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

The spotted seal (Phoca largha) 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 P. largha 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 P. largha as sister to Phoca vitulina 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 (KRT) and matrix metalloproteinase (MMP) families reveal contrasting chromosomal organisation and evolutionary dynamics: KRTs form large chromosomal clusters with broadly conserved synteny across Carnivora but lineage-dependent remodelling within clusters, whereas MMPs 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.