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Spatially resolved transcriptomics reveals plant host responses to pathogens

By Michael Giolai, Walter Verweij, Ashleigh Lister, Darren Heavens, Iain C Macaulay, Matthew D Clark

Posted 31 Jul 2019
bioRxiv DOI: 10.1101/720086 (published DOI: 10.1186/s13007-019-0498-5)

Background 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. Here we present Grid-seq, 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. Results We compare the Grid-seq method with widely used library preparation methods (Illumina TruSeq). In spatial experiments we show that the Grid-seq method is sensitive enough to identify expression differences across a plant organ. We further assess the spatial transcriptome response of Arabidopsis thaliana leaves exposed to the bacterial molecule flagellin-22. Conclusion We show that our method can be used to identify known, rapidly flagellin-22 elicited genes, plant immune response pathways to bacterial attack and spatial expression patterns of genes associated with these pathways.

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