Whole Genome Assembly of the Atlantic Bluefin Tuna Thunnus thynnus, with Phased Haplotypes

Abstract Atlantic bluefin tuna ( Thunnus thynnus ) are highly migratory fish, the largest tuna in the genus Thunnus . These fish possess a unique suite of traits, including regional endothermy, in their swimming muscle, viscera, brain and eyes that elevates tissue temperatures significantly above ambient water temperatures. Bluefin tuna also have an efficient ‘thunniform’ locomotory style, involving a fusiform low drag external shape and a novel musculoskeletal system that enhances elastic energy storage. Together the unique swimming form and warm muscle temperatures enable this species to move across large expanses of the ocean. Atlantic bluefin tuna are targeted by high-value international fisheries of over fifty nations. Populations have recovered in recent years and the species is now actively farmed extensively within the Mediterranean Sea and eastern Atlantic. To date, fisheries management and evolutionary studies have been hampered by a lack of genomic resources. Here, we report a novel de novo chromosome-level phased genome assembly for the Atlantic bluefin tuna obtained using PacBio HiFi reads and Dovetail Omni-C scaffolding. This assembly was scaffolded into 24 chromosomes containing 98% of the genes in the BUSCO reference dataset, demonstrating a high level of contiguity with a contig N50 of 26.54 and assembly size of ∼800Mbp. We compare a diploid-resolved (2N) genome assembly of Atlantic bluefin tuna with a haplotype-collapsed (1N) genome assembly from a Pacific bluefin tuna caught in the eastern Pacific off California. We show the two species have a 98.47% sequence identity. These high-quality genomes for northern bluefin tunas provide the genomic tools necessary for improving phylogenomic and evolutionary physiology analyses of this lineage and are important for potential functional assays for population biology of these commercially important species.