Long read genome assemblies complemented by single cell RNA-sequencing reveal genetic and cellular mechanisms underlying the adaptive evolution of yak

Xue Gao, Sheng Wang, Yan-Fen Wang, Shuang Li, Shi-Xin Wu, Rong-Ge Yan, Yi-Wen Zhang, Rui-Dong Wan, Zhen He, Ren- De Song, Xin-Quan Zhao (), Dong-Dong Wu () and Qi-En Yang ()
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Xue Gao: Chinese Academy of Sciences
Sheng Wang: Chinese Academy of Sciences
Yan-Fen Wang: University of Chinese Academy of Sciences
Shuang Li: Chinese Academy of Sciences
Shi-Xin Wu: Chinese Academy of Sciences
Rong-Ge Yan: Chinese Academy of Sciences
Yi-Wen Zhang: Chinese Academy of Sciences
Rui-Dong Wan: Chinese Academy of Sciences
Zhen He: Chinese Academy of Sciences
Ren- De Song: Center for Animal Disease Control and Prevention
Xin-Quan Zhao: Chinese Academy of Sciences
Dong-Dong Wu: Chinese Academy of Sciences
Qi-En Yang: Chinese Academy of Sciences

Nature Communications, 2022, vol. 13, issue 1, 1-14

Abstract: Abstract Wild yak (Bos mutus) and domestic yak (Bos grunniens) are adapted to high altitude environment and have ecological, economic, and cultural significances on the Qinghai-Tibetan Plateau (QTP). Currently, the genetic and cellular bases underlying adaptations of yak to extreme conditions remains elusive. In the present study, we assembled two chromosome-level genomes, one each for wild yak and domestic yak, and screened structural variants (SVs) through the long-read data of yak and taurine cattle. The results revealed that 6733 genes contained high-FST SVs. 127 genes carrying special type of SVs were differentially expressed in lungs of the taurine cattle and yak. We then constructed the first single-cell gene expression atlas of yak and taurine cattle lung tissues and identified a yak-specific endothelial cell subtype. By integrating SVs and single-cell transcriptome data, we revealed that the endothelial cells expressed the highest proportion of marker genes carrying high-FST SVs in taurine cattle lungs. Furthermore, we identified pathways which were related to the medial thickness and formation of elastic fibers in yak lungs. These findings provide new insights into the high-altitude adaptation of yak and have important implications for understanding the physiological and pathological responses of large mammals and humans to hypoxia.

Date: 2022
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DOI: 10.1038/s41467-022-32164-9

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