The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling

• Published in: Communications Biology
• Main Authors: Noh, Hyun Ji., Turner-Maier, Jason, Schulberg, S. Anne, Fitzgerald, Michael L., Johnson, Jeremy, Allen, Kaitlin N., Huckstadt, Luis A., Batten, Annabelle J., Alfoldi, Jessica, Costa, Daniel P., Karlsson, Elinor K., Zapol, Warren M., Buys, Emmanuel S., Lindblad-Toh, Kerstin, Hindle, Allyson G.
• Other Authors: Program in Bioinformatics and Integrative Biology
• Format: Article in Journal/Newspaper
• Language: English
• Published: 2022
• Subjects: Cardiovascular biology; Evolutionary biology; Ecology and Evolutionary Biology; Genetics and Genomics; Antarctic; The Antarctic; Weddell; Antarc*; harbor seal; Weddell Seal; Weddell Seals
• Online Access: https://doi.org/10.1038/s42003-022-03089-2; https://hdl.handle.net/20.500.14038/25960; https://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=1182&context=bioinformatics_pubs&unstamped=1; https://escholarship.umassmed.edu/bioinformatics_pubs/171

The Weddell seal (Leptonychotes weddellii) thrives in its extreme Antarctic environment. We generated the Weddell seal genome assembly and a high-quality annotation to investigate genome-wide evolutionary pressures that underlie its phenotype and to study genes implicated in hypoxia tolerance and a lipid-based metabolism. Genome-wide analyses included gene family expansion/contraction, positive selection, and diverged sequence (acceleration) compared to other placental mammals, identifying selection in coding and non-coding sequence in five pathways that may shape cardiovascular phenotype. Lipid metabolism as well as hypoxia genes contained more accelerated regions in the Weddell seal compared to genomic background. Top-significant genes were SUMO2 and EP300; both regulate hypoxia inducible factor signaling. Liver expression of four genes with the strongest acceleration signals differ between Weddell seals and a terrestrial mammal, sheep. We also report a high-density lipoprotein-like particle in Weddell seal serum not present in other mammals, including the shallow-diving harbor seal.