The genome architecture of a copepod invading novel habitats

Abstract With climate change, salinity is rapidly changing in marine and freshwater habitats throughout the globe. In addition, many of the most destructive aquatic invaders are crossing salinity boundaries. Populations of the copepod Eurytemora affinis species complex are numerically dominant and highly invasive, with the exceptional capacity to rapidly invade and adapt to novel salinities. Prior studies have found striking patterns of parallel adaptation in E. affinis complex populations, with selection acting on the same sets of ion transporter genes during independent saline to freshwater invasions. Our chromosome-level genome of Eurytemora carolleeae (Atlantic clade of the E. affinis complex) revealed a peculiar genome architecture that might contribute to its remarkable capacity to acclimate and evolve during salinity invasions. We assembled the highest quality copepod genome to date, using high-coverage PacBio and Hi-C sequencing of an inbred line generated through 30 generations of full-sib mating. Our new genome consisted of 529.3 Mb (contig N50 = 4.2 Mb, scaffold N50 = 140.6 Mb) anchored onto four chromosomes. Of its predicted 20,262 protein-coding genes, we found an extraordinary expansion of ion transporter gene families based on a comparative analysis of 13 arthropod genomes, with many of these expansions being recent. Notably, we found extreme CpG depletion of the ion transporter gene bodies, indicating high rates of methylation at these genes and suggesting transcriptional robustness of ion transporter gene regulation. This high-quality genome provides an invaluable resource that could help yield fundamental insights into the capacity of populations to expand their ranges into novel habitats.