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Zhang R, Liu Q, Pan S, Zhang Y, Qin Y, Du X, Yuan Z, Lu Y, Song Y, Zhang M, Zhang N, Ma J, Zhang Z, Jia X, Wang K, He S, Liu S, Ni M, Liu X, Xu X, Yang H, Wang J, Seim I, Fan G. A single-cell atlas of West African lungfish respiratory system reveals evolutionary adaptations to terrestrialization. Nat Commun 2023; 14:5630. [PMID: 37699889 PMCID: PMC10497629 DOI: 10.1038/s41467-023-41309-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
The six species of lungfish possess both lungs and gills and are the closest extant relatives of tetrapods. Here, we report a single-cell transcriptome atlas of the West African lungfish (Protopterus annectens). This species manifests the most extreme form of terrestrialization, a life history strategy to survive dry periods that can last for years, characterized by dormancy and reversible adaptive changes of the gills and lungs. Our atlas highlights the cell type diversity of the West African lungfish, including gene expression consistent with phenotype changes of terrestrialization. Comparison with terrestrial tetrapods and ray-finned fishes reveals broad homology between the swim bladder and lung cell types as well as shared and idiosyncratic changes of the external gills of the West African lungfish and the internal gills of Atlantic salmon. The single-cell atlas presented here provides a valuable resource for further exploration of the respiratory system evolution in vertebrates and the diversity of lungfish terrestrialization.
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Affiliation(s)
- Ruihua Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, 266555, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, China
| | - Qun Liu
- BGI Research, 266555, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, China
- Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Shanshan Pan
- BGI Research, 266555, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, China
| | - Yingying Zhang
- BGI Research, 266555, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, China
| | - Yating Qin
- BGI Research, 266555, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, China
| | - Xiao Du
- BGI Research, 266555, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, China
- BGI Research, 518083, Shenzhen, China
| | - Zengbao Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI Research, 266555, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, China
| | - Yongrui Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China
| | - Yue Song
- BGI Research, 266555, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, China
| | | | - Nannan Zhang
- BGI Research, 266555, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, China
| | - Jie Ma
- BGI Research, 266555, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, China
| | | | - Xiaodong Jia
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, 252000, Liaocheng, Shandong, P.R. China
| | - Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, 710072, Xi'an, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China
| | - Shanshan Liu
- BGI Research, 518083, Shenzhen, China
- MGI Tech, 518083, Shenzhen, China
| | - Ming Ni
- BGI Research, 518083, Shenzhen, China
- MGI Tech, 518083, Shenzhen, China
| | - Xin Liu
- BGI Research, 518083, Shenzhen, China
| | - Xun Xu
- BGI Research, 518083, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, 518083, Shenzhen, China
| | | | - Jian Wang
- BGI Research, 518083, Shenzhen, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China.
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, 4000, Australia.
| | - Guangyi Fan
- BGI Research, 266555, Qingdao, China.
- Qingdao Key Laboratory of Marine Genomics, BGI Research, 266555, Qingdao, China.
- BGI Research, 518083, Shenzhen, China.
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