A chromosome-level reference genome for the black-legged kittiwake (Rissa tridactyla), a declining circumpolar seabird.

Amidst the current biodiversity crisis, the availability of genomic resources for declining species can provide important insights into the factors driving population decline. In the early 1990s, the black-legged kittiwake (Rissa tridactyla), a pelagic gull widely distributed across the arctic, subarctic and temperate zones, suffered a steep population decline following an abrupt warming of sea-surface temperature across its distribution range and is currently listed as Vulnerable by the IUCN. Kittiwakes have long been the focus for field studies of physiology, ecology, and ecotoxicology, and are primary indicators of fluctuating ecological conditions in arctic and subarctic marine ecosystems. We present a high-quality chromosome-level annotated reference genome and annotation for the black-legged kittiwake using a combination of PacBio HiFi sequencing, Bionano optical maps, Hi-C reads and RNA-Seq data. The final assembly spans 1.35 Gbp across 32 chromosomes, with a scaffold N50 of 88.21 Mbp, and a BUSCO completeness of 97.4%. This genome assembly substantially improves the quality of a previous draft genome, showing a ∼5X increase in contiguity and a more complete annotation. Using this new chromosome-level reference genome and three more chromosome-level assemblies of Charadriiformes, we uncover several lineage-specific chromosome fusions and fissions, but find no shared rearrangements, suggesting that interchromosomal rearrangements have been commonplace throughout the Charadriiformes diversification. This new high-quality genome assembly will enable population genomic, transcriptomic, and phenotype-genotype association studies in a widely studied sentinel species, which may provide important insights into the impacts of global change on marine systems.