RNA-seq and qPCR analyses of food conditions and their influence on gene expression in the Manila clam (Ruditapes philippinarum)

An understanding of the food conditions to which clams are exposed and the associated differences in physiologyical conditions is important for identifying the mechanisms that affect resource fluctuations. We performed RNA-seq and quantitative PCR with juveniles reared under two different feeding conditions: non-feeding (N) and feeding (F). RNA-seq with 18 libraries contained a total of 167733 unigenes of which 6093 were determined to be differentially expressed genes (DEGs) in the comparison of N and F on days 3, 5 and 20 during the rearing period. From the pathway analysis of DEGs, ECM-receptor interaction and Focal adhesion pathways were well enriched, and they are characteristic pathways that respond to changes in food conditions. From changes in the defensin, ependymin-related protein-1, heat shock protein 22 and thioredoxin expression patterns, we could categorize the physiological conditions of juveniles in starvation into short-term starvation (1–3 days), during which genes expression in the non-feeding (N) relative to the feeding (F) declined rapidly; medium-term starvation (3–15 days), during which genes expression then increased rapidly; and long-term starvation (15 days and longer), during which genes expression declined again.