The Euphausia superba transcriptome database, SuperbaSE: An online, open resource for researchers

A thorough annotation of the krill transcriptome offers new insights for the study of physiological processes

The krill species Euphausia superba plays a critical role in the food chain of the Antarctic ecosystem. Significant changes in climate conditions observed in the Antarctic Peninsula region in the last decades have already altered the distribution of krill and its reproductive dynamics. A deeper understanding of the adaptation capabilities of this species is urgently needed. The availability of a large body of RNA-seq assays allowed us to extend the current knowledge of the krill transcriptome. Our study covered the entire developmental process providing information of central relevance for ecological studies. Here we identified a series of genes involved in different steps of the krill moulting cycle, in the reproductive process and in sexual maturation in accordance with what was already described in previous works. Furthermore, the new transcriptome highlighted the presence of differentially expressed genes previously unknown, playing important roles in cuticle development as well as in energy storage during the krill life cycle. The discovery of new opsin sequences, specifically rhabdomeric opsins, one onychopsin, and one non-visual arthropsin, expands our knowledge of the krill opsin repertoire. We have collected all these results into the KrillDB2 database, a resource combining the latest annotation of the krill transcriptome with a series of analyses targeting genes relevant to krill physiology. KrillDB2 provides in a single resource a comprehensive catalog of krill genes; an atlas of their expression profiles over all RNA-seq datasets publicly available; a study of differential expression across multiple conditions. Finally, it provides initial indications about the expression of microRNA precursors, whose contribution to krill physiology has never been reported before.

Transcriptome-proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes

The Antarctic krill (Euphausia superba Dana) is a keystone species in the Southern Ocean that uses an arsenal of hydrolases for biomacromolecule decomposition to effectively digest its omnivorous diet. The present study builds on a hybrid-assembled transcriptome (13,671 ORFs) combined with comprehensive proteome profiling. The analysis of individual krill compartments allowed detection of significantly more different proteins compared to that of the entire animal (1,464 vs. 294 proteins). The nearby krill sampling stations in the Bransfield Strait (Antarctic Peninsula) yielded rather uniform proteome datasets. Proteins related to energy production and lipid degradation were particularly abundant in the abdomen, agreeing with the high energy demand of muscle tissue. A total of 378 different biomacromolecule hydrolysing enzymes were detected, including 250 proteases, 99 CAZymes, 14 nucleases and 15 lipases. The large repertoire in proteases is in accord with the protein-rich diet affiliated with E. superba's omnivorous lifestyle and complex biology. The richness in chitin-degrading enzymes allows not only digestion of zooplankton diet, but also the utilization of the discharged exoskeleton after moulting. This article is protected by copyright. All rights reserved.

In silico Identification of a Molecular Circadian System With Novel Features in the Crustacean Model Organism Parhyale hawaiensis

The amphipod Parhyale hawaiensis is a model organism of growing importance in the fields of evolutionary development and regeneration. A small, hardy marine crustacean that breeds year-round with a short generation time, it has simple lab culture requirements and an extensive molecular toolkit including the ability to generate targeted genetic mutant lines. Here we identify canonical core and regulatory clock genes using genomic and transcriptomic resources as a first step in establishing this species as a model in the field of chronobiology. The molecular clock of P. hawaiensis lacks orthologs of the canonical circadian genes cryptochrome 1 and timeless, in common with the mammalian system but in contrast to many arthropods including Drosophila melanogaster. Furthermore the predicted CLOCK peptide is atypical and CRY2 shows an extended 5′ region of unknown function. These results appear to be shared by two other amphipod species.

Sex identification from distinctive gene expression patterns in Antarctic krill (Euphausia superba)

Antarctic krill (Euphausia superba) is a highly abundant keystone species of the Southern Ocean ecosystem, directly connecting primary producers to high-trophic level predators. Sex ratios of krill vary remarkably between swarms and this phenomenon is poorly understood, as identification of krill sex relies on external morphological differences that appear late during development. Sex determination mechanisms in krill are unknown, but could include genetic, environmental or parasitic mechanisms. Similarly, virtually nothing is known about molecular sex differentiation. The krill genome has to date not been sequenced, and due to its enormous size and large amount of repetitive elements, it is currently not feasible to develop sex-specific DNA markers. To produce a reliable molecular marker for sex in krill and to investigate molecular sex differentiation we therefore focused on identifying sex-specific transcriptomic differences. Through transcriptomic analysis, we found large gene expression differences between testes and ovaries and identified three genes exclusively expressed in female whole krill from early juvenile stages onwards. The sex-specific expression of these three genes persisted through sexual regression, although our regressed samples originated from a krill aquarium and may differ from wild-regressed krill. Two slightly male-biased genes did not display sufficient expression differences to clearly differentiate sexes. Based on the expression of the three female-specific genes we developed a molecular test that for the first time allows the unambiguous sex determination of krill samples lacking external sex-specific features from juvenile stages onwards, including the sexually regressed krill we examined.

De novo sequencing of the Antarctic krill (Euphausia superba) transcriptome to identify functional genes and molecular markers

To provide massive genetic resources for the Antarctic krill (Euphausia superba), we sequenced and analysed the transcriptome by using high-throughput Illumina paired-end sequencing technology. A total of 77.1 million clean reads representing ~11.0Gb data were generated. The average length of these reads was 142 bp. De novo assembly yielded 125,211 transcripts with a N50 of 690 bp. Further analysis produced 106,250 unigenes, of which 31,683 were annotated based on protein homology searches against protein databases. Gene ontology analysis showed that ion binding, organic substance, metabolic process, and cell part were the most abundantly used terms in molecular function, biological process and cellular component categories, respectively. In addition, 3067 unigenes were mapped onto 311 signal pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Finally, 15,224 simple sequence repeats were identified from 13,535 transcripts, and 103,593 single-nucleotide polymorphisms were found from 21.6% of total transcripts. These genetic resources obtained in this study forms a good foundation for investigating gene function, and evaluating population genetic diversity for this important Southern Ocean fisheries resource, E. superba.

Functional characterization of the circadian clock in the Antarctic krill, Euphausia superba

Antarctic krill (Euphausia superba) is a key species in Southern Ocean ecosystem where it plays a central role in the Antarctic food web. Available information supports the existence of an endogenous timing system in krill enabling it to synchronize metabolism and behavior with an environment characterized by extreme seasonal changes in terms of day length, food availability, and surface ice extent. A screening of our transcriptome database “KrillDB” allowed us to identify the putative orthologues of 20 circadian clock components. Mapping of conserved domains and phylogenetic analyses strongly supported annotations of the identified sequences. Luciferase assays and co-immunoprecipitation experiments allowed us to define the role of the main clock components. Our findings provide an overall picture of the molecular mechanisms underlying the functioning of the endogenous circadian clock in the Antarctic krill and shed light on their evolution throughout crustaceans speciation. Interestingly, the core clock machinery shows both mammalian and insect features that presumably contribute to an evolutionary strategy to cope with polar environment’s challenges. Moreover, despite the extreme variability characterizing the Antarctic seasonal day length, the conserved light mediated degradation of the photoreceptor EsCRY1 suggests a persisting pivotal role of light as a Zeitgeber.