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The lipid-rich copepodNeocalanus flemingeriis abundant throughout the subarctic Pacific, with a biogeographic range that includes the open ocean, marginal seas and fjord systems. Two distinct genetic variants have been reported based on differences in size: the ‘small form’, with a 1 yr life cycle, is found throughout the region, and the ‘large form’, with a 2 yr life cycle, is found in the western Pacific, where it is most abundant in the Sea of Okhotsk. Using a molecular approach, this study examined the genetic composition ofN. flemingeripopulations in the Gulf of Alaska from multiple stations over a 9 yr period. This is the first report of the occurrence of the large form in the eastern Pacific, where it exhibits a significant presence in fjord systems. However, in this region, both the small- and large-formN. flemingerihave annual life cycles. Collections from nearshore to offshore locations over multiple years indicated both interannual and spatial differences in the relative proportion of the 2 variants. Our results show that the forms inhabit overlapping yet distinct habitats, potentially due to adaptation to contrasting environmental conditions. 

Abstract This study presents eight new high-qualityde novotranscriptomes from six co-occurring species of calanoid copepods, the first published forNeocalanus plumchrus,N. cristatus, Eucalanus bungiiandMetridia pacificaand additional ones forN. flemingeriandCalanus marshallae. They are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. ‘Omics data for this diverse and numerous taxonomic group are sparse and difficult to obtain. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Quality filtered reads were assembled with Trinity software and validated using multiple criteria. The study’s primary purpose is to provide a resource for gene expression studies. The integrated database can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes. An example of an additional use is provided for discovering novel and evolutionarily-significant proteins within the Calanoida. A workflow was designed to find and characterize unannotated transcripts with homologies acrossde novoassemblies that have also been shown to be eco-responsive. 

Abstract Molecular tools have changed the understanding of zooplankton biodiversity, speciation, adaptation, population genetics and global patterns of connectivity. However, the molecular resources needed to capitalize on these advances continue to be limited in comparison with those available for other eukaryotic plankton. This deficiency could be addressed through an Ocean Zooplankton Open ‘Omics Project (Ocean ZOOP) that would generate de novo assembled transcriptomes for hundreds of metazoan plankton species. A collection of comparable reference transcriptomes would generate a new framework for ecological and physiological studies. Defining species niches, identifying optimal habitats, assessing adaptive capacity and predicting changes in phenology are just a few examples of how such a resource could transform studies on zooplankton ecology. 

Background: Diapause is a seasonal dormancy that allows organisms to survive unfavorable conditions and optimizes the timing of reproduction and growth. Emergence from diapause reverses the state of arrested development and metabolic suppression returning the organism to an active state. The physiological mechanisms that regulate the transition from diapause to post-diapause are still unknown. In this study, this transition has been characterized for the sub-arctic calanoid copepod Neocalanus flemingeri, a key crustacean zooplankter that supports the highly productive North Pacific fisheries. Transcriptional profiling of females, determined over a two-week time series starting with diapausing females collected from > 400m depth, characterized the molecular mechanisms that regulate the post-diapause trajectory. Results: A complex set of transitions in relative gene expression defined the transcriptomic changes from diapause to post-diapause. Despite low temperatures (5–6 °C), the switch from a “diapause” to a “post-diapause” transcriptional profile occurred within 12 h of the termination stimulus. Transcriptional changes signaling the end of diapause were activated within one-hour post collection and included the up-regulation of genes involved in the 20E cascade pathway, the TCA cycle and RNA metabolism in combination with the down-regulation of genes associated with chromatin silencing. By 12 h, females exhibited a post-diapause phenotype characterized by the up-regulation of genes involved in cell division, cell differentiation and multiple developmental processes. By seven days post collection, the reproductive program was fully activated as indicated by up-regulation of genes involved in oogenesis and energy metabolism, processes that were enriched among the differentially expressed genes. Conclusions: The analysis revealed a finely structured, precisely orchestrated sequence of transcriptional changes that led to rapid changes in the activation of biological processes paving the way to the successful completion of the reproductive program. Our findings lead to new hypotheses related to potentially universal mechanisms that terminate diapause before an organism can resume its developmental program. 

Abstract Organisms inhabiting high-latitude environments have evolved adaptations, such as diapause to time reproduction and growth to optimize their survival. However, the physiological regulation of the timing of complex life histories is poorly understood, particularly for marine copepods, that diapause at depth. A member of the pelagic community of the sub-Arctic Pacific Ocean,Neocalanus flemingerienters diapause in June. Egg production occurs in winter/spring. In order to characterize the transition from diapause to egg release, females were collected in late September from 400–700 m depth, incubated in the dark at 4–5 °C and sampled for RNASeq at weekly intervals. The diapause phenotype showed down-regulation of protein turnover and up-regulation of stress genes. Activation of the reproductive program was marked by the up-regulation of genes involved in germline development. Thereafter, progress through phases of oocyte development could be linked to changes in gene expression. At 5 weeks, females showed up-regulation of spermatogenesis, indicating that stored sperm had been in a quiescent stage and completed their maturation inside the female. Gene expression profiles provide a framework to stage field-collected females. The 7-week progression from diapause to late oogenesis suggests that females typically spawning in January initiated the reproductive program in November. 

Abstract How individual organisms adapt to nonoptimal conditions through physiological acclimatization is central to predicting the consequences of unusual abiotic and biotic conditions such as those produced by marine heat waves. The Northeast Pacific, including the Gulf of Alaska, experienced an extreme warming event (2014–2016, “The Blob”) that affected all trophic levels and led to large‐scale changes in the community. The marine copepodNeocalanus flemingeriis a key member of the subarctic Pacific pelagic ecosystem. During the spring phytoplankton bloom this copepod builds substantial lipid stores as it prepares for its nonfeeding adult phase. A 3‐year comparison of gene expression profiles of copepods collected in Prince William Sound in the Gulf of Alaska between 2015 and 2017 included two high‐temperature years (2015 and 2016) and one year with very low phytoplankton abundances (2016). The largest differences in gene expression were between high and low chlorophyll years, and not between warm and cool years. The observed gene expression patterns were indicative of physiological acclimatization. The predominant signal in 2016 was the down‐regulation of genes involved in glycolysis and its incoming pathways, consistent with the modulation of metabolic rates in response to prolonged low food conditions. Despite the down‐regulation of genes involved in metabolism, there was no evidence of suppression of protein synthesis based on gene expression or behavioural activity. Genes involved in muscle function were up‐regulated, and the copepods were actively swimming and responsive to stimuli at collection. However, genes involved in fatty acid metabolism were down‐regulated in 2016, suggesting reduced lipid accumulation.