Spatially resolved transcriptomics reveals plant host responses to pathogens

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.

Data and Resources

Additional Info

Field Value
Author Giolai, Michael
Last Updated November 20, 2019, 16:52 (UTC)
Created November 4, 2019, 17:57 (UTC)
Article Host Type publisher
Article Is Open Access true
Article License Type cc-by
Article Version Type publishedVersion
Citation Report https://scite.ai/reports/10.1186/s13007-019-0498-5
DOI 10.1186/s13007-019-0498-5
Date Last Updated 2019-10-31T19:05:05.276904
Evidence open (via page says license)
Funder code(s) Biotechnology and Biological Sciences Research Council (BB/J004669/1, BB/CSP17270/1, BB/M011216/1, BB/J010375/1)
Journal Is Open Access true
Open Access Status gold
PDF URL https://plantmethods.biomedcentral.com/track/pdf/10.1186/s13007-019-0498-5
Publisher URL https://doi.org/10.1186/s13007-019-0498-5