Spatiotemporal transcriptome atlas reveals gene regulatory patterns during the organogenesis of the rapid growing bamboo shoots

• Published in: The New phytologist Vol. 244; no. 3; pp. 1057 - 1073
• Main Authors: Guo, Jing, Luo, Dan, Chen, Yamao, Li, Fengjiao, Gong, Jiajia, Yu, Fen, Zhang, Wengen, Qi, Ji, Guo, Chunce
• Format: Journal Article
• Language: English
• Published: England Wiley Subscription Services, Inc 01.11.2024
• Subjects: Bamboo; bamboos; Cell differentiation; Cell Nucleus - genetics; Cell Nucleus - metabolism; Developmental stages; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; gene regulatory network; Gene sequencing; Genes; Genes, Plant; Genetic analysis; Genomic analysis; genomics; Growth rate; Hormones; Landscape architecture; Liliopsida; Lipid metabolism; Lipids; Meristem - genetics; Meristem - growth & development; Meristems; Metabolism; Molecular modelling; Molecular structure; Moso bamboo; Nuclei (cytology); Nucleus; Organogenesis; Organogenesis - genetics; Organogenesis, Plant - genetics; Parenchyma; Pattern analysis; Plant Shoots - genetics; Plant Shoots - growth & development; Plant tissues; Sasa - genetics; Sasa - growth & development; Shoots; single‐nucleus transcriptome; Spatial analysis; spatial transcriptome; Spatio-Temporal Analysis; Time Factors; transcriptome; Transcriptome - genetics; Transcriptomes; transcriptomics; Vascular tissue; Moso bamboo; spatial transcriptome; single‐nucleus transcriptome; organogenesis; gene regulatory network
• ISSN: 0028-646X; 1469-8137; 1469-8137
• DOI: 10.1111/nph.20059

Summary Bamboo with its remarkable growth rate and economic significance, offers an ideal system to investigate the molecular basis of organogenesis in rapidly growing plants, particular in monocots, where gene regulatory networks governing the maintenance and differentiation of shoot apical and intercalary meristems remain a subject of controversy. We employed both spatial and single‐nucleus transcriptome sequencing on 10× platform to precisely dissect the gene functions in various tissues and early developmental stages of bamboo shoots. Our comprehensive analysis reveals distinct cell trajectories during shoot development, uncovering critical genes and pathways involved in procambium differentiation, intercalary meristem formation, and vascular tissue development. Spatial and temporal expression patterns of key regulatory genes, particularly those related to hormone signaling and lipid metabolism, strongly support the hypothesis that intercalary meristem origin from surrounded parenchyma cells. Specific gene expressions in intercalary meristem exhibit regular and dispersed distribution pattern, offering clues for understanding the intricate molecular mechanisms that drive the rapid growth of bamboo shoots. The single‐nucleus and spatial transcriptome analysis reveal a comprehensive landscape of gene activity, enhancing the understanding of the molecular architecture of organogenesis and providing valuable resources for future genomic and genetic studies relying on identities of specific cell types.