Extended Data Fig. 1: Experimental design and Stereo-Seq at single-cell resolution.

a, Inoculation of potato leaves with P. infestans strain 88069td. Morphological observations of P. infestans at different developmental stages. c: cyst; gt: germ tube; a: appressorium; h: haustoria; m: mycelium. Scale bars presented in each time point. All images are representative of results repeated three times with similar results. b, Representative images showing fluorescent brightener (FB) staining of the plant cell walls (left panel) and Qubit ssDNA staining of oligonucleotide (right panel) on the chip to visualize cell-cell boundary. All images are representative of results repeated four times with similar results. c, Representative images showing single-cell segmentations based on the cell wall boundary and nucleus. Purple dots represent the corresponding leaf cells as showing in this paper. d, Statistics of cell numbers (left panel), gene counts (middle panel) and UMI (right panel) of each cell type. UEC, upper epidermal cell; PMC, palisade mesophyll cell; SMC, spongy mesophyll cell; LEC, lower epidermal cell; GC, guard cell; VC, vascular related cell. The box plots displaying the 25th to 75th percentiles, with a center line representing the median and whiskers extending to the minimum and maximum values within 1.5 times the interquartile range. The sample sizes for these box plots are provided in Supplementary Table 6. e, Spatial visualization of all leaf samples at four time points classified by cell type. Each dot represented a segmented cell and the color indicated cell type.