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Nature communications
12 06, 2021;12 (1): 7083.

Single cell atlas for 11 non-model mammals, reptiles and birds.

Dongsheng Chen, Jian Sun, Jiacheng Zhu, Xiangning Ding, Tianming Lan, Xiran Wang, Weiying Wu, Zhihua Ou, Linnan Zhu, Peiwen Ding, Haoyu Wang, Lihua Luo, Rong Xiang, Xiaoling Wang, Jiaying Qiu, Shiyou Wang, Haimeng Li, Chaochao Chai, Langchao Liang, Fuyu An, Le Zhang, Lei Han, Yixin Zhu, Feiyue Wang, Yuting Yuan, Wendi Wu, Chengcheng Sun, Haorong Lu, Jihong Wu, Xinghuai Sun, Shenghai Zhang, Sunil Kumar Sahu, Ping Liu, Jun Xia, Lijing Zhang, Haixia Chen, Dongming Fang, Yuying Zeng, Yiquan Wu, Zehua Cui, Qian He, Sanjie Jiang, Xiaoyan Ma, Weimin Feng, Yan Xu, Fang Li, Zhongmin Liu, Lei Chen, Fang Chen, Xin Jin, Wei Qiu, Tianjiao Wang, Yang Li, Xiumei Xing, Huanming Yang, Yanchun Xu, Yan Hua, Yahong Liu, Huan Liu, Xun Xu
Author Information
  1. Dongsheng Chen: BGI-Shenzhen, Shenzhen, 518083, China.
  2. Jian Sun: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, 510642, China.
  3. Jiacheng Zhu: BGI-Shenzhen, Shenzhen, 518083, China.
  4. Xiangning Ding: BGI-Shenzhen, Shenzhen, 518083, China.
  5. Tianming Lan: BGI-Shenzhen, Shenzhen, 518083, China.
  6. Xiran Wang: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, 510642, China.
  7. Weiying Wu: BGI-Shenzhen, Shenzhen, 518083, China.
  8. Zhihua Ou: BGI-Shenzhen, Shenzhen, 518083, China.
  9. Linnan Zhu: BGI-Shenzhen, Shenzhen, 518083, China.
  10. Peiwen Ding: BGI-Shenzhen, Shenzhen, 518083, China. ORCID
  11. Haoyu Wang: BGI-Shenzhen, Shenzhen, 518083, China.
  12. Lihua Luo: BGI-Shenzhen, Shenzhen, 518083, China.
  13. Rong Xiang: BGI-Shenzhen, Shenzhen, 518083, China.
  14. Xiaoling Wang: BGI-Shenzhen, Shenzhen, 518083, China.
  15. Jiaying Qiu: BGI-Shenzhen, Shenzhen, 518083, China.
  16. Shiyou Wang: BGI-Shenzhen, Shenzhen, 518083, China. ORCID
  17. Haimeng Li: BGI-Shenzhen, Shenzhen, 518083, China.
  18. Chaochao Chai: BGI-Shenzhen, Shenzhen, 518083, China.
  19. Langchao Liang: BGI-Shenzhen, Shenzhen, 518083, China.
  20. Fuyu An: Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China.
  21. Le Zhang: College of Wildlife Resources Northeast Forestry University, Harbin, 150040, China.
  22. Lei Han: College of Wildlife Resources Northeast Forestry University, Harbin, 150040, China.
  23. Yixin Zhu: BGI-Shenzhen, Shenzhen, 518083, China.
  24. Feiyue Wang: BGI-Shenzhen, Shenzhen, 518083, China.
  25. Yuting Yuan: BGI-Shenzhen, Shenzhen, 518083, China.
  26. Wendi Wu: BGI-Shenzhen, Shenzhen, 518083, China.
  27. Chengcheng Sun: BGI-Shenzhen, Shenzhen, 518083, China.
  28. Haorong Lu: China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China.
  29. Jihong Wu: Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.
  30. Xinghuai Sun: Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.
  31. Shenghai Zhang: Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.
  32. Sunil Kumar Sahu: BGI-Shenzhen, Shenzhen, 518083, China. ORCID
  33. Ping Liu: BGI-Shenzhen, Shenzhen, 518083, China.
  34. Jun Xia: BGI-Shenzhen, Shenzhen, 518083, China.
  35. Lijing Zhang: BGI-Shenzhen, Shenzhen, 518083, China.
  36. Haixia Chen: BGI-Shenzhen, Shenzhen, 518083, China.
  37. Dongming Fang: BGI-Shenzhen, Shenzhen, 518083, China.
  38. Yuying Zeng: BGI-Shenzhen, Shenzhen, 518083, China.
  39. Yiquan Wu: HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892-1868, USA.
  40. Zehua Cui: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, 510642, China.
  41. Qian He: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, 510642, China.
  42. Sanjie Jiang: BGI-Shenzhen, Shenzhen, 518083, China.
  43. Xiaoyan Ma: Department of Biochemistry, University of Cambridge, Cambridge, CB21QW, UK.
  44. Weimin Feng: BGI-Shenzhen, Shenzhen, 518083, China.
  45. Yan Xu: BGI-Shenzhen, Shenzhen, 518083, China.
  46. Fang Li: Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China.
  47. Zhongmin Liu: Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai, 200120, China.
  48. Lei Chen: College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.
  49. Fang Chen: BGI-Shenzhen, Shenzhen, 518083, China.
  50. Xin Jin: BGI-Shenzhen, Shenzhen, 518083, China. ORCID
  51. Wei Qiu: Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, China.
  52. Tianjiao Wang: Institute of Special Animal and Plant Sciences (ISAPS) of Chinese Academy of Agricultural Sciences, Changchun, China.
  53. Yang Li: Institute of Special Animal and Plant Sciences (ISAPS) of Chinese Academy of Agricultural Sciences, Changchun, China.
  54. Xiumei Xing: Institute of Special Animal and Plant Sciences (ISAPS) of Chinese Academy of Agricultural Sciences, Changchun, China.
  55. Huanming Yang: BGI-Shenzhen, Shenzhen, 518083, China.
  56. Yanchun Xu: College of Wildlife Resources Northeast Forestry University, Harbin, 150040, China.
  57. Yan Hua: Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China. wildlife530@hotmail.com.
  58. Yahong Liu: National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, 510642, China. gale@scau.edu.cn.
  59. Huan Liu: BGI-Shenzhen, Shenzhen, 518083, China. liuhuan@genomics.cn. ORCID
  60. Xun Xu: BGI-Shenzhen, Shenzhen, 518083, China. xuxun@genomics.cn. ORCID
PMID: 34873160 DOI: 10.1038/s41467-021-27162-2

Abstract

The availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening of animal cells could reveal the expression patterns of viral entry genes in different hosts. However, such exploration for SARS-CoV-2 remains limited. Here, we perform single-nucleus RNA sequencing for 11 non-model species, including pets (cat, dog, hamster, and lizard), livestock (goat and rabbit), poultry (duck and pigeon), and wildlife (pangolin, tiger, and deer), and investigated the co-expression of ACE2 and TMPRSS2. Furthermore, cross-species analysis of the lung cell atlas of the studied mammals, reptiles, and birds reveals core developmental programs, critical connectomes, and conserved regulatory circuits among these evolutionarily distant species. Overall, our work provides a compendium of gene expression profiles for non-model animals, which could be employed to identify potential SARS-CoV-2 target cells and putative zoonotic reservoirs.

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MeSH Term

Angiotensin-Converting Enzyme 2
Animals
Atlases as Topic
Birds
Cell Communication
Evolution, Molecular
Gene Regulatory Networks
Host-Pathogen Interactions
Lung
Mammals
Receptors, Virus
Reptiles
SARS-CoV-2
Serine Endopeptidases
Single-Cell Analysis
Transcriptome
Viral Tropism
Virus Internalization

Chemicals

Receptors, Virus
Angiotensin-Converting Enzyme 2
Serine Endopeptidases
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

GEN: GEND000567 (Single cell atlas for mammals, reptiles and birds)
GEN: GEND000568 (Single cell atlas for mammals, reptiles and birds)
GEN: GEND000569 (Single cell atlas for mammals, reptiles and birds)
GEN: GEND000570 (Single cell atlas for mammals, reptiles and birds)
GEN: GEND000571 (Single cell atlas for mammals, reptiles and birds)
GEN: GEND000572 (Single cell atlas for mammals, reptiles and birds)
GEN: GEND000573 (Single cell atlas for mammals, reptiles and birds)
GEN: GEND000574 (Single cell atlas for mammals, reptiles and birds)
GEN: GEND000575 (Single cell atlas for mammals, reptiles and birds)
GEN: GEND000576 (Single cell atlas for mammals, reptiles and birds)

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