Background: The study of stress response in natural populations is crucial for understanding species local adaptation and evolution. In Drosophila, significant genetic diversity across populations from different geographical origins has been observed, emphasizing the influence of local environments.

Results: In this study, we explored the impact of starvation and cold stress on the phenotypic and transcriptomic response of two natural populations of D. melanogaster and D. simulans from temperate and tropical regions. Additionally, we investigated the behavior and influence of transposable elements (TEs) in these types of stress, combining RNA-seq and ChIP-seq experiments, with high-quality long-read genome assemblies of all the strains. Our findings in D. melanogaster revealed that the transcriptomic response to stress is similar across geographical origins, whereas in D. simulans there is more variability. Notably, neither starvation nor cold induced a general activation of TEs in D. melanogaster or D. simulans, at least in the tissue and strains analysed in this study. Finally, we found three polymorphic TEs producing TE-chimeric transcripts associated with changes in nearby gene expression levels after stress.

Conclusions: Overall, this study highlights the complexity of stress-TE interactions and their potential impact on adaptation. Understanding these dynamics contributes to the broader knowledge of how genetic and environmental factors interact to modulate gene expression, shaping an organism's ability to adapt to varying conditions.