Gene expression of the marine copepod Calanus finmarchicus: Responses to small-scale environmental variation in the Gulf of Maine (NW Atlantic Ocean)

• Field collected C. finmarchicus were examined for differential gene expression.
• Deep females/CVs showed activation in protein synthesis and early development.
• Deep CVs showed less evidence of activation than deep females.
• Multiple emergent processes from diapause were pronounced in deep females and CVs.
• Surface females showed activation in protein turnover, homeostasis and immunity.

The pelagic copepod Calanus finmarchicus is one of the most important zooplankton species in the North Atlantic Ocean. Despite its ecological importance and pivotal role in the food chain, the molecular mechanisms underlying this species' complex life history (ontogenetic development, reproduction, molting, and diapause) and physiology (digestion, neural processes, and membrane physiology) have remained poorly characterized. This study examined differential expression of nearly 1000 genes, selected based on physiological function and hypothesized ecological importance, for C. finmarchicus collected in the Gulf of Maine (NW Atlantic Ocean) using an oligonucleotide DNA microarray. Replicate analyses compared adult females and final-stage juveniles (Copepodite-V stages) collected from surface (0–30 m) and deep (130–170 m) layers during April, 2008. Differentially expressed genes were identified by statistical analysis of multiple replicates, including a control for False Discovery Rate (FDR). Functional relationships of selected genes and/or proteins were evaluated using the Gene Ontology Enrichment Analysis Software Toolkit (GOEAST). Genes involved in protein synthesis, cell-cycle and tissue buildup were shown to be up-regulated (i.e., significantly higher expression levels) in deep females and juveniles; genes related to protein turnover, cellular homeostasis, activity, and stress/immunity responses were up-regulated in surface females. Additional functional analyses using KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis indicated up-regulation of genes encoding enzymes related to energy metabolism and osmoregulation in surface females, and citric acid cycle and anaerobic metabolism in deep females and juveniles. Overall, an active physiological state was pronounced in surface females, and a number of processes related with emergence from diapause were pronounced in deep females and juveniles.