Molecular profiling of the gilthead sea bream (Sparus aurata L.) response to chronic exposure to the myxosporean parasite Enteromyxum leei

► The response of gilthead sea bream after challenge with Enteromyxum leei was investigated by cDNA microarray. ► In infected fish, 371 and 373 genes were differentially regulated in intestine and head kidney. ► In non-infected fish, 175 and 501 genes were differentially regulated in intestine and head kidney. ► A marked gene down-regulation was evident in infected fish, mainly in immune response genes. ► In the head kidney of non-infected fish a marked depression of genes involved in the APR was evident. ► In the intestine of non-infected fish, IFN-stimulated and MHC class II genes were up-regulated.