Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap

Tatsuya Nobori, Marina Oliva, Ryan Lister, Joseph R Ecker

Research output: Contribution to journalArticlepeer-review

34 Citations (Web of Science)

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.

Original languageEnglish
Pages (from-to)1026-1033
Number of pages8
JournalNature Plants
Volume9
Issue number7
Early online date12 Jun 2023
DOIs
Publication statusPublished - Jul 2023

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