De novo assembly and functional characterisation of Calanus hyperboreus using state-of-the-art genomics technologies

Background: Climate change is impacting marine ecosystems, including important zooplankton communities. While genetic adaptation could help populations survive under warmer conditions, this process is poorly understood in zooplankton. The Calanus hyperboreus copepod is a keystone species in high-latitude waters. It is polymorphic for genome size, ranging from 12 Gb in the Arctic Ocean to 9 Gb around Scandinavia. Aims: to assemble the first genome of any species of Calanus, characterising structural variation in the genome to gain insights into the evolutionary history of C. hyperboreus and to assess the role of genome size evolution in adaptation. Methods/Materials: Long-read DNA sequencing data from a single specimen was used to produce and polish a genome assembly, which was then annotated using RNA-seq data. Structural variants and repeats were studied using multiple bioinformatics tools. Results: The genome assembly spanned 8.8 Gb and was highly fragmented (233,848 contigs, N50: 53,059 bp) but relatively complete (94.3% complete BUSCO genes), with a third of the genes duplicated. SVs occupied 3% of the genome, with altered patterns of certain elements near contig ends. Gene Ontology terms enriched in the set of duplicated genes included terms associated with lipid metabolism. Conclusions: We have shown that a fragmented genome assembly with a high level of completeness can be assembled from low coverage sequence data, providing a basis for further analyses. The duplicated genes may have evolved through numerous segmental duplications rather than whole-genome duplication, that may be related to life-history traits in C. hyperboreus, suggesting that these duplications might have been necessary for adaptation to Arctic conditions.