Zhou Chuang, Zheng Xiaofeng, Feng Kaize, Peng Kexin, Zhang Yanni, Zhao Guangqing, Meng Yang, Zhang Li, Yue Bisong, Wu Yongjie
Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China.
Chinese Institute for Brain Research, Beijing (CIBR), Beijing, China.
J Hered. 2023 Apr 6;114(2):175-188. doi: 10.1093/jhered/esac069.
The Tibetan partridge (Perdix hodgsoniae) is a widely distributed endemic species in high-altitude areas across the Tibetan Plateau where the hypoxia, lower temperature and high ultraviolet radiation are pivotal factors influencing survival. However, the underlying genetic adaptation of the Tibetan partridge to extreme environments remains uncertain due to limited genomic resources. Similarly, the phylogenetic position of Perdix within Phasianidae remains controversial due to lacking information. Consequently, we de novo assembled and annotated the whole genome of the Tibetan partridge. The genome size was 1.15 Gb with contig N50 of 3.70 Mb. A total of 202.30 Mb (17.61%) repetitive elements and 445,876 perfect microsatellites were identified. A total of 16,845 functionally annotated protein-coding genes were identified in the Tibetan partridge. Genomic phylogenetic analysis across 30 Galliformes species indicated a close relationship between Perdix and typical pheasants composed of Chrysolophus, Symaticus, Phasianus, Crossopilon, and Lophura. However, the phylogenetic relationship of (Perdix + (Chrysolophus + (Syrmaticus + other pheasants))) was different from those of (Perdix + (Syrmaticus + (Chrysolophus + other pheasants))) in previous studies. Comparative genomic results identified NFKB1 and CREBBP positively selected genes related to hypoxia with 3 and 2 Tibetan partridge-specific missense mutations, respectively. Expanded gene families were mainly associated with energy metabolism and steroid hydroxylase activity, meanwhile, contracted gene families were mainly related to immunity and olfactory perception. Our genomic data considerably contribute to the phylogeny of Perdix and the underlying adaptation strategies of the Tibetan partridge to a high-altitude environment.
藏雪鸡（Perdix hodgsoniae）是青藏高原高海拔地区广泛分布的特有物种，该地区的缺氧、低温和高紫外线辐射是影响其生存的关键因素。然而，由于基因组资源有限，藏雪鸡对极端环境的潜在遗传适应性仍不明确。同样，由于缺乏相关信息，雪鸡属在雉科中的系统发育位置也存在争议。因此，我们对藏雪鸡的全基因组进行了从头组装和注释。基因组大小为1.15 Gb，重叠群N50为3.70 Mb。共鉴定出202.30 Mb（17.61%）的重复元件和445,876个完美微卫星。在藏雪鸡中总共鉴定出16,845个具有功能注释的蛋白质编码基因。对30种鸡形目物种的基因组系统发育分析表明，雪鸡属与由锦鸡属、长尾雉属、雉属、角雉属和火背鹇属组成的典型雉类关系密切。然而，（雪鸡属 + （锦鸡属 + （长尾雉属 + 其他雉类）））的系统发育关系与先前研究中的（雪鸡属 + （长尾雉属 + （锦鸡属 + 其他雉类）））不同。比较基因组结果确定NFKB1和CREBBP为与缺氧相关的正选择基因，分别有3个和2个藏雪鸡特异性错义突变。基因家族的扩张主要与能量代谢和类固醇羟化酶活性相关，同时，基因家族的收缩主要与免疫和嗅觉感知相关。我们的基因组数据为雪鸡属的系统发育以及藏雪鸡对高海拔环境的潜在适应策略提供了重要贡献。
