ArticleNature communications2022
A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed.
- Decoding the landscape of cell-type-specific co-expressed transcription factors in soybean.Nature plants · 2026Article
- Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026Review
- The role of geometry in morphogenesis.Development (Cambridge, England) · 2026Review
- Single-nucleus transcriptomics resolves multiple fate dynamics between inflorescence meristem and primary stem.Science advances · 2026Article
- Spatial and single-cell transcriptomics uncover brassinosteroid-mediated coordination of sepal elongation in Arabidopsis.Genome biology · 2026Article
- Review
- Atlas-based spatiotemporal MRI phenotyping of 3D fungal spread in grapevine wood.Plant phenomics (Washington, D.C.) · 2026Article
- Cellular Heterogeneity and Developmental Dynamics of Aril in Papaya.International journal of molecular sciences · 2026Article
- Single-nucleus and spatial transcriptomics reveal the cell populations of intercalary meristems in bamboo.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Large-scale single-cell profiling of stem cells identifies redundant regulators of shoot development and yield trait variation.Developmental cell · 2025Article
- Single-cell transcriptome atlas unveils transcriptional regulation networks of banana root tips in response toHorticulture research · 2025Article
- Evolution of petal patterning: blooming floral diversity at the microscale.The New phytologist · 2025Review
- Spatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organisms.Nucleic acids research · 2025Article
- Brassinosteroids mediate proper coordination of sepal elongation.bioRxiv : the preprint server for biology · 2025Article
- Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics.The New phytologist · 2025Article
- Strigolactones optimise plant water usage by modulating vessel formation.Nature communications · 2025Article
- Investigating biological nitrogen fixation via single-cell transcriptomics.Journal of experimental botany · 2025Review
- Orthologous marker groups reveal broad cell identity conservation across plant single-cell transcriptomes.Nature communications · 2025Article
- CUC/auxin patterning of decanalised petal number inQuantitative plant biology · 2025Article
- Single-cell transcriptomic and cell‑type‑specific regulatory networks in Polima temperature-sensitive cytoplasmic male sterility of Brassica napus L.BMC plant biology · 2024Article
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11 authors.
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Abstract
Cellular heterogeneity in growth and differentiation results in organ patterning. Single-cell transcriptomics allows characterization of gene expression heterogeneity in developing organs at unprecedented resolution. However, the original physical location of the cell is lost during this methodology. To recover the original location of cells in the developing organ is essential to link gene activity with cellular identity and function in plants. Here, we propose a method to reconstruct genome-wide gene expression patterns of individual cells in a 3D flower meristem by combining single-nuclei RNA-seq with microcopy-based 3D spatial reconstruction. By this, gene expression differences among meristematic domains giving rise to different tissue and organ types can be determined. As a proof of principle, the method is used to trace the initiation of vascular identity within the floral meristem. Our work demonstrates the power of spatially reconstructed single cell transcriptome atlases to understand plant morphogenesis. The floral meristem 3D gene expression atlas can be accessed at http://threed-flower-meristem.herokuapp.com .
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