Genome architecture of an exceptionally invasive copepod crossing salinity boundaries

Abstract

Abstract Background: Copepods are among the most abundant organisms on the planet and play critical functions in aquatic ecosystems. Among copepods, populations of the Eurytemora affinis species complex are numerically dominant in many coastal habitats and serve as the food source for major fisheries. Intriguingly, certain populations possess the unusual capacity to invade novel salinities on rapid time scales. Despite their ecological importance, high-quality genomic resources have been absent for calanoid copepods, limiting our ability to comprehensively dissect the genomic mechanisms underlying this highly invasive and adaptive capacity. Results: Here, we present the first chromosome-level genome of a calanoid copepod, from the Atlantic clade (Eurytemora carolleeae) of the E. affinis species complex. This genome was assembled using high-coverage PacBio and Hi-C sequences of an inbred line, generated through 30 generations of full-sib mating. This genome consisting of 529.3 Mb (contig N50 = 4.2 Mb, scaffold N50 = 140.6 Mb) was anchored onto four chromosomes. Genome annotation predicted 20,262 protein-coding genes, of which ion transporter gene families were substantially expanded based on comparative analyses of 12 additional arthropod genomes. Also, we found genome-wide signatures of historical gene body methylation of the ion transporter genes and significant clustering of these genes on each chromosome. Conclusions: This genome represents one of the most contiguous copepod genomes to date and among the highest quality of marine invertebrate genomes. As such, this genome provides an invaluable resource that could help yield fundamental insights into the ability of this copepod to adapt to rapid environmental transitions.