ArticleNature plants2023
Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap.
Article in Nature plants, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward.The Plant cell · 2026Review
- Problems With GO Enrichment as an Endpoint for Ecological Omics Interpretation.Molecular ecology · 2026Article
- 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
- Quantitative RNA spatial profiling using single-molecule RNA FISH on plant tissue cryosections.Plant communications · 2026Article
- DeSpaST: deconvoluting spatial transcriptomics signals to cell-level resolution using histology images.Briefings in bioinformatics · 2026Article
- Genetic regulation of stem elongation and thickening in ornamental plants: a review.Horticulture research · 2026Article
- Review
- Integrated single cell transcriptomics analysis for unraveling heterogeneity and plasticity of root cells for sustainable and regenerative agriculture.Frontiers in plant science · 2026Review
- Plant-Compatible Xenium In Situ Sequencing: Protocol for Spatial Transcriptomics in Medicago truncatula Roots and Nodules.Methods in molecular biology (Clifton, N.J.) · 2026Article
- RNA tomography reveals spatial gene expression maps of Arabidopsis thaliana roots infected with Heterodera schachtii.The New phytologist · 2026Article
- Why "Where" Matters as Much as "How Much": Single-Cell and Spatial Transcriptomics in Plants.International journal of molecular sciences · 2025Review
- FX-Cell: a method for single-cell RNA sequencing on difficult-to-digest and cryopreserved plant samples.Nature methods · 2025Article
- Single-Cell Omics in Legumes: Research Trends and Applications.Plants (Basel, Switzerland) · 2025Review
- Genomics-assisted breeding for designing salinity-smart future crops.Plant biotechnology journal · 2025Review
- Exploring the untapped potential of single-cell and spatial omics in plant biology.The New phytologist · 2025Review
- A timeline of discovery and innovation in Arabidopsis.The Plant cell · 2025Article
- Deep-tissue transcriptomics and subcellular imaging at high spatial resolution.Science (New York, N.Y.) · 2025Article
- A space for time. Exploring temporal regulation of plant development across spatial scales.The Plant journal : for cell and molecular biology · 2025Review
- Rearranging development makes a slippery slope: a commentary on 'Carnivorous Nepenthes pitcher plants combine common developmental processes to make a complex epidermal trapping surface'.Annals of botany · 2025Article
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Abstract
Retrieving the complex responses of individual cells in the native three-dimensional tissue context is crucial for a complete understanding of tissue functions. Here, we present PHYTOMap (plant hybridization-based targeted observation of gene expression map), a multiplexed fluorescence in situ hybridization method that enables single-cell and spatial analysis of gene expression in whole-mount plant tissue in a transgene-free manner and at low cost. We applied PHYTOMap to simultaneously analyse 28 cell-type marker genes in Arabidopsis roots and successfully identified major cell types, demonstrating that our method can substantially accelerate the spatial mapping of marker genes defined in single-cell RNA-sequencing datasets in complex plant tissue.
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