Methods for analysing spatial gene expression in plants have been limited in their throughput. Now the imaging method PHYTOMap allows the spatial expression of dozens of genes to be analysed in three-dimensional whole-mount tissue at single-cell resolution, in a transgene-free manner.
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References
Seyfferth, C. et al. Advances and opportunities of single-cell transcriptomics for plant research. Annu. Rev. Plant Biol. 1–20 (2021). A review article highlighting how single-cell transcriptomics is advancing plant research.
Nobori, T. et al. Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack. Preprint at bioRxiv https://doi.org/10.1101/2023.04.10.536170 (2023). This study integrates spatial transcriptomics and single-cell multiomics in A. thaliana leaf sections.
Rozier, F., Mirabet, V., Vernoux, T. & Das, P. Analysis of 3D gene expression patterns in plants using whole-mount RNA in situ hybridization. Nat. Protoc. 9, 2464–2475 (2014). This protocol details whole-mount RNA in situ hybridization in plants.
Wang, X. et al. Three-dimensional intact-tissue sequencing of single-cell transcriptional states. Science 361, eaat5691 (2018). A study introducing STARmap, the target amplification approach that was adopted by PHYTOMap.
Gyllborg, D. et al. Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue. Nucleic Acids Res. 48, e112–e112 (2020). This study introduces the sequence-by-hybridization method, which was adopted in PHYTOMap.
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This is a summary of: Nobori, T. et al. Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap. Nat. Plants https://doi.org/10.1038/s41477-023-01439-4 (2023).
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A tool for multiplexed spatial gene expression analysis in plant tissues. Nat. Plants 9, 1012–1013 (2023). https://doi.org/10.1038/s41477-023-01440-x
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DOI: https://doi.org/10.1038/s41477-023-01440-x
