Studying plant cell type-specific biology through spatial transcriptomics

Abstract

To understand a plants biological complexity, characterising different cell types can help us explain the role of each cell in a tissue, organ or whole system. A cells function can be studied effectively through the transcriptome, which is linked to cell lineage and identity. Traditional transcriptomic methods like bulk RNA-sequencing or microarrays capture the transcriptome effectively, but average gene expression across many cells and lose heterogeneity in cell behaviour based on cell type or location. Recently, single-cell RNA sequencing and spatial transcriptomic methods have been developed, making it possible to cluster cells with similar transcriptomes and retain single-cell spatial information. In the following review, I explore how spatial transcriptomics can be used to study cell type specific biology in plants. In summary, single-cell transcriptomics data has partly shifted cell type classification from a morphology and lineage-based, to a data-driven approach, revealing new complexity in clustering similar cell populations. Some technical limitations still require improved protocols, for example for cell wall permeabilization or imaging with autofluorescence. However, spatial transcriptomics provide a very promising tool to link single-cell gene expression to tissue morphology, improving our understanding of plant biology from developmental processes to plant stress responses.