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Genome-wide analysis sheds light on the high-altitude adaptation of the buff-throated partridge (Tetraophasis szechenyii)

  • Chuang Zhou
  • Jake George James
  • Yu Xu
  • Hongmei Tu
  • Xingcheng He
  • Qinchao Wen
  • Megan Price
  • Nan Yang
  • Yongjie Wu
  • Jianghong Ran
  • Yang MengEmail author
  • Bisong YueEmail author
Original Article
  • 53 Downloads

Abstract

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.

Keywords

Buff-throated partridge Comparative genomics High-altitude adaptation Positive selection Missense mutation 

Notes

Acknowledgements

We are very grateful to Haoran Yu, Yang Geng, and Wei Wu for their valuable suggestions.

Author contributions

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.

Funding

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.

Supplementary material

438_2019_1601_MOESM1_ESM.pdf (1 mb)
Supplementary material 1 (PDF 1049 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Chuang Zhou
    • 1
  • Jake George James
    • 1
  • Yu Xu
    • 2
  • Hongmei Tu
    • 1
  • Xingcheng He
    • 1
  • Qinchao Wen
    • 3
  • Megan Price
    • 1
  • Nan Yang
    • 4
  • Yongjie Wu
    • 1
  • Jianghong Ran
    • 1
  • Yang Meng
    • 1
    Email author
  • Bisong Yue
    • 1
    Email author
  1. 1.Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life SciencesSichuan UniversityChengduPeople’s Republic of China
  2. 2.School of Life SciencesGuizhou Normal UniversityGuiyangPeople’s Republic of China
  3. 3.Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life SciencesSichuan UniversityChengduPeople’s Republic of China
  4. 4.Institute of Qinghai-Tibetan PlateauSouthwest Minzu UniversityChengduPeople’s Republic of China

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