Differentiation Trajectory of Virus-Induced Tumour Cells in Rice Revealed by Single-Cell RNA Sequencing

Many plant viruses trigger abnormal differentiation and development of host cells, causing distinct symptoms. Here, in a single-cell RNA sequence analysis, we find transcriptional heterogeneity between cells from rice leaf sheaths that are infected with rice black streaked dwarf virus (RBSDV) and from those that are virus-free. Using 106 973 cells, we construct a single-cell transcriptome atlas with 12 cell types and find that parenchyma and vascular parenchyma cells are the two major cell types affected by RBSDV. Notably, in RBSDV-infected plants, virus-induced tumours are observed to proliferate and show to differentiate from vascular parenchyma cells in a pseudotime analysis. During the differentiation of RBSDV-induced tumour cells, genes that involved in such processes as nucleosome assembly and chromatin remodeling are upregulated, and those involved in photosynthesis and energy metabolism are downregulated. A gene module of DGP1-GLK1-LHCBs that functions in regulating chloroplast development is repressed in the process of tumour cell formation. Moreover, a jasmonate-inducible pathogenesis-related gene, JiPR10, is expressed specifically in RBSDV-induced tumour cells and endows host resistance to RBSDV by inhibiting the proliferation and expansion of tumours. Our cell-type-specific atlas for plant responses to viral infection provides a valuable resource for further study of virus-induced abnormal development of host plants.