Sablefish (Anoplopoma fimbria) chromosome-level genome assembly

Abstract

Sablefish (Anoplopoma fimbria) are in the suborder Cottioidei, which also includes stickleback and lumpfish. This species inhabits coastal regions of the northeastern and northwestern Pacific Ocean from California to Japan. A commercial fishery for sablefish began to flourish in the 1960s, though a downward trend in stock biomass and landings has been observed since 2010. Aquaculture protocols have been developed for sablefish; eggs and sperm from wild-caught and hatchery-reared captive broodstock are used to generate offspring that reach market size in about two years. Parentage analyses show that survival in aquaculture varies among families. Growth rate and disease resistance also vary among individuals and cohorts, but the extent to which genetics and the environment contribute to this variation is unclear. The sablefish genome assembly reported here will form the foundation for SNP-based surveys designed to detect genetic markers associated with survival, growth rate, and pathogen resistance. Beyond its contribution to sablefish domestication, the sablefish genome can be a resource for the management of the wild sablefish fishery. The assembly generated in this study had a length of 653 Mbp, a scaffold N50 of 26.74 Mbp, a contig N50 of 2.57 Mbp, and contained more than 98% of the 3640 Actinopterygii core genes. We placed 620.9 Mbp (95% of the total) onto 24 chromosomes using a genetic map derived from six full-sib families and Hi-C contact data.

Keywords: Anoplopoma fimbria; cottioidei; genome assembly; sablefish; teleostei.

Fig. 1.

Threespine stickleback and sablefish Circos ribbon plot showing chromosome-level alignments. Threespine stickleback has 21 chromosomes, 19 and Y are homologs, but displayed as distinct chromosomes. Sablefish have 24 chromosomes. Threespine stickleback fusion chromosomes 1, 4, and 7 align to sablefish chromosomes 1 + 22, 4 + 23 and 7 + 24, respectively. A sablefish-specific, ∼2 Mbp, translocation (chromosome 3 to chromosome 8) is also shown. Chromosome-level alignments/dot plots (Supplementary Figs. 2–4) show that this translocation is derived in sablefish. This figure also shows the relationship between chromosome length in cM (X-axis) and length in base pairs (y-axis) for each sex. Each dot on the figure represents a genetic marker with the female cM position (blue) and male cM position (orange) on the Y-axis, and the physical position on the X-axis.