draft genome of the Tibetan partridge (Perdix hodgsoniae) provides insights into its phylogenetic position and high-altitude adaptation.

This article focuses on the de novo assembly and analysis of the whole genome of the Tibetan partridge (Perdix hodgsoniae), an endemic high-altitude bird species of the Tibetan Plateau, to clarify its phylogenetic position within the Phasianidae family and to investigate its genetic adaptations to extreme environmental conditions such as hypoxia and high ultraviolet radiation. The assembled genome is approximately 1.15 Gb in size, containing 16,845 protein-coding genes, with phylogenomic analysis indicating that Perdix is closely related to typical pheasants but diverges earlier than previously thought. Comparative genomics identified positively selected genes related to hypoxia response, including NFKB1 and CREBBP with Tibetan partridge-specific missense mutations, as well as expanded gene families involved in energy metabolism and steroid hydroxylase activity, while contracted gene families were associated with immunity and olfactory perception. These findings provide genomic insights into the evolutionary history of Perdix and the molecular mechanisms underlying the Tibetan partridge’s adaptation to high-altitude environments.