Lamprey 3D single-cell transcriptomics reveals ancestral and specialized features of the vertebrate brain
- Haixu Wu
- Duoyuan Chen
- Jun Li
- Tao Zhou
- Zhenkun Zhuang
- Zhiwei Niu
- Zeyu Du
- Yongjie Chen
- Shunqin Chuan
- Chunyan Xu
- Xun Liao
- Xiaoyu Meng
- Jiali Lu
- Wenxue Cui
- Youning Lin
- Fubaoqian Huang
- Kuo Liao
- Yan Liu
- Tao Yang
- Jing Chen
- Hui Wang
- Zhiqiang Dong
- Longqi Liu
- Xiaodong Fang
- Xun Xu
- Qingwei Li
- Yue Pang
- Shiping Liu
- Bing Su
2026-06-18
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.