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A chromosome-length assembly of the Hawaiian Monk seal (Neomonarchus schauinslandi) confirms genomic stability in the Pinnipeds and a prolonged history of “genetic purging”

David W. Mohr, Stephen J. Gaughran, Justin Paschall, Ahmed Naguib, Andy Wing Chun Pang, Olga Dudchenko, Erez Lieberman Aiden, Deanna M. Church, Alan F. Scott
doi: https://doi.org/10.1101/2022.03.31.486393
David W. Mohr
1Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore MD 21287
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  • For correspondence: dwmohr@jhmi.edu afscott@jhmi.edu
Stephen J. Gaughran
2Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544
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Justin Paschall
1Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore MD 21287
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Ahmed Naguib
3Bionano Genomics, Inc., 9640 Towne Centre Dr., Suite 100, San Diego CA 92121
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Andy Wing Chun Pang
3Bionano Genomics, Inc., 9640 Towne Centre Dr., Suite 100, San Diego CA 92121
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Olga Dudchenko
4The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
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Erez Lieberman Aiden
4The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030
5Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX 77030, USA
6UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia
7Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
8Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
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Deanna M. Church
9Inscripta, Boulder, 5500 Central Ave., Colorado 80301
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Alan F. Scott
1Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore MD 21287
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  • For correspondence: dwmohr@jhmi.edu afscott@jhmi.edu
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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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://www.ncbi.nlm.nih.gov/genome/?term=txid29088[orgn]

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 31, 2022.
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A chromosome-length assembly of the Hawaiian Monk seal (Neomonarchus schauinslandi) confirms genomic stability in the Pinnipeds and a prolonged history of “genetic purging”
David W. Mohr, Stephen J. Gaughran, Justin Paschall, Ahmed Naguib, Andy Wing Chun Pang, Olga Dudchenko, Erez Lieberman Aiden, Deanna M. Church, Alan F. Scott
bioRxiv 2022.03.31.486393; doi: https://doi.org/10.1101/2022.03.31.486393
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A chromosome-length assembly of the Hawaiian Monk seal (Neomonarchus schauinslandi) confirms genomic stability in the Pinnipeds and a prolonged history of “genetic purging”
David W. Mohr, Stephen J. Gaughran, Justin Paschall, Ahmed Naguib, Andy Wing Chun Pang, Olga Dudchenko, Erez Lieberman Aiden, Deanna M. Church, Alan F. Scott
bioRxiv 2022.03.31.486393; doi: https://doi.org/10.1101/2022.03.31.486393

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