Chromosome-level genome assembly, annotation, and population genomic resource of argali (Ovis ammon).

Argali stands as the largest species among wild sheep in Central and East Asia, with a concerning rate of decline estimated at 30%. The intraspecific taxonomy of argali remains contentious due to limited genomic data and unclear geographic separation. In this study, we constructed a chromosome-level genome assembly and annotation for the Tibetan argali (O. a. hodgsoni), together with population genomic resequencing of 32 individuals representing four subspecies. The contig-level genome was 2.64 Gb in size, with a contig N50 length of 71.69 Mb and an estimated genomic completeness of 96.01%. Using Hi-C sequencing data scaffolding, 99.90% of initially assembled sequences were mapped and oriented onto 28 pseudo-chromosomes except the Y chromosome. Annotation uncovered 21,564 protein-coding genes and 46.38% repeat sequences. The average coverage of the population resequencing data was 23.74 with mean mapping ratio up to of 97.19%. The high-quality genome assembly and annotation of the Tibetan argali, coupled with the high-depth population genomic data, will serve as a valuable genetic resource for studies on the taxonomy and conservation of argali.