Data from: Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness

The Antarctic fur seal (Arctocephalus gazella) is an important top
predator and indicator of the health of the Southern Ocean
ecosystem. Although abundant, this species narrowly escaped
extinction due to historical sealing and is currently declining as a
consequence of climate change. Genomic tools are essential for
understanding these anthropogenic impacts and for predicting long-term
viability. However, the current reference genome (“arcGaz3”)
shows considerable room for improvement in terms of both completeness and
contiguity. We therefore combined PacBio sequencing, haplotype
aware HiRise assembly and scaffolding based on Hi-C information to
generate a refined assembly of the Antarctic fur seal reference genome
(“arcGaz4_h1”). The new assembly is 2.53 Gb long, has a scaffold
N50 of 55.6 Mb and includes 18 chromosome-sized scaffolds, which
correspond to the 18 chromosomes expected in otariids. Genome
completeness is greatly improved, with 23,408 annotated genes and a
Benchmarking Universal Single-Copy Orthologs (BUSCO) score raised from
84.7% to 95.2%. We furthermore included the new genome in a
reference-free alignment of the genomes of eleven pinniped species to
characterize evolutionary conservation across the Pinnipedia using
genome-wide genomic evolutionary rate profiling (GERP). We then
implemented gene ontology (GO) enrichment analyses to identify biological
processes associated with those genes showing the highest levels of either
conservation or differentiation between the two major pinniped families,
Otariidae and Phocidae. We show that processes linked to neuronal
development, the circulatory system and osmoregulation are overrepresented
both in conserved as well as in differentiated regions of the genome.