Evidence map›Paper›PMID 42612643›Full record

ArticleCell genomics2026

A cross-vertebrate single-cell and spatial atlas reveals evolutionary trajectories of gastrointestinal cellular innovation.

Lidong Guo, Baichuan Tong, Xiaomin Gao, Xiaodong Jia, Xiang Liu, Lei Li, Mengyang Xu, Yaolei Zhang, Jiahao Wang, Qun Liu and 28 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed
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1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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3 · Its place in the literature

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

38 authors.

Lidong GuoQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China; BGI Research, Chongqing 401329, China; Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
Baichuan TongState Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China.
Xiaomin GaoQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China; School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
Xiaodong JiaJoint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, Shandong 252000, China.
Xiang LiuQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China; Department of Biology, University of Copenhagen, 2100 Copenhagen OE, Denmark; State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266071, China.
Lei LiQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China.
Mengyang XuQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China.
Yaolei ZhangQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China; BGI Research, Chongqing 401329, China; Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
Jiahao WangQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China.
Qun LiuQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China; Department of Biology, University of Copenhagen, 2100 Copenhagen OE, Denmark.
Kai HanQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China; Department of Biology, University of Copenhagen, 2100 Copenhagen OE, Denmark.
Ruihua ZhangQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China.
Zeyu LinState Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China.
Liyan HeState Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China.
Xiao DuQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China.
Yating QinQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China.
Yue SongQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China; Department of Biology, University of Copenhagen, 2100 Copenhagen OE, Denmark.
Zengbao YuanQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China.
Xiaobin LiuQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China.
Yao LiQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China; Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hong Kong 999077, China.
Jiaxin LuoQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China.
Tao YangBGI Research, Shenzhen 518120, China; Guangdong Provincial Genomics Data Center BGl Research, Shenzhen 518120, China.
Jing ChenBGI Research, Shenzhen 518120, China; Guangdong Provincial Genomics Data Center BGl Research, Shenzhen 518120, China.
Yangyang LiQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China; Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
Xizi WangJoint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, Shandong 252000, China.
Zhaona SongJoint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, Shandong 252000, China.
Inge SeimMarine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4000, Australia.
Long ZhaoKey Laboratory of Evolution and Marine Biodiversity (Ministry of Education) and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; College of Fisheries, Ocean University of China, Qingdao 266003, China.
Bin ZhangCollege of Medical Imaging and Laboratory, Jining Medical University, Jining 272067, China.
Ruijiao ChenCollege of Medical Imaging and Laboratory, Jining Medical University, Jining 272067, China.
Baoyu HeCollege of Medical Imaging and Laboratory, Jining Medical University, Jining 272067, China.
Changwei ShaoState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong 266071, China.
Huanming YangBGI Research, Shenzhen 518120, China.
Xun XuState Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Shenzhen 518083, China.
Fengming SunKey Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China. Electronic address: sunfengming@cqmu.edu.cn.
Qingming QuState Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China. Electronic address: quqingming@xmu.edu.cn.
Songlin ChenYellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China. Electronic address: chensl@ysfri.ac.cn.
Guangyi FanQingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao 266555, China; BGI Research, Shenzhen 518120, China; College of Medical Imaging and Laboratory, Jining Medical University, Jining 272067, China; Shenzhen Key Laboratory of Marine Biology Genomics, BGI Research, Shenzhen 518083, China. Electronic address: fanguangyi@genomics.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The cellular innovations underlying vertebrate gastrointestinal diversification remain largely unknown. Here, we constructed a single-cell and spatial transcriptomic atlas comprising nearly 1 million cells from 10 species, spanning 500 million years of vertebrate evolution. Analysis of conserved gene co-expression modules shows that the repurposing of existing genetic programs, together with de novo gene emergence, drives cellular evolution. We link module remodeling to lineage-specific dynamics, including ciliated cell loss and the tuft cell emergence. Furthermore, we identify lymphoid aggregates in lungfish, suggesting that intestinal immune organization may be prior to the tetrapod lineage, and demonstrate that fish oxynticopeptic cells exhibit functional polarization that prefigures mammalian gastric specialization. Our atlas provides a global view of gastrointestinal evolution, highlighting the role of regulatory repurposing in defining organ function.

Indexed as

Biological EvolutionGastrointestinal TractSingle-Cell AnalysisVertebratesAnimalsHumansSingle-Cell Gene Expression AnalysisSpatial TranscriptomicsTranscriptomeCoRCcross-speciesgastrointestinalsingle cell

Identifiers

PMID42612643
PMCPMC13689627

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