Digital gene expression analysis in the gills of Ruditapes philippinarum exposed to short- and long-term exposures of ammonia nitrogen.

•Long-term exposure of ammonia caused more DEGs.•Short-term exposure disturbed 4 pathways in cancer formation and protein folding.•Long-term exposure affected 7 pathways in immunity, metabolism and cancer formation.•Clam immunity was suggested to be weakened heavily by ammonia exposure.