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The first draft genome of Lophophorus: A step forward for Phasianidae genomic diversity and conservation

Cui, Kai, Li, Wujiao, James, Jake George, Peng, Changjun, Jin, Jiazheng, Yan, Chaochao, Fan, Zhenxin, Du, Lianming, Price, Megan, Wu, Yongjie, Yue, Bisong
Genomics 2019 v.111 no.6 pp. 1209-1215
Lophophorus lhuysii, altitude, birds, color, databases, evolution, genes, genetic variation, genomics, high-throughput nucleotide sequencing, life history, mammals, microsatellite repeats, mountains, non-coding RNA, plumage, temperature, China
The monal genus (Lophophorus) is a branch of Phasianidae and its species inhabit the high-altitude mountains of the Qinghai-Tibet Plateau. The Chinese monal, L. lhuysii, is a threatened endemic bird of China that possesses high-altitude adaptability, diversity of plumage color and potentially low reproductive life history. This is the first study to describe the monal genome using next generation sequencing technology. The Chinese monal genome size is 1.01 Gb, with 16,940 protein-coding genes. Gene annotation yielded 100.93 Mb (9.97%) repeat elements, 785 ncRNA, 5,465,549 bp (0.54%) SSR and 15,550 (92%) genes in public databases. Compared to other birds and mammals, the genome evolution analysis showed numerous expanded gene families and positive selected genes involved in high-altitude adaptation, especially related to the adaptation of low temperature and hypoxia. Consequently, this gene data can be used to investigate the molecular evolution of high-altitude adaptation in future bird research. Our first published genome of the genus Lophophorus will be integral for the study of monal population genetic diversity and conservation, genomic evolution and Galliformes species differentiation in the Qinghai-Tibetan Plateau.