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

Abstract

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.

Comparative population genomics provide new insight into the evolutionary history and adaptive potential of World Ocean krill

“…Cuticular protein genes are among the largest gene families in arthropod genomes (Magkrioti et al 2004), and help build the exoskeleton. In krill, cuticular development and gene expression are closely linked to physiological and seasonal cycles of ecdysis (molting), growth and reproduction (Buchholz and Buchholz 2010;Urso et al 2022). In krill native to warm waters, we detect potentially selective substitutions in Ecdysone-induced protein 75B (Eip75B), a gene encoding a nuclear receptor that regulates the timing of molting, reproduction and circadian oscillation in insects and crustaceans (Kumar et al 2014;Gouveia et al 2018), that could contribute to adaptation.…”

“…S9B), automatically annotated as Rh5. However, queries against KrillDB 2 (Urso et al 2022) and NCBI Genbank suggest it is a peropsin, a light-sensitive yet non-visual receptor with poorly understood function in crustaceans but with expression patterns that oscillate daily in Antarctic krill (Henze and Oakley 2015;Biscontin et al 2016;Palecanda et al 2022).…”

“…M. norvegica). This includes efforts to uncover and functionally characterize the photoreceptor and circadian clock gene repertoires (Biscontin et al 2016;Christie et al 2017;Palecanda et al 2022;Urso et al 2022) or genes involved in regulating the molting cycle (Seear et al 2010), seasonal dynamics (Seear et al 2012;Höring et al 2021) and heat shock response (Huenerlage et al 2016;Papot et al 2016). However, analyses of how specific genes may contribute to environmental adaptation through natural selection have only been performed in heat shock proteins hsp70 genes of Antarctic species before.…”

“…Both E. superba and E. crystallorophias appear to have experienced diversifying selection between hsp70 paralogs, but E. superba hsps are characterized by greater functional diversity and balancing selection associated with a more heterogeneous environment, while E. crystallorophias hsps may have evolved under stronger directional selection in a more constantly cold environment (Cascella et al 2015;Papot et al 2016). In the Antarctic krill, genes involved in controlling seasonal metabolic, molting, growth and reproductive cycles have been shown to be differentially expressed between summer and winter seasons (Urso et al 2022). These cycles are thought to be driven by photoperiodic environmental cues such as day light, temperature and food availability and involve genetic pathways for photoreception and circadian clocks (Teschke et al 2008;Biscontin et al 2017;Piccolin et al 2018;Höring et al 2021).…”

Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins

“…Moreover, we detected expansions of the opsin gene repertoire, which encodes the light-sensitive receptors in ommatidia. Fourteen opsins have previously been identified from RNA in the Antarctic krill E. superba (34), which are thought to enable vision under the divergent light conditions experienced throughout its life cycle and vertical migrations (35), while 16 opsins have recently been inferred from M. norvegica RNA (36). We queried our M. norvegica gene-set and the KrillDB 2 E. superba RNA database against the curated crustacean opsin dataset in ref 35.…”