Lamprey 3D single-cell transcriptomics reveals ancestral and specialized features of the vertebrate brain
The lamprey occupies a pivotal position for elucidating vertebrate brain evolution. Using spatial transcriptomics and single-nucleus RNA sequencing, we generated a three-dimensional molecular atlas of the lamprey brain, identifying 209 distinct cell clusters across 14 regions. Cross-species comparisons revealed broad conservation of regional spatial architecture, defining an ancestral organizational blueprint. Within this conserved framework, however, marked lineage-specific divergence emerged. We observed extensive neuronal specialization across vertebrate lineages, accompanied by regulatory shifts associated with spatial reorganization and functional diversification of neuronal populations. Additionally, our results suggest that a cerebellum-like architecture predates the jawed vertebrate cerebellum. Together, these findings identified constraints on neural organization and detected cellular innovations driving evolutionary diversification.
Authors
- Haixu Wu
- Shiping Liu (ORCID: https://orcid.org/0000-0003-0019-619X)
- Zhenkun Zhuang (ORCID: https://orcid.org/0009-0001-5258-9203)
- Bing Su (ORCID: https://orcid.org/0000-0002-4379-9014)
- Longqi Liu (ORCID: https://orcid.org/0000-0002-5828-5542)
- Xiaodong Fang (ORCID: https://orcid.org/0000-0001-7061-3337)
- Fubaoqian Huang
- Zhiqiang Dong (ORCID: https://orcid.org/0000-0001-6259-915X)
- Yue Pang (ORCID: https://orcid.org/0000-0002-9869-2863)
- Duoyuan Chen (ORCID: https://orcid.org/0000-0001-8621-340X)
- Xun Liao (ORCID: https://orcid.org/0000-0002-6789-4358)
- Jiali Lu (ORCID: https://orcid.org/0000-0003-3493-7857)
- Zeyu Du
- Tao Yang (ORCID: https://orcid.org/0000-0003-4211-5183)
- Jun Li (ORCID: https://orcid.org/0000-0003-2845-7566)
- Jing Chen (ORCID: https://orcid.org/0000-0001-7974-3090)
- Xun Xu (ORCID: https://orcid.org/0000-0002-5338-5173)
- Ying Liu (ORCID: https://orcid.org/0000-0002-1312-0146)
- Yongjie Chen (ORCID: https://orcid.org/0000-0002-9056-0604)
- Qingwei Li (ORCID: https://orcid.org/0000-0001-5802-365X)
- H Wang
- Youning Lin (ORCID: https://orcid.org/0000-0002-0047-026X)
- Kuo Liao (ORCID: https://orcid.org/0009-0008-2473-6131)
- Chunyan Xu (ORCID: https://orcid.org/0000-0003-4095-9569)
- Xiaoyu Meng (ORCID: https://orcid.org/0000-0002-1025-3314)
- Tao Zhou (ORCID: https://orcid.org/0009-0007-5122-082X)
- Zhiwei Niu
- Wenxue Cui (ORCID: https://orcid.org/0000-0001-8656-0954)
- Shunqin Chuan
Institutions
- BGI Group (China) (CN)
- Liaoning Normal University (CN)
- Kunming Institute of Zoology (CN)
- Chinese Academy of Sciences (CN)
- Huazhong Agricultural University (CN)
- Westlake University (CN)
- State Key Laboratory of Chemical Engineering (CN)
- University of Chinese Academy of Sciences (CN)
- BGI Research (CN)
Publication Details
- Journal
- Science
- Published
- 2026-06-18
- DOI
- https://doi.org/10.1126/science.aea2535
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 0.00