• Single-nucleus and spatial tra...

*Result*: Single-nucleus and spatial transcriptomics reveal the cell populations of intercalary meristems in bamboo.

Title:
Single-nucleus and spatial transcriptomics reveal the cell populations of intercalary meristems in bamboo.
Authors:
Qin N; Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China.; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing 100102, China., Liu X; Beijing Genomics Institute Research, Beijing 102601, China.; Beijing Genomics Institute Research, Shenzhen, Guangdong 518083, China., Li S; Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China.; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing 100102, China., Sun L; Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China.; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing 100102, China., Chen C; Beijing Genomics Institute Research, Beijing 102601, China.; State Key Laboratory of Genome and Multi-omics Technologies, Beijing Genomics Institute Research, Shenzhen 518083, China., Lou W; State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210000, China., Wang X; Institute of New Bamboo and Rattan Based Biomaterials, International Centre for Bamboo and Rattan, Beijing 100102, China., Bao P; Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China.; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing 100102, China., Cao B; Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China.; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing 100102, China., Zhang H; Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China.; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing 100102, China., Gan J; Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China.; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing 100102, China., Hou Y; Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China.; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing 100102, China., Fan Z; Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China.; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing 100102, China., Liu J; Beijing Genomics Institute Research, Beijing 102601, China., Wang Y; Beijing Genomics Institute Research, Shenzhen, Guangdong 518083, China.; Shenzhen Key Laboratory of Transomics Biotechnologies, Beijing Genomics Institute Research, Shenzhen 518083, China., Yang H; Beijing Genomics Institute Research, Shenzhen, Guangdong 518083, China., Zhao H; Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China.; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing 100102, China.
Source:
Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2025 Dec 23; Vol. 122 (51), pp. e2511701122. Date of Electronic Publication: 2025 Dec 18.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: National Academy of Sciences Country of Publication: United States NLM ID: 7505876 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1091-6490 (Electronic) Linking ISSN: 00278424 NLM ISO Abbreviation: Proc Natl Acad Sci U S A Subsets: MEDLINE
Imprint Name(s):
Original Publication: Washington, DC : National Academy of Sciences
MeSH Terms:
Meristem*/genetics , Meristem*/cytology , Meristem*/growth & development , Meristem*/metabolism , Transcriptome*/genetics , Cell Nucleus*/genetics , Cell Nucleus*/metabolism , Poaceae*/genetics , Poaceae*/growth & development, Gene Expression Regulation, Plant
Grant Information:
32430072 National Natural Science Foundation of China; 32271975 National Natural Science Foundation of China; 2021YFD2201000 National Key Research and Development Program of China
Contributed Indexing:
Keywords: Moso bamboo; intercalary meristems; internode elongation; single-nucleus transcriptome; spatial transcriptome
Entry Date(s):
Date Created: 20251218 Date Completed: 20251218 Latest Revision: 20251231
Update Code:
20260130
PubMed Central ID:
PMC12745733
DOI:
10.1073/pnas.2511701122
PMID:
41410774
Database:
MEDLINE

*Further Information*

*Intercalary meristems (IcMs), specialized developmental zones that drive rapid stem elongation in monocots, exhibit distinct spatiotemporal dynamics; however, their genetic basis remains poorly understood due to their transient activity and cellular heterogeneity. Moso bamboo ( Phyllostachys edulis )-with its exceptional daily growth rates of up to 114.5 cm, prolonged IcM activity spanning 45 to 60 d, and large, accessible culm structure-provides an ideal system for building a comprehensive IcM cell atlas. Here, we integrated a chromosome-level genome assembly of Moso bamboo with a high-resolution anatomical atlas to delineate three critical developmental stages of IcM activity: the initial cell division phase (ID), the rapid cell division phase (RD), and the rapid cell elongation phase (RE). By combining single-nucleus RNA sequencing (snRNA-seq) and spatial transcriptomics, we reconstructed a dynamic single-nucleus transcriptomic continuum spanning from proliferative to elongation states. Multiomics integration, along with in situ hybridization and ultrastructural imaging, identified IcM cells as short-columnar cells adjacent to elongating ground tissue parenchyma (Gp) cells, with the IcM1 subpopulation functioning as stem-like cells essential for maintaining the proliferative capacity. Pseudotemporal trajectory analysis revealed transcriptional transitions from stem-like IcM states to differentiated Gp cells. Functional experiments revealed that clrGene008562 , a WOX2 homolog, enhances callus regeneration, indicating its potential role in promoting cell division and differentiation processes relevant to IcM development. These findings provide a comprehensive molecular and cellular framework for understanding IcM function and offer valuable multiomics resources for advancing meristem research in bamboo and other Poaceae species.*

*Competing interests statement:The authors declare no competing interest.*