Whole-body regeneration of planarians is a natural wonder but how it occurs remains elusive. It requires coordinated responses from each cell in the remaining tissue with spatial awareness to regenerate new cells and missing body parts. While previous studies identified new genes essential to regeneration, a more efficient screening approach that can identify regeneration-associated genes in the spatial context is needed. Here, we present a comprehensive three-dimensional spatiotemporal transcriptomic landscape of planarian regeneration. We describe a pluripotent neoblast subtype, and show that depletion of its marker gene makes planarians more susceptible to sub-lethal radiation. Furthermore, we identified spatial gene expression modules essential for tissue development. Functional analysis of hub genes in spatial modules, such as plk1, shows their important roles in regeneration. Our three-dimensional transcriptomic atlas provides a powerful tool for deciphering regeneration and identifying homeostasis-related genes, and provides a publicly available online spatiotemporal analysis resource for planarian regeneration research.  

　　Publication:  

　　Nature Communications 14, 3205 (2023).  

　　https://doi.org/10.1038/s41467-023-39016-0  

　　Author:  

　　Guanshen Cui  

　　CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China  

　　China National Center for Bioinformation, Beijing, 100101, China  

　　Kangning Dong  

　　NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China  

　　School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China  

　　Jia-Yi Zhou  

　　CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China  

　　China National Center for Bioinformation, Beijing, 100101, China  

　　Shang Li  

　　NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China  

　　School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China  

　　Ying Wu  

　　CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China  

　　China National Center for Bioinformation, Beijing, 100101, China  

　　Qinghua Han  

　　NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China  

　　School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China  

　　Bofei Yao  

　　CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China  

　　China National Center for Bioinformation, Beijing, 100101, China  

　　Qunlun Shen  

　　NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China  

　　School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China  

　　Yong-Liang Zhao  

　　CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China  

　　China National Center for Bioinformation, Beijing, 100101, China  

　　University of Chinese Academy of Sciences, Beijing, China  

　　Ying Yang  

　　CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China  

　　China National Center for Bioinformation, Beijing, 100101, China  

　　Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China  

　　Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China  

　　Jun Cai  

　　CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China  

　　China National Center for Bioinformation, Beijing, 100101, China  

　　University of Chinese Academy of Sciences, Beijing, China  

　　Shihua Zhang  

　　NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China  

　　School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China  

　　Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China  

　　Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China