Reference sequences of the Saimaa ringed seal. The reference sequences of the Saimaa ringed seal (Pusa hispida saimensis)

We report a highly contiguous de novo assembly of the Saimaa ringed seal genome. We employ a multi-platform next-generation sequencing approach where the around 50 X coverage backbone of the genome was produced by Pacific Biosciences long-read technologies and further corrected with 200 X coverage of Illumina NextSeq paired-end read technologies. Finally, we composed a next-to chromosome level assembly of the genome using specialized sequencing data from the 10x genomics platform. We used a LD-based method called Lep-Anchor (Rastas, 2020) that was refined (Kivikoski et al., 2021) and proved efficient in finding links between the pre-assembled contigs and combining them to superscaffolds. Additional population level sequencing using short-read technologies allowed us to investigate the level of variation within species and between some of the subpopulations. Despite both ancient and recent bottlenecks in the population, the Saimaa ringed seal genome appears viable with little evidence of genome-level defects or genomic erosion. In addition, we observe that Saimaa ringed seal phenotypes are virtually free of malignant neoplasia when compared with other marine mammals. The phenotypes of the Saimaa ringed seal are peculiar with respect to the population history of the subspecies. Due to the conservation and monitoring of the population, an autopsy is performed to all Saimaa ringed seals that are found deceased. Currently, the autopsies of hundreds of Saimaa ringed seals have shown virtually no evidence of malignant neoplasia, suggesting that cancers that are common in many marine mammal species are rare in the Saimaa ringed seal.