Interactions between chromatin accessibility and transposable elements in native and invasive isofemale lines of Drosophila suzukii

Transposable elements (TEs) have been predicted to facilitate the spread of invasive species into new environments. If invasive populations do carry novel TE insertions, they are likely to also display new patterns of epigenetic regulation, as the host genome attempts to silence or control the expression of these TEs. The spotted wing drosophila, Drosophila suzukii, is native to Asia but was recorded in Europe and continental North America in 2008, and since then has spread through both continents causing widespread economic damage to fruit production. We investigated the interactions between TE insertions and chromatin accessibility in six isofemale D.suzukii lines. Two lines were from the native range in Japan (Tokyo and Sapporo), while the other four lines were collected from the newly invaded range: two from France (Montpellier and Paris) and two from the USA (Watsonville and Dayton).In this experiment, we carried out whole genome resequencing for isofemale lines from Tokyo (T20), Paris (L6) and Dayton (Sok1). We combined this with previously published DNA sequence data for lines from Sapporo (S29), Montpellier (MT47), and Watsonville (W120) (Marin et al 2021, GBE, PRJNA610892) to characterize TE insertions in the 6 lines. We then collected data on chromatin accessibility from all six lines using ATAC-seq. All ATAC-seq samples consisted of pooled ovary samples (21-22 individuals), while DNA for whole genome resequencing was collected from pooled samples of the bodies of the same flies used in ATAC-sequencing. All ATAC-seq samples were triplicated.