The mode of expression divergence in fat body is infection-specific.

Transcription is controlled by interactions of -acting DNA elements with diffusible -acting factors. Changes in or factors can drive expression divergence within and between species, and their relative prevalence can reveal the evolutionary history and pressures that drive expression variation. Previous work delineating the mode of expression divergence in animals has largely used whole-body expression measurements in one condition. Because -acting elements often drive expression in a subset of cell types or conditions, these measurements may not capture the complete contribution of -acting changes. Here, we quantify the mode of expression divergence in the fat body, the primary immune organ, in several conditions, using two geographically distinct lines of and their F1 hybrids. We measured expression in the absence of infection and in infections with Gram-negative or Gram-positive bacteria, which trigger the two primary signaling pathways in the innate immune response. The mode of expression divergence strongly depends on the condition, with -acting effects dominating in response to Gram-negative infection and -acting effects dominating in Gram-positive and preinfection conditions. Expression divergence in several receptor proteins may underlie the infection-specific effects. Before infection, when the fat body has a metabolic role, there are many compensatory effects, changes in and that counteract each other to maintain expression levels. This work shows that within a single tissue, the mode of expression divergence varies between conditions and suggests that these differences reflect the diverse evolutionary histories of host-pathogen interactions.