The Transcriptome of the Eastern Oyster Crassostrae virginica in Response to Bacterial Challenge

The eastern oyster Crassostrea virginica is an ecologically and economically important estuarine organism.  Roseovarius Oyster Disease (ROD), caused by the bacterium Roseovarius crassostreae, went unreported before 1988 and presently affects oysters from the Long Island Sound north to Maine. The identification of potential genes and pathways of the effective host defense response in the eastern oyster to R. crassostreae is important not only to provide a basis for enhanced breeding techniques, but also contributes to the understanding of innate immunity in a broader, evolutionary sense.  The goal of this study is to uncover genes and general processes potentially involved in disease resistance to ROD in the eastern oyster and identify diversified gene families involved in immunity. ROD-resistant and ROD-susceptible families of oysters were exposed to R. crassostreae and cDNA from samples collected at 1, 5, 15, and 30 days after challenge was sequenced using Illumina GAIIx. Patterns of differential gene expression were analyzed at the gene and gene family levels. We used sequence similarity clustering to define gene families and further explored the size, composition, and phylogeny of several groups of diversified proteins.  The eastern oyster host defense response to R. crassostreae involved serine proteases, serine protease inhibitors, c-type lectins, C1q domain-containing proteins, fibrinogen domain-containing proteins (FREPs), interferon-induced protein 44 family proteins, scavenger receptors with class B SRCR domains, and GTPase of the immunity associated protein family (GIMAP) proteins.  Further, similarity clustering of proteins and translated transcripts from diverse invertebrates suggested that GIMAP proteins are expanded in molluscs and IFI44 proteins are expanded in bivalves.  We have also identified several diversified gene families of unknown identity that appear to be involved in oyster immunity against R. crassostreae. This research provides candidate genetic markers to aid in the breeding of disease-resistant strains of oysters.