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

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.