Spatially resolved transcriptomics reveals plant host responses to pathogens

Thorough understanding of complex model systems requires the characterisation of processes in different cell types of an organism. This can be achieved with high-throughput spatial transcriptomics at a large scale. However, for plant model systems this is still challenging as suitable transcriptomics methods are sparsely available. Researchers at the John Innes Centre have developed GaST-seq (Grid-assisted, Spatial Transcriptome sequencing), an easy to adopt, micro-scale spatial-transcriptomics workflow that allows to study expression profiles across small areas of plant tissue at a fraction of the cost of existing sequencing-based methods.

The researchers compare the GaST-seq method with widely used library preparation methods (Illumina TruSeq). In spatial experiments they show that the GaST-seq method is sensitive enough to identify expression differences across a plant organ. They further assess the spatial transcriptome response of Arabidopsis thaliana leaves exposed to the bacterial molecule flagellin-22, and show that with eukaryotic (Albugo laibachii) infection both host and pathogen spatial transcriptomes are obtained.

Overview of the GaST-seq workflow

a tissue sections of approximately 1 mm² size are mechanically extracted (e.g. a cross-section of a leaf) and after mRNA extraction (b) prepared into uniquely barcoded Illumina sequencing libraries. After c Illumina sequencing d transcript specific, spatial expression data can be assessed and analysed