To accomplish DROSADAPTATION objectives, we have used an integrative approach that combines -omics methodologies, such as long-read DNA sequencing, transcriptomics, and chromatin analysis (ATAC-seq, ChIP-seq, Hi-C), with in depth individual characterization of adaptive mutations, using RT-qPCR, allele-specific expression, in vivo reporter gene assays, and CRISPR/Cas9 genome editing. We have generated 32 new reference Drosophila melanogaster genomes that have allowed us to identify 58% more transposable element insertions than previously described. We have identified hundreds of transposable element insertions that affect the expression of their nearby genes. We have showed that environmental variables related with wind are relevant for adaptation in Drosophila. Regarding the molecular mechanisms of adaptive mutations, we have showed that transposable elements contribute to the regulation of stress-response genes by adding transcription factor binding sites, and that the effect that transposable elements have on gene expression through epigenetic changes is body part specific. Finally, stress response, development, behaviour, morphogenesis and pigmentation are the phenotypic traits most often shaped by transposable elements, and their role in oxidative stress and insecticide resistance appears to be more prevalent than in other stress responses. The DROSADAPTATION results have been shared with the scientific community through research, review, protocol, and commentary articles and through conference, workshop, and seminar presentations across the world. All the datasets and scripts generated during the project are publicly available.
