A Near-Telomere-to-Telomere Genome Assembly of the Spotted Seal (Phoca largha) Reveals Genomic Architecture Underlying Skin and Fur Adaptation

The spotted seal (<i>Phoca largha</i>) is an ice-associated pinniped in the Northwest Pacific and is a subject of conservation concern under increasing environmental and anthropogenic pressures; however, genomic studies have been constrained by the absence of a high-quality reference genome. Here, we present a near-telomere-to-telomere (near-T2T), gap-free genome assembly of <i>P. largha</i> spanning 2.39 Gb and comprising 16 chromosome-length sequences, with a scaffold N50 of 184.39 Mb and high completeness (99.34% complete BUSCOs). Compared with the previous chromosome-level assembly, the new genome improves contiguity and gene-space completeness. Comparative analyses across 20 carnivoran species resolve <i>P. largha</i> as sister to <i>Phoca vitulina</i> with an estimated divergence time of ~2.1 Ma. Branch-site positive-selection analyses and gene-family evolution analyses identify lineage-associated changes, and enrichment results motivate focused investigation of integument-related gene families. Targeted analyses of keratin (<i>KRT</i>) and matrix metalloproteinase (<i>MMP</i>) families reveal contrasting chromosomal organisation and evolutionary dynamics: <i>KRT</i>s form large chromosomal clusters with broadly conserved synteny across Carnivora but lineage-dependent remodelling within clusters, whereas <i>MMP</i>s are dispersed and display largely conserved orthologous correspondence. This high-quality genome provides a high-quality resource for pinniped comparative genomics and for elucidating the genomic architecture of skin and fur adaptation.