Chromosome-level Genome Assembly of the South African Lion (Panthera leo melanochaita)

Hadebe, S.; Tshilate, T. S.; Hlongwane, N.; Nesengani, L. T.; Mdyogolo, S.; Molotsi, A.; Smith, R. M.; Labuschagne, K.; Masebe, T.; Mapholi, N.

doi:10.64898/2026.03.10.710750

bioRxiv · 10.64898/2026.03.10.710750

Chromosome-level Genome Assembly of the South African Lion (Panthera leo melanochaita)

Hadebe, S.·Tshilate, T. S.·Hlongwane, N.·Nesengani, L. T.·Mdyogolo, S.·Molotsi, A.·Smith, R. M.·Labuschagne, K.·Masebe, T.·Mapholi, N.

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Abstract

The lion (Panthera leo melanochaita) is one of the most iconic species and part of the big five, maintaining ecological balance and a major wildlife-based tourism attraction in South Africa. Despite its importance, it is currently threatened by rapid population decline and increasing population fragmentation. Therefore, there is a need for a high-quality genomic resource that captures the diverse genetic landscape of South African lion populations. To address this, we present a high-quality genome assembly of the lion, generated using PacBio HiFi and Omni-C sequencing technologies. The final assembly comprises 2.45 Gb, with a scaffold N50 of 148 Mb and a contig N50 of 22 Mb. Remarkably, 94.8% of the genome is anchored to 19 scaffolds, reflecting the high degree of contiguity and near-complete chromosomal level. Completeness assessment of the genome showed 98.2% BUSCO, 98.2% k-mer completeness and QV of 65.6 underscoring high accuracy and biological integrity. Genome annotation predicted 831.4 Mb (33.9%) of repetitive sequences and 21 739 protein-coding genes. This work provides high-quality genomic resource to establish a foundation for future population genomic and conservation-focused investigations of the lion populations in South Africa.

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Hadebe, S., Tshilate, T. S., Hlongwane, N., Nesengani, L. T., Mdyogolo, S., Molotsi, A., Smith, R. M., Labuschagne, K., Masebe, T., Mapholi, N.. 2026-03-12. Chromosome-level Genome Assembly of the South African Lion (Panthera leo melanochaita). https://doi.org/10.64898/2026.03.10.710750

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