First Genome Assembly of the Critically Endangered Arabian Leopard (Panthera pardus nimr)

The Arabian leopard (Panthera pardus nimr), native to the Arabian Peninsula, is critically endangered and faces acute threats from habitat fragmentation, low population size, and genetic erosion. As a continuation of our previous study on the complete mitochondrial genome of this subspecies, we now report the first nuclear genome assembly of P. p. nimr, generated from the same wild-born male individual sampled in the Oman. Using PacBio HiFi long-read sequencing, we produced 162.9 gigabases (Gb) of high-fidelity data and assembled a haplotype-aware draft genome with HiFiasm. The assembly spans approximately 2.43 Gb across 94 contigs, achieving a contig N50 of 62.4 Mb and zero gap content, with BUSCO completeness of 99.4%. Genome annotation predicted 23,459 protein-coding genes with annotation BUSCO completeness of 95.0%, and 84.1% of proteins were classified as consistent with the Panthera lineage by OMArk. Repetitive elements occupy 34.01% of the assembly, with retroelements dominating and L1/CIN4 LINEs (15.44%) and SINEs (9.61%) representing the two largest subclasses. Comparative simple sequence repeat (SSR) analysis across six Panthera genomes confirmed a conserved repeat motif architecture, with no lineage-specific expansions detected in P. p. nimr. This nuclear genome complements the mitochondrial reference and provides a foundational resource for future studies on genetic diversity, demographic history, inbreeding load, and conservation planning for the Arabian leopard and other Panthera lineages.