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Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long read data

View ORCID ProfileEllie E. Armstrong, Ryan W. Taylor, Danny E. Miller, Christopher Kaelin, Gregory Barsh, Elizabeth A. Hadly, Dmitri Petrov
doi: https://doi.org/10.1101/705483
Ellie E. Armstrong
1Department of Biology, Stanford University, Stanford, California, USA
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Ryan W. Taylor
1Department of Biology, Stanford University, Stanford, California, USA
2End2EndGenomics, LLC, Davis, California, USA
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Danny E. Miller
3Department of Pediatrics, Seattle Children’s Hospital and The University of Washington, Seattle, Washington, USA
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Christopher Kaelin
4HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
5Department of Genetics, Stanford University, Stanford, California, USA
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Gregory Barsh
4HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
5Department of Genetics, Stanford University, Stanford, California, USA
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Elizabeth A. Hadly
1Department of Biology, Stanford University, Stanford, California, USA
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Dmitri Petrov
1Department of Biology, Stanford University, Stanford, California, USA
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Abstract

The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly for the captive African lion from the Exotic Feline Rescue Center as a resource for current and subsequent genetic work of the sole social species of the Panthera clade. Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore long-read data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length and levels of homozygosity across the genomes of the lion sequenced here and other previous published resequence data, indicating contrasting histories of recent and ancient small population sizes and/or inbreeding. Demographic analyses reveal similar histories across all individuals except the Asiatic lion, which shows a more rapid decline in population size. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion.

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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-NC-ND 4.0 International license.
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Posted July 17, 2019.
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Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long read data
Ellie E. Armstrong, Ryan W. Taylor, Danny E. Miller, Christopher Kaelin, Gregory Barsh, Elizabeth A. Hadly, Dmitri Petrov
bioRxiv 705483; doi: https://doi.org/10.1101/705483
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Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long read data
Ellie E. Armstrong, Ryan W. Taylor, Danny E. Miller, Christopher Kaelin, Gregory Barsh, Elizabeth A. Hadly, Dmitri Petrov
bioRxiv 705483; doi: https://doi.org/10.1101/705483

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