hsp gene promoters, chromatin accessibility could be one of the factors explaining the recurrent insertions of roo elements in CG18446 promoter region.
Highlights
Recurrent insertion of transposable elements in specific genomic regions has been described in the Drosophila melanogaster reference genome
Twenty roo solo Long Terminal Repeat (LTR) insertions are present in the CG18446 promoter region in natural populations To check whether there were more roo insertions in the CG18446 promoter region, we performed a PCR screening in 218 strains from 15 natural populations: 13 European, one North American [16], and one African population collected in the ancestral range of the species (Zambia) (Additional file 1) [17]. 143 strains gave a band consistent with the presence of an insertion, in homozygous or heterozygous state, and 75 strains gave a band consistent with the absence of an insertion (Table 1 and Additional file 2A)
Besides the nine roo solo-LTRs found in Merenciano et al (2016) [10], we have discovered 11 new roo insertions in the CG18446 promoter region
Summary
Recurrent insertion of transposable elements in specific genomic regions has been described in the Drosophila melanogaster reference genome. The analysis of 50 kb genomic windows identified 23 regions with a high density of TE insertions, most of them located in pericentromeric regions or on chromosome 4 [1]. Besides TEs annotated in the reference genome, non-reference TE insertions can be analyzed. Based on these population analyses, some genes have been reported to accumulate many TE insertions, such as the 106.5 kb klarsicht, and the 24 kb derailed-2 that were analyzed in 146 strains of the Drosophila Synthetic Population Resource [5, 6]. While the majority of strains analyzed so far contain a roo insertion (26 out of 39), none of them contains more than one insertion [10]
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