Spatially resolved transcriptomics reveals plant host responses to pathogens

Giolai, Michael, Verweij, Walter, Lister, Ashleigh, Heavens, Darren, MacAulay, Iain and Clark, Matthew D. (2019) Spatially resolved transcriptomics reveals plant host responses to pathogens. Plant Methods, 15 (1). ISSN 1746-4811

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Abstract

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 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. Results: We compare the GaST-seq method with widely used library preparation methods (Illumina TruSeq). In spatial experiments we show that the GaST-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, and show that with eukaryotic (Albugo laibachii) infection both host and pathogen spatial transcriptomes are obtained. 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.

Item Type:	Article
Additional Information:	Funding Information: This work was strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC), Institute Strategic Programme Grant (BB/ J004669/1) at the Earlham Institute (formerly The Genome Analysis Centre, Norwich), a BBSRC National Capability Grant (BB/J010375/1), a BBSRC Core Strategic Programme Grant (BB/CSP17270/1), a BBSRC DTP Studentship Award (BB/M011216/1) and by the Natural History Museum. Publisher Copyright: © 2019 The Author(s).
Uncontrolled Keywords:	biotic interaction,flare,flg22,gast-seq,oomycete,pamp,plant defence response,plant immunity,rna-seq,spatial transcriptomics,transcriptome landscape,transcriptomics,biotechnology,genetics,plant science ,/dk/atira/pure/subjectarea/asjc/1300/1305
Faculty \ School:	Faculty of Science > School of Biological Sciences
Related URLs:	http://www.scopus.com/inward/record.url?...
Depositing User:	LivePure Connector
Date Deposited:	01 Nov 2022 16:30
Last Modified:	01 Nov 2022 16:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/89488
DOI:	10.1186/s13007-019-0498-5

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