show Abstracthide AbstractInfections induce a large suite of gene expression change in organisms responding to immune challenges. Despite much evidence that the sequence of proteins in the immune system can evolve very rapidly, the evolution of gene expression is comparatively poorly understood. Under constant environmental pressure, the gene regulation during immune response evolves rapidly and diverge between related species. The divergence between gene expression results from the accumulation of changes in both cis- and trans-regulatory elements between species. By sequencing the tissue-specific transcriptomes of D. simulans, D. sechellia and their F1 hybrids, we reveal the regulatory divergence between these two species in their immune response to parasitoid wasps, the contributions from cis-regulatory changes and trans-regulatory changes. The study adds to the better understanding of immune regulation evolution in Drosophila species.