LAUSR

The Tibetan Partridge (Perdix hodgsoniae), an endemic species distributed in high-altitude areas of 3,600-5,600 m on the Qinghai-Tibet Plateau (QTP). To explore on how the species is adapted to the high elevation environment, we assembled a draft genome based on both the Illumina and PacBio sequencing platforms with its population genetics and genomics analysis. In total, 134.74 Gb short reads and 30.81 Gb long reads raw data were generated. The 1.05 Gb assembled genome had a contig N50 of 4.56 Mb, with 91.94% complete BUSCOs. The 17,457 genes were annotated, and 11.35% of the genome was composed of repeat sequences. The phylogenetic tree showed that P. hodgsoniae was located at the basal position of the clade, including Golden Pheasant (Chrysolophus pictus), Common Pheasant (Phasianus colchicus) and Mikado Pheasant (Syrmaticus mikado). We found that 1,014, 2,595 and 2,732 of the 6,641 one-to-one orthologous genes were under positive selection in P. hodgsoniae, detected using PAML, BUSTED, and aBSREL programs respectively, of which 965 genes were common under positive selection with three different programs. Several positively selected genes (PSGs) and immunity pathways relevant to high-altitude adaptation were detected. Gene family evolution showed that 99 gene families experienced significant expansion events, while six gene families were under contraction. The total number of olfactory receptor (OR) genes was relatively low in P. hodgsoniae. Genomic data provide an important resource for a further study on evolutionary history of P. hodgsoniae, which provides a new insight into its high-altitude adaptation mechanisms. This article is protected by copyright. All rights reserved.