A de novo assembled genome of the Tibetan Partridge (Perdix hodgsoniae) and its high-altitude adaptation  

作　　者：Xuejuan LI Xiaoyang WANG Chao YANG Liliang LIN Hao YUAN Fumin LEI Yuan HUANG 

机构地区：[1]College of Life Sciences,Shaanxi Normal University,Xi’an,China [2]School of Biological and Environmental Engeering,Xi’an University,Xi’an,China [3]Shaanxi Institute of Zoology,Xi’an,China [4]Key Laboratory of the Zoological Systematics and Evolution,Institute of Zoology,the Chinese Academy of Sciences,Beijing,China

出　　处：《Integrative Zoology》2023年第2期225-236,共12页整合动物学（英文版）

基　　金：The National Center for Biotechnology Information(NCBI)BioProject and BioSample accession numbers of Perdix hodgsoniae are PRJNA760267 and SAMN21212221,respectively;The raw reads have been deposited in the NCBI SRA database with the accession numbers SRR15900414(Illumina),SRR15900412,and SRR15900413(PacBio).

摘　　要：The Tibetan Partridge(Perdix hodgsoniae)is an endemic species distributed in high-altitude areas of 3600–5600 m on the Qinghai–Tibet Plateau.To explore how the species is adapted to the high elevation environment,we as-sembled 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 17457 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 1014,2595,and 2732 of the 6641 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 selec-tion with 3 different programs.Several positively selected genes and immunity pathways relevant to high-altitude adaptation were detected.Gene family evolution showed that 99 gene families experienced significant expansion events,while 6 gene families were under contraction.The total number of olfactory receptor genes was relatively low in P.hodgsoniae.Genomic data provide an important resource for a further study on the evolutionary history of P.hodgsoniae,which provides a new insight into its high-altitude adaptation mechanisms.

关 键 词：comparative genome genome assembly high-altitude adaptation Perdix hodgsoniae 

分 类 号：Q95[生物学—动物学]