RT Journal Article SR Electronic T1 A chromosome-length assembly of the Hawaiian Monk seal (Neomonarchus schauinslandi) confirms genomic stability in the Pinnipeds and a prolonged history of “genetic purging” JF bioRxiv FD Cold Spring Harbor Laboratory SP 2022.03.31.486393 DO 10.1101/2022.03.31.486393 A1 Mohr, David W. A1 Gaughran, Stephen J. A1 Paschall, Justin A1 Naguib, Ahmed A1 Chun Pang, Andy Wing A1 Dudchenko, Olga A1 Aiden, Erez Lieberman A1 Church, Deanna M. A1 Scott, Alan F. YR 2022 UL http://biorxiv.org/content/early/2022/03/31/2022.03.31.486393.abstract AB The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here we report a chromosomal reference assembly for a male animal produced using a variety of methods including linked-read sequencing, Hi-C contiguity mapping, optical genome mapping, and nanopore long read sequencing. The final assembly consisted of 16 autosomes, an X and portions of the Y chromosomes. We compared variants in the reference animals to nine other HMS and to the human reference NA12878 confirming a low level of variation within the species and one-eighth that of the human reference. A lack of variation in several MHC genes was documented suggesting that this species may be at risk for infectious disease. Lastly, the HMS chromosomal assembly confirmed significant synteny with other pinnipeds. This reference should be a useful tool for long-term management of HMS and evolutionary studies of other carnivorans.Competing Interest StatementThe authors have declared no competing interest.