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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.