Where do plants make their medicine? Mapping chemical defence one cell at a time (NOBORI_T27DTP)

When a pathogen attacks, a plant fights back with chemistry. However, not every cell uses the same defence. Our recent single-cell study revealed an unexpected division of labour in infected leaves: different groups of cells activate genes for different chemical defence pathways. Which cells take on these roles, how are they organised around infection sites, and why does this organisation matter?

This PhD will map that hidden cellular geography and ask whether it can help us discover new pathways. Most genes involved in plant specialised metabolism remain uncharacterised. Bulk tissue analyses average gene expression across whole tissues, potentially hiding pathways used by rare or transient cell states.

You will create fluorescent reporter plants (Arabidopsis thaliana) and use advanced microscopy to follow defence-pathway activation as bacteria and fungi invade. You will then analyse gene-activity and chromatin profiles from around 100,000 infected leaf nuclei, combining them with a curated catalogue of biosynthetic enzymes to identify groups of genes activated together in the same cell state. Finally, you will use multiplex genome editing, pathogen assays, and metabolomics to test what the strongest candidates make and whether they help plants resist infection.

Based at The Sainsbury Laboratory and working with the Osbourn group at the John Innes Centre, you will be trained in plant molecular biology, advanced imaging, single-cell data analysis, genome editing, plant pathology, and natural-product chemistry. The project offers a supported start with established data and methods, followed by real intellectual ownership as you choose and investigate the most promising candidate gene modules.

This PhD would suit someone curious about how plants defend themselves and keen to connect experimental biology with data analysis and chemistry. Experience in all areas is not expected; full training and day-to-day support will be provided.