  The innate immune system in insects consists of a conserved core signaling
network and rapidly diversifying effector and recognition components, often
containing a high proportion of taxonomically-restricted genes. In the absence
of functional annotation, genes encoding immune system proteins can thus be
difficult to identify, as homology-based approaches generally cannot detect
lineage-specific genes. Here, we use RNA-seq to compare the uninfected and
infection-induced transcriptome in the parasitoid wasp Nasonia vitripennis to
identify genes regulated by infection. We identify 183 genes significantly
up-regulated by infection and 61 genes significantly down-regulated by
infection. We also produce a new homology-based immune catalog in N.
vitripennis, and show that most infection-induced genes are not assigned an
immune function from homology alone, suggesting the potential for substantial
novel immune components in less-well-studied systems. Finally, we show that a
high proportion of these novel induced genes are taxonomically-restricted,
highlighting the rapid evolution of immune gene content. The combination of
functional annotation using RNA-seq and homology-based annotation provides a
robust method to characterize the innate immune response across a wide variety
of insects, and reveals significant novel features of the Nasonia immune
response.
