PT  - JOURNAL ARTICLE
AU  - Ellie E. Armstrong
AU  - Ryan W. Taylor
AU  - Danny E. Miller
AU  - Christopher Kaelin
AU  - Gregory Barsh
AU  - Elizabeth A. Hadly
AU  - Dmitri Petrov
TI  - Long live the king: chromosome-level assembly of the lion (<em>Panthera leo</em>) using linked-read, Hi-C, and long read data
AID  - 10.1101/705483
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 705483
4099  - http://biorxiv.org/content/early/2019/07/17/705483.short
4100  - http://biorxiv.org/content/early/2019/07/17/705483.full
AB  - 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.