Some key insect recognition, signaling and response genes are missing in the pea aphid. Previously sequenced genomes of other insects (flies, mosquitoes, bees, beetles) have indicated that immune signaling pathways, seen here, are conserved across insects. In aphids, missing IMD pathway members (dashed lines) include those involved in recognition (PGRPs) and signaling (IMD, dFADD, Dredd, REL). Genes encoding antimicrobial peptides common in other insects, including defensins and cecropins, are also missing. In contrast, we found putative homologs for most genes central to the Toll, JNK and JAK/STAT signaling pathways.