Single-cell transcriptomic analysis highlights specific cell types manipulated by Fusarium head blight fungus leading to wheat susceptibility

Most invading fungi can be recognized by the plant immune system and trigger host defenses, but adapted pathogens can cause susceptibility. Multicellular plants might use cell-differentiated strategies to restrict non-adapted fungi invasion and to yield adapted fungi colonization. Here, we employed single-cell RNA sequencing (scRNA-seq) to identify the responses of wheat coleoptiles to the adapted Fusarium graminearum (Fgr) and the non-adapted Fusarium oxysporum f. sp. cubense (Foc) at 1, 2, and 3 days post inoculation. We profiled the transcriptomes of over 90,000 cells and identified cell-type-specific responses of eight major cell types: stomata, epidermis, chlorenchyma, parenchyma, outer sheath, inner sheath, phloem, and procambium. Differential expression analyses indicated that the upregulation of immune pathways was compartmentalized in nonhost resistance to Foc but widespread in susceptible interaction with Fgr. Pseudotime analyses showed continuous state transitions of mesophyll cells along disease progression and that Fgr induces a state of low transcriptional activity in chlorenchyma cells.