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First Arabian Leopard Nuclear Genome Assembly Provides a Reference for Conservation Genomics

Wild Arabian leopard walking through rocky desert terrain
Research · Genetics & genomics

The Arabian leopard (Panthera pardus nimr) now has its first nuclear genome assembly built directly from DNA of the subspecies. Published on 8 July 2026, the reference genome, named Nimr1, was assembled from a wild-born male in Oman — the same animal used for the complete mitochondrial genome published in 2025.

Mitochondrial DNA follows the maternal line and represents only a small part of an animal’s genetic material. Earlier work had produced whole-genome sequence data from two captive Arabian leopards, but those reads were mapped to a domestic-cat reference rather than used to build a new Arabian leopard genome. Nimr1 therefore provides a reference sequence from the subspecies itself.

A high-quality draft genome

The blood sample was collected during a routine veterinary assessment connected to a relocation in September 2023. PacBio HiFi sequencing produced long DNA reads with high accuracy. The resulting assembly spans about 2.43 gigabases in 94 contiguous sequences, or contigs, with no sequence gaps. Its contig N50 is 62.4 megabases, meaning that half of the assembly lies in contigs at least that long.

A BUSCO assessment recovered 99.4% of 13,727 conserved carnivore genes, indicating that the draft contains almost all of the expected gene set. The researchers predicted 23,459 protein-coding genes. A comparison of simple sequence repeats across six Panthera genomes found broadly conserved patterns and no repeat expansion unique to the Arabian leopard.

One genome is not a population survey

Nimr1 was assembled from a single male. It therefore cannot show how much genetic diversity remains across wild and captive Arabian leopards, or provide population-wide estimates of inbreeding and harmful mutation load. The assembly also remains at contig level rather than chromosome level, so its sequences have not yet been fully organised into individual chromosomes.

Nimr1 can anchor population comparisons

The authors describe the genome as a foundation for comparing DNA from additional animals. Future resequencing can use Nimr1 to examine genetic diversity, relatedness, long homozygous regions—stretches where the two inherited chromosome copies carry the same variants, which can reveal shared ancestry and inbreeding—demographic history and gene flow. They also identify possible uses in captive-breeding decisions and in developing DNA markers for individual identification, parentage and seized wildlife material.

The assembly, annotation and raw HiFi reads are openly available through NCBI. The value of the reference will therefore grow as more samples are added: Nimr1 supplies the genomic map, while population-level conclusions still require DNA from many more Arabian leopards.

Sources and image credit

  1. Alqahtani, F. H., Măndoiu, I. I., Al-Shomrani, B. M., Al-Hashmi, S., Jamshidi-Adegani, F., Al-Kindi, J., Golachowski, A., Golachowska, B., Al-Jabri, A. K., & Manee, M. M. (2026). First Genome Assembly of the Critically Endangered Arabian Leopard (Panthera pardus nimr). International Journal of Molecular Sciences, 27(14), 6115.
  2. Panthera pardus nimr — The Genome of the Arabian LeopardPrimary genome-data record for Nimr1; includes assembly GCA_038088395.2 and the associated sequencing data.

Image: Yossi Aud / PikiWiki Israel / Wikimedia Commons — wild Arabian leopard near Ein Gedi in the Judean Desert, photographed in 1985; representative subspecies image · CC BY 2.5 · Source

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