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IntroductionCalanus finmarchicus, a highly abundant copepod that is an important primary consumer in North Atlantic ecosystems, has a flexible life history in which copepods in the last juvenile developmental stage (fifth copepodid, C5) may either delay maturation and enter diapause or molt directly into adults. The factors that regulate this developmental plasticity are poorly understood, and few tools have been developed to assess the physiological condition of individual copepods.ResultsWe sampled a cultured population of C. finmarchicus copepods daily throughout the C5 stage and assessed molt stage progression, gonad development and lipid storage. We used high-throughput sequencing to identify genes that were differentially expressed during progression through the molt stage and then used qPCR to profile daily expression of individual genes. Based on expression profiles of twelve genes, samples were statistically clustered into three groups: (1) an early period occurring prior to separation of the cuticle from the epidermis (apolysis) when expression of genes associated with lipid synthesis and transport (FABP and ELOV) and two nuclear receptors (ERR and HR78) was highest, (2) a middle period of rapid change in both gene expression and physiological condition, including local minima and maxima in several nuclear receptors (FTZ-F1, HR38b, and EcR), and (3) a late period when gonads were differentiated and expression of genes associated with molting (Torso-like, HR38a) peaked. The ratio of Torso-like to HR38b strongly differentiated the early and late groups.ConclusionsThis study provides the first dynamic profiles of gene expression anchored with morphological markers of lipid accumulation, development and gonad maturation throughout a copepod molt cycle. Transcriptomic profiling revealed significant changes over the molt cycle in genes with presumed roles in lipid synthesis, molt regulation and gonad development, suggestive of a coupling of these processes in Calanus finmarchicus. Finally, we identified gene expression profiles that strongly differentiate between early and late development within the C5 copepodid stage. We anticipate that these findings and continued development of robust gene expression biomarkers that distinguish between diapause preparation and continuous development will ultimately enable novel studies of the intrinsic and extrinsic factors that govern diapause initiation in Calanus finmarchicus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12983-014-0091-8) contains supplementary material, which is available to authorized users.

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29The copepod Calanus finmarchicus is a key component of northern Atlantic food webs, linking 30 energy-transfer from phytoplankton to higher trophic levels. We examined the effect of different 53The carbonate concentration in seawater is declining due to increased pCO2 4 , and meta-analyses 54 indicate that calcifying organisms may be negatively affected by this phenomenon 5 . Marine 55 metazoans rely on a positive CO2 gradient from their body fluids to excrete metabolic CO2 by 56 diffusion. Elevated seawater pCO2 can therefore lead to hypercapnia and acidosis 6 which in turn 57 may result in a reallocation of resources away from growth and reproduction, due to mobilization 58 of energy demanding acid-base regulatory processes to counteract internal pH reduction. 59Accordingly, ocean acidification has been shown to negatively affect processes such as 60 reproduction 7 , development 8 and behavior 9 in non-calcifying organisms also. 61Copepods of the genus Calanus constitute a large part of the zooplankton biomass in the North 62 Atlantic 10, 11 . During the development from eggs, these copepods develop through six nauplii 63 stages (N1-N6), of which the two first (N1-2) are non-feeding, and five copepodite stages (C1-64 C5), before reaching maturity as either male or female 12 . These cold water species concentrate 65 and store energy through synthesis and accumulation of lipids and therefore represent an 66 important energy link between phytoplankton and higher trophic level predators such as fish 13, 14 67

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