A genome wide model for estimating DNA transposable element excision rates in Drosophila virilis
Authors: Stefan Cerbin 1; Danny Miller 2,3; Justin Blumenstiel 1
Affiliations: 1) Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS; 2) Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; 3) Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children’s Hospital, Seattle, WA
Keywords: a. genome evolution; n. other (repetitive sequences)
DNA transposons are sequences that are capable of moving in the genome resulting in profligate DNA damage and genome instability. Estimating transposon mobilization rates and the damage they cause is important for understanding genome evolution and genome stability. Drosophila virilis has several strains with varying copy number of DNA transposons and differences in germline piRNAs profiles. Transposons become activated when females lacking the requisite piRNAs to unique transposons inherited paternally, resulting in hybrid dysgenesis. With these strains we can study global transposon mobilization to determine the rates of excision and the overall change in copy number. In this study, we use pooled long-read DNA sequencing to identify elements mobilized in dysgenic crosses. These reads will be analyzed to estimate an excision rate using a likelihood model for estimating global excision rates for DNA transposons. This model will incorporate specific DNA transposon insertions, family, and piRNA profiles as parameters. We predict that differences in piRNA profiles, DNA transposon family identity, location, and internal deletion status will jointly determine the excision rate.