Genome-wide analysis sheds light on the high-altitude adaptation of the buff-throated partridge (Tetraophasis szechenyii)
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The buff-throated partridge (Tetraophasis szechenyii) is a hypoxia-tolerant bird living in an extremely inhospitable high-altitude environment, which has high ultraviolet (UV) radiation as well as a low oxygen supply when compared with low-altitude areas. To further understand the molecular genetic mechanisms of the high-altitude adaptation of the buff-throated partridges, we de novo assembled the complete genome of the buff-throated partridge. Comparative genomics revealed that positively selected hypoxia-related genes in the buff-throated partridge were distributed in the HIF-1 signaling pathway (map04066), response to hypoxia (GO:0001666), response to oxygen-containing compound (GO:1901700), ATP binding (GO:0005524), and angiogenesis (GO:0001525). Of these positively selected hypoxia-related genes, one positively selected gene (LONP1) had one buff-throated partridge-specific missense mutation which was classified as deleterious by PolyPhen-2. Moreover, positively selected genes in the buff-throated partridge were enriched in cellular response to DNA damage stimulus (corrected P value: 0.028006) and DNA repair (corrected P value: 0.044549), which was related to the increased exposure of the buff-throated partridge to UV radiation. Compared with other avian genomes, the buff-throated partridge showed expansion in genes associated with steroid hormone receptor activity and contractions in genes related to immune and olfactory perception. Furthermore, comparisons between the buff-throated partridge genome and red junglefowl genome revealed a conserved genome structure and provided strong evidence of the sibling relationship between Tetraophasis and Lophophorus. Our data and analysis contributed to the study of Phasianidae evolutionary history and provided new insights into the potential adaptation mechanisms to the high altitude employed by the buff-throated partridge.
KeywordsBuff-throated partridge Comparative genomics High-altitude adaptation Positive selection Missense mutation
We are very grateful to Haoran Yu, Yang Geng, and Wei Wu for their valuable suggestions.
CZ, YM and BSY designed and supervised the project. CZ, JGJ, YX, HMT, XCH, and QCW performed the bioinformatic analyses. CZ wrote the manuscript. All authors contributed to revising the manuscript.
This work was supported by the National Natural Science Foundation of China (No. 31702017, 31772478); and the National Key Program of Research and Development, Ministry of Science and Technology (2016YFC0503200).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no competing interests.
Human and animal rights
This article does not contain any studies with human participants or animals performed by any of the authors.
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