Alqahtani FH, Măndoiu II, Al-Shomrani BM, Al-Hashmi S, Jamshidi-Adegani F, Al-Kindi J, Golachowski A, Golachowska B, Al-Jabri AK, Manee MM. · International journal of molecular sciences · 2026

First Genome Assembly of the Critically Endangered Arabian Leopard (<i>Panthera pardus nimr</i>).

Resumo original em inglês

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.