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. 2019 Mar 13:10:10.
doi: 10.1186/s13100-019-0152-9. eCollection 2019.

A unique cluster of roo insertions in the promoter region of a stress response gene in Drosophila melanogaster

Miriam Merenciano  1 , Camillo Iacometti  1   2 , Josefa González  1
Affiliations

A unique cluster of roo insertions in the promoter region of a stress response gene in Drosophila melanogaster

Miriam Merenciano et al. Mob DNA. .

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.

Keywords: Fecundity; Natural population; Recurrent insertion; Target site duplication; Transposable element; Viability.

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Conflict of interest statement

Not applicable.Not applicable.The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Twenty roo solo-LTR insertions are located in the promoter region of CG18446 gene in different natural strains. Schematic representation of the CG18446 promoter region where the 20 roo solo-LTRs are inserted. The black line represents the CG18446 promoter region. Note that although only one insertion was found in any given strain, we have represented them together for simplicity. The white box represents CG18446 5’UTR. Regions depicted with dotted lines are not drawn to scale. Insertions present in 5′-3′ orientation are shown above the black line and insertions present in 3′-5′ orientation are shown below the black line
Fig. 2
Fig. 2
The majority of the insertions in the CG18446 promoter region are present at very low allelic frequencies. Allelic frequencies of the 20 roo solo-LTRs insertions in populations from Europe, North America, and Africa. The number of strains analyzed in each population is given in parenthesis and the pie chart size is proportional to this number. Blue, yellow, and red lines represent populations with cold, temperate, and arid climates, respectively
Fig. 3
Fig. 3
The 20 roo solo-LTR insertions found in CG18446 promoter region are the result of several bursts of transposition. Phylogenetic tree including the 20 roo solo-LTR insertions found in CG18446 promoter region and 115 other roo insertions annotated in the reference genome. roo solo-LTRs found in this work are highlighted in red. When several TEs with the same exact sequence were identified, we removed all of them but one. The TEs included in the tree are marked with *. The TEs that were eliminated are: (*) FBti0019017, FBti0019394, FBti0019438, FBti0020009, FBti0020080, roo+ 7, roo− 90, roo− 19, roo− 28, roo− 64, roo+ 37, and roo+7inv, (**) roo− 291, (***) roo− 44, and (****) FBti0019608
Fig. 4
Fig. 4
Egg-to-adult viability and fecundity are not likely to reduce the probability of finding flies with more than one roo element in the CG18446 promoter region. a. Percentage of emerged flies from the four crosses tested. b. Average number of eggs laid per day during the first 48 h for each of the four crosses analyzed. c. Average number of eggs laid per day during 18 days for each of the four crosses analyzed
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