A chromosome-level genome assembly of the mountain lion, Puma concolor - PubMed (original) (raw)

. 2025 Jul 21;116(4):479-487.

doi: 10.1093/jhered/esae063.

Merly Escalona 3, Nicolas Alexandre 1 2, Michael R Buchalski 4, Seth P D Riley 5, Justin A Dellinger 6, T Winston Vickers 7, Ruta Sahasrabudhe 8, Oanh Nguyen 8, Colin W Fairbairn 1, William E Seligmann 1, Christopher C Wilmers 9, Beth Shapiro 1 2

Affiliations

A chromosome-level genome assembly of the mountain lion, Puma concolor

Megan A Supple et al. J Hered. 2025.

Abstract

Mountain lions, Puma concolor, are widespread and adaptable carnivores. However, due to their large home ranges and long distance dispersals, they are strongly impacted by habitat fragmentation, which results in small and isolated populations. Genomic analyses play an important role in understanding and predicting the impacts of increased isolation of populations, such as decreased genetic diversity and increased levels of inbreeding. Here we report a high-quality, chromosome-level reference genome of P. concolor that was generated as part of the California Conservation Genomics Project. The primary assembly has a total length of 2.5 Gb contained in 258 scaffolds, a contig N50 of 42.3 Mb, a scaffold N50 of 149.8 Mb, and a BUSCO completeness score of 95%. This P. concolor genome assembly will provide an important resource for genomic analyses that aid decision-makers in managing the species in fragmented landscapes.

Keywords: California Conservation Genomics Project; conservation genomics; felidae; wildlife management.

© The American Genetic Association. 2024.

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Figures

Fig. 1.

Fig. 1.

Charlie, the captive mountain lion who provided a blood sample for the genome assembly. Photo courtesy of Sonoma County Wildlife Rescue.

Fig. 2.

Fig. 2.

Visualization of assembly metrics. A) K-mer frequencies from the adapter-trimmed PacBio HiFi data used to estimate genome size, sequencing error rate, and heterozygosity. The main peak at ~44-fold coverage corresponds to homozygous regions of the genome, whereas the peak at ~22-fold corresponds to heterozygous regions of the genome. The peak near zero corresponds to probable sequencing errors. B) Snail plot displaying assembly metrics for the primary assembly. C) Omni-C contact map for the primary assembly after manual curation shows the 3D organization of the genome, with darker areas indicating closer proximity. D) Omni-C contact map for the alternate assembly.

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