A chromosome-length assembly of the Hawaiian Monk seal ( Neomonarchus schauinslandi ) confirms genomic stability in the Pinnipeds and a prolonged history of “genetic purging”
A chromosome-length assembly of the Hawaiian Monk seal ( Neomonarchus schauinslandi ) confirms genomic stability in the Pinnipeds and a prolonged history of “genetic purging”
Abstract 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.
Mohr David W.、Naguib Ahmed、Chun Pang Andy Wing、Church Deanna M.、Scott Alan F.、Dudchenko Olga、Paschall Justin、Gaughran Stephen J.、Aiden Erez Lieberman
Department of Genetic Medicine, Johns Hopkins University School of MedicineBionano Genomics, Inc.Bionano Genomics, Inc.InscriptaDepartment of Genetic Medicine, Johns Hopkins University School of MedicineThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of MedicineDepartment of Genetic Medicine, Johns Hopkins University School of MedicineDepartment of Ecology & Evolutionary Biology, Princeton UniversityThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine||Center for Theoretical Biological Physics and Department of Computer Science, Rice University||UWA School of Agriculture and Environment, The University of Western Australia||Broad Institute of MIT and Harvard||Shanghai Institute for Advanced Immunochemical Studies
遗传学动物学分子生物学
Mohr David W.,Naguib Ahmed,Chun Pang Andy Wing,Church Deanna M.,Scott Alan F.,Dudchenko Olga,Paschall Justin,Gaughran Stephen J.,Aiden Erez Lieberman.A chromosome-length assembly of the Hawaiian Monk seal ( Neomonarchus schauinslandi ) confirms genomic stability in the Pinnipeds and a prolonged history of “genetic purging”[EB/OL].(2025-03-28)[2025-05-28].https://www.biorxiv.org/content/10.1101/2022.03.31.486393.点此复制
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