Draft nuclear and complete mitochondrial genome assemblies of the flare-horned markhor (Capra falconeri): genomic resources for conservation and phylogenetics.

The flare-horned markhor (Capra falconeri), a near-threatened mountain ungulate endemic to the Western Himalayas, remains vulnerable to habitat fragmentation, human disturbance, and environmental change. Although localized conservation efforts have stabilized some populations, genomic resources for this species remain limited. Here, we report nuclear and mitochondrial genome assemblies for C. falconeri, including a nuclear genome assembly (GCA_038502695.1) and a complete mitochondrial genome (OR799853.1), and place these data within an ecological context derived from field surveys. A structured winter survey conducted between 2020 and 2022 documented 225 individuals across 14 sites, indicating a demographically stable population with marked spatial heterogeneity. Genome-completeness assessment with BUSCO indicated that the short-read nuclear assembly is a fragmented draft (49.4% complete), and should be regarded as a preliminary genomic resource rather than a reference-quality genome. The complete mitochondrial genome is 16,639 bp in length and exhibits conserved gene organization and pronounced AT bias; comparison with the reference mitogenome identified high-confidence coding-region substitutions, exclusively transitions, distributed across the major mitochondrial protein-coding gene groups. Codon usage analyses revealed moderate bias, whereas Ka/Ks ratios across the mitochondrial protein-coding genes were consistently below one, indicating pervasive purifying selection. Comparative phylogenetic analyses based on mitochondrial and nuclear data resolved the evolutionary placement of C. falconeri within the genus Capra. Together, these results provide genomic assemblies supported by ecological context and establish a foundation for future comparative, population, and conservation genomics studies of this species.