ArticleDevelopmental cell2022
A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.
Article in Developmental cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 202 papers, 1 of them a synthesis that pooled it.
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Who cites it
202 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic review of single-cell RNA sequencing applications and insights in Oryza sativa response to environmental stresses.Molecular biology reports · 2025Pooled it
- Cyclin' Through the Root: Developmental Control of Cell Cycle Progression in theAnnual review of cell and developmental biology · 2026Review
- A binding-activated CRISPR/dCas13X imaging system enables precise RNA tracking in plants.PLoS biology · 2026Article
- Advances in single-cell and spatial multi-omics for plant development and stress responses.Plant diversity · 2026Review
- Temperature regulation of cell cycle and growth dynamics in Arabidopsis.Biochemical Society transactions · 2026Review
- Integrating single-cell omic techniques to resolve the spatio-temporal complexity of arbuscular mycorrhizal symbiosis.Journal of experimental botany · 2026Review
- Longitudinal zone- and cell type-specific pattern-triggered immune responses in Arabidopsis roots.Developmental cell · 2026Article
- Dissecting root-specific non-conventional effector-triggered immunity and its role in defense and shifting the microbiome.Nature communications · 2026Article
- Novel Cell-Type-Specific Drought-Responsive Proteins in Root Tips of Field-Grown Perennial Switchgrass.ACS omega · 2026Article
- Quantitative RNA spatial profiling using single-molecule RNA FISH on plant tissue cryosections.Plant communications · 2026Article
- Single-Cell and Spatial Omics Technologies in Rice Abiotic Stress Biology: A Methodological Review.International journal of molecular sciences · 2026Review
- Sample Preparation for Imaging-Based Spatial Transcriptomics in Rigid Plant Tissues (Roots, Shoots).Bio-protocol · 2026Article
- Global StationaryOT: trajectory inference for aging time courses of single-cell snapshots.Bioinformatics (Oxford, England) · 2026Article
- GhNAC47 activates GhSKS6-mediated cell wall remodeling to promote cotton chemical defoliation.The New phytologist · 2026Article
- Cell-type specific early perception of nine phytohormones revealed by single-nucleus transcriptomics in Arabidopsis.Nature communications · 2026Article
- Tyrosine-sulfated peptide-induced flavonol biosynthesis controls elongation and differentiation in Arabidopsis primary root.The Plant cell · 2026Article
- Integrated signaling mechanisms governing root hair growth via transcriptional master regulators.The Plant journal : for cell and molecular biology · 2026Review
- Intermolecular-Interaction-Driven Adaptive Remodeling: A Network Perspective on Plant Abiotic Stress Responses.Plants (Basel, Switzerland) · 2026Review
- Single-nucleus transcriptomics resolves multiple fate dynamics between inflorescence meristem and primary stem.Science advances · 2026Article
- Arabidopsis KASH domains are differentially required for distinct LINC complex roles in stomata, roots and pollen.Journal of cell science · 2026Article
142 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
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Abstract
In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal transcriptional signatures underlying developmental trajectories. To map gene expression dynamics across root cell types and developmental time, we built a comprehensive, organ-scale atlas at single-cell resolution. In addition to estimating developmental progressions in pseudotime, we employed the mathematical concept of optimal transport to infer developmental trajectories and identify their underlying regulators. To demonstrate the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single-cell resolution, shortroot and scarecrow. We report transcriptomic and in vivo evidence for tissue trans-differentiation underlying a mixed cell identity phenotype in scarecrow. Our results support the atlas as a rich community resource for unraveling the transcriptional programs that specify and maintain cell identity to regulate spatiotemporal organ development.
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