A Chromosome-Level Genome Assembly of the Snow Leopard, Panthera Uncia

Abstract The snow leopard (Panthera uncia), a vulnerable big cat native to Central Asia, faces an ongoing population decline due to habitat loss and human activities. Despite its conservation importance, genomic resources for this species remain limited. High-quality reference genomes are essential for assessing genetic diversity, structural variation, and evolutionary history. To address this gap, we have generated a long-read-based and proximity-ligation scaffolded de novo genome assembly of a male snow leopard. The final assembly has a total length of 2.46 Gb in 280 scaffolds, of which the 19 largest correspond to the 18 autosomes and the X chromosome. The scaffold N50 is 145.76 Mb, and the L50 is seven scaffolds. BUSCO and compleasm scores are 98.7% and 98.9% of identified Carnivora orthologs. Telomeric sequences were identified on at least one end of 18 out of 19 chromosomes. Scaffolds corresponding to the Y chromosome were identified and mapped. Additionally, the assembly's annotation identified a repeat content of 42.27% and 25 391 genes. We produced a high-quality, long-read-based chromosome-level assembly of a male snow leopard, as evidenced by the data above. As a first assembly of a male genome, it can serve as a suitable reference genome for the species. The Y chromosome scaffolds provide a glimpse into the chromosome organization and interspecies differences.