Supplementary Tables

We performed an RNA-seq based comparison of gene expression levels in the antennae of honey bee drones and time-trained foragers (workers) collected at different times of the day and different activity states. Interestingly, olfaction-related genes (i.e. odorant receptor (Ors), odorant binding proteins (Obps), carboxyl esterases (CEst) etc.) showed stable gene expression differences between drone and worker antennae. Drone antennae showed higher expression of 24 Ors, of which 21 belong to the clade X which comprises the receptor for the major queen pheromone compound 9-ODA. This high number of drone-biased Ors suggests that more Ors than previously expected play a role in sex-pheromone communication. In addition, we found higher expression levels for many non-olfaction related genes including nitric oxide synthase (NOS), and the potassium channel Shaw. In contrast, workers showed higher expression of 67 Ors, which belong to different Or clades that are involved in pheromone communication as well as the perception of cuticular hydrocarbons and floral scents. Further, drone antennae showed higher expression of genes involved in energy metabolism, whereas worker antennae showed higher expression of genes involved in neuronal communication consistent with earlier reports on peripheral olfactory plasticity. Finally, drones that perform mating flight in the afternoon (innate) and foragers that are trained to forage in the afternoon (adapted) showed similar daily changes in the expression of two major clock genes, period and cryptochrome2. Most of the other genes showing changes with time or onset of daily flight activity were specific to drones and foragers.