Genomic comparison of male and female spotted seals in the Liaodong Gulf, China

Accumulated genomic resources and molecular markers should facilitate the assessment of biodiversity and the conservation of marine mammals. The spotted seal (Phoca largha) is an endangered species and the only pinniped species that breeds in China, yet limited genomic information of this endangered species has been reported till now. In this study, whole genome sequencing data was used to implement genomic comparison of male and female P. largha collected from the Liaodong Gulf. The genomic sizes of P. largha were estimated to be 2.39 (male) and 2.49 (female) Gb, respectively. The estimated genomic features and identification of the male-specific gene (SRY gene) suggested the spotted seal should be male heterogamety. Using a two-step assembly strategy, the scaffold N50 of genome assemblies in our study were about 39 Mb, with the BUSCO estimates of over 94%, showing high genome continuity and completeness. A total of 1,444,553 and 1,464,251 microsatellite motifs were identified in the male and female genome assemblies, respectively. Besides, a total of 3,055,239 genome-wide SNPs were identified and annotated, among which 569 were categorized as high-impact mutations. Using these identified SNPs, the PSMC analyses revealed recent population decline of the spotted seals in the Liaodong Gulf. Phylogenomics analysis was also conducted to confirm the close relationship between the spotted seal and harbor seal. The genomic resources and molecular markers reported in this study will facilitate further conservation genetics and evolutionary biology investigations of the spotted seal.