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, 18 (1), 3

Long Live the King: Chromosome-Level Assembly of the Lion (Panthera Leo) Using Linked-Read, Hi-C, and Long-Read Data

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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 et al. BMC Biol.

Abstract

Background: 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 from a captive African lion from the Exotic Feline Rescue Center (Center Point, IN) as a resource for current and subsequent genetic work of the sole social species of the Panthera clade.

Results: 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 of runs of homozygosity across lion genomes, indicating contrasting histories of recent and possibly intense inbreeding and bottleneck events. Demographic analyses reveal similar ancient histories across all individuals during the Pleistocene except the Asiatic lion, which shows a more rapid decline in population size. We show a substantial influence on the reference genome choice in the inference of demographic history and heterozygosity.

Conclusions: We demonstrate that the choice of reference genome is important when comparing heterozygosity estimates across species and those inferred from different references should not be compared to each other. In addition, estimates of heterozygosity or the amount or length of runs of homozygosity should not be taken as reflective of a species, as these can differ substantially among individuals. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion, which is rapidly moving towards becoming a species in danger of extinction.

Keywords: 10x Genomics Chromium; African lion; Conservation genomics; Dovetail Hi-C; Genome assembly; Oxford Nanopore; Panthera leo; Reference bias.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
(Left panel) Schematic showing the different improvements made via various technologies in the three assembly phases for the lion genome. (Right panel) Assembly statistics for the three assembly phases of the lion genome
Fig. 2
Fig. 2
Phylogenetic reconstruction of de novo felid genomes using RAxML and 4039 highly conserved genes from BUSCO mammalia_odb9 dataset. Node annotations indicate posterior probabilities
Fig. 3
Fig. 3
Circos plot of alignments between domestic cat (left) and lion (right) chromosomes. Colors represent different chromosomes indicated by their felCat9 linkage group names (e.g. A1)
Fig. 4
Fig. 4
Average genome-wide heterozygosity of various felids when mapped to a reference genome from their own species, if available (blue) vs. when mapped to the domestic cat (red)
Fig. 5
Fig. 5
Distribution of lengths of homozygosity across various lion individuals
Fig. 6
Fig. 6
Demographic history of the lion as inferred by PSMC, with the PanLeo1.0 used as the reference genome. Generation time used was 5 years, and mutation rate applied was 0.5 × 10−8
Fig. 7
Fig. 7
Demographic history of the lion as inferred by PSMC, with felCat9 used as the reference genome. Generation time used was 5 years, and mutation rate applied was 0.5 × 10−8

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