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Host microenvironment in potato–Phytophthora infestans interaction revealed by single-cell spatiotemporal transcriptome

Nature Plants volume 12, pages 241–257 (2026)Cite this article

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Abstract

Late blight, caused by Phytophthora infestans (P. infestans), is one of the most destructive diseases in potato production. Yet, the interaction landscape between potato and the late blight pathogen at single-cell and spatial resolution remains elusive. Here we utilize Stereo-seq to present the spatiotemporal transcriptome atlas in potato leaves inoculated with P. infestans at single-cell resolution. We retrieve the major cell types of potato leaves, highlighting the coordination and specialization of immune responses among distinct cell types. We also conduct a comprehensive analysis to elucidate the multifaceted infection strategies employed by P. infestans to facilitate successful host colonization. Furthermore, we distinguish pathogen-targeted cells (PTCs) and surrounding PTC cells (SPCs) on the basis of pathogen distribution, thereby revealing the cellular and spatial heterogeneity of plant immune responses. Specifically, transcriptional profiling indicates that PTCs are mainly involved in cell wall reinforcement and regulation of redox homeostasis, whereas SPCs probably play a role in coordinating systemic immune signalling. Collectively, our findings elucidate a regulatory paradigm wherein PTCs and SPCs integrate with the cell-type-specific responses and dynamic expression patterns of P. infestans, orchestrating a complex and finely tuned host microenvironment during the interaction between potato and P. infestans. These findings provide a resource for advancing our understanding of the dynamic and heterogeneous nature of plant–pathogen interactions, offering novel insights to enhance crop disease resistance.

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Fig. 1: Spatiotemporal transcriptomic atlas of potato leaves infected by P. infestans at single-cell resolution.
Fig. 2: Coordination and heterogeneity of cell-type expression patterns in response to P. infestans infection.
Fig. 3: Spatial and dynamic gene expression patterns associated with the P. infestans infection process.
Fig. 4: Spatiotemporal cellular responses in PTCs and SPCs.
Fig. 5: Intercellular spatial dynamic expression patterns across leaf tissue.

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Data availability

All datasets supporting the findings of this study are available in the main text or Extended Data. All raw sequence data are available in CNSA at https://db.cngb.org/data_resources/project/CNP0007678 (ref. 99). The biological materials used in this study are available from S.D. on reasonable request. Source data are provided with this paper.

Code availability

The codes related to analysis are available in GitHub at https://github.com/jkfo002/Potato-Phytophthora-Spatial-Alts (ref. 100).

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Acknowledgements

We thank S. Raffaele, T. Zhang, X. Yang, X. Guo, K. Ye, L. Wang, F. Zhang and H. Shu for project discussion and critical comments; Y. Xia, H. Qin, J. Chen and Q. Zhong for supporting cell segmentation and database construction. This work was supported by Guangdong Major Project of Basic and Applied Basic Research (2021B0301030004), the National Natural Science Foundation of China (32488302 and 32001601), the Joint Research Program of State Key Laboratory of Agricultural and Forestry Biosecurity (SKLJRP2506), the Guangdong Provincial Genomics Data Center (2021B1212100001) and the Guangdong Laboratory of Lingnan Morden Agriculture (AGIS-ZDXM202203).

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Author notes

  1. These authors contributed equally: Yuying Li, Jichen Dai.

Authors and Affiliations

  1. State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China

    Yuying Li, Jichen Dai, Zhaonian Dong, Xuming Luo & Sanwen Huang

  2. College of Horticulture, Nanjing Agricultural University, Nanjing, China

    Jichen Dai

  3. BGI Research, Wuhan, China

    Wenwen Shao, Yingsi Cui & Xinxin Xu

  4. College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China

    Wenwen Shao

  5. BGI Research, Shenzhen, China

    Tao Yang & Xizheng Ma

  6. Guangdong Provincial Genomics Data Center, BGl research, Shenzhen, China

    Tao Yang & Xizheng Ma

  7. State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, Nanjing Agricultural University, Nanjing, China

    Liang Kong & Suomeng Dong

  8. National Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, China

    Sanwen Huang

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  1. Yuying Li
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Contributions

S.H. and S.D. conceived the project. S.H., S.D., Y.L. and J.D. designed the study. Y.L., J.D. and Z.D. performed data analyses. Y.L., J.D. and W.S. performed experiments. X.L., Y.C., X.X., T.Y., X.M. and L.K. gave technical support and conceptual advice. Y.L. and J.D. wrote the draft manuscript. Y.L., J.D., S.D. and S.H. revised the manuscript.

Corresponding authors

Correspondence to Sanwen Huang or Suomeng Dong.

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The authors declare no competing interests.

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Nature Plants thanks Doil Choi, Edouard Evangelisti and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

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.

Extended Data Fig. 2 Spatiotemporal transcriptomic atlas of mock-treated potato leaves.

a, Spatial visualization of representative marker genes from each cell type of mock-treated sample. Scale bar, 100 μm. b, Dot plots showing the expression of selected marker genes for each cell type. The dot size suggests the percentage of cells expressing the corresponding marker genes, color intensity indicates the relative expression level. c, The UMAP visualization of the unsupervised clustering results for cells from mock-treated sample, each dot represented a segmented cell and the color indicated the cell type. d, Recall and precision rates of cell type segmentation. UEC, upper epidermal cell; PMC, palisade mesophyll cell; SMC, spongy mesophyll cell; LEC, lower epidermal cell; VC, vascular related cell; GC, guard cell.

Extended Data Fig. 3 Spatiotemporal transcriptomic atlas of all samples.

a, The UMAP visualization (upper panel) and spatial visualization (lower panel) of the unsupervised clustering results for cells from each separated time point, each dot represented a segmented cell and the color indicated cluster identity. b, Statistics of UMI (left panel) and gene counts (right panel) of each cluster. 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. c, Spatial visualization of clusters showcasing the align with experimental design. Clusters were labeled as infected or non-infected based on their location within the actual P. infestans zoospore droplet-treated area. Each dot represented a segmented cell, with red, blue and green colors indicating clusters from inoculated, non-inoculated and mock regions, respectively. d, Statistics of cell number in each cluster. e, UMAP visualization presenting the clusters categorized as Inoculated, Non-inoculated and Mock-treated parts (left panel) and cell types (right panel). Each dot represented a segmented cell, red color: Inoculated cells; blue color: Non-inoculated cells; green: Mock-treated cells.

Extended Data Fig. 4 Coordination gene expression patterns responding to pathogen infection in potato leaf.

a, Bubble plot showing the enriched GO terms of the commonly upregulated (left panel) and down-regulated (right panel) genes across different cell types. The size of bubble represents the counts of genes within indicated GO terms, and the color indicated the P value adjusted with Benjamini-Hochberg method. Enrichment of GO terms were assessed using two-tailed Fisher’s exact test implemented in the clusterProfiler package. b, c, Line graph (b) and spatial visualization (c) showing the representative commonly up and down-regulated genes across different cell types. Scale bar, 100 μm. SMC, spongy mesophyll cell; UEC, upper epidermal cell; LEC, lower epidermal cell; VC, vascular related cell; PMC, palisade mesophyll cell.

Extended Data Fig. 5 Coordination gene expression patterns across all major cell types.

a, b, Line graph (a) and spatial visualization (b) showing the representative genes expression pattern across different cell types. Scale bar, 100 μm. SMC, spongy mesophyll cell; UEC, upper epidermal cell; LEC, lower epidermal cell; VC, vascular related cell; PMC, palisade mesophyll cell.

Extended Data Fig. 6 Spatial visualization of the expression patterns of P. infestans gene modules.

Spatial visualization of the expression patterns of the GHs and AAs (a), transporters (b), RxLRs and other pathogenic factors (c). Scale bar, 100 μm. GH: Glycoside Hydrolase; AA: Auxiliary Activity; RxLR: Arg-X-Leu-Arg effector.

Extended Data Fig. 7 Representative gene expression profiles associated with PTCs.

a, The images showing the NMF factors across potato leaf cells at each time point. Arrows indicate the direction of the gradients, and the color intensity in the cells reflects the loading values of the NMF factors, corresponding to the levels of gene expression in individual cells. Representative enlarged images are shown in Fig. 4c. b, Spatial visualization showing the representative genes expression pattern across infected potato leaves. The right side of the leaf indicated the inoculated side. Scale bar, 100 μm. c, The scatterplot showcasing the pseudo-temporal expression pattern of representative genes, with smooth expression curve represented by the red line.

Extended Data Fig. 8 Spatial dynamic profiles of representative clusters in potato leaves at 6hpi.

a, Neighborhood enrichment analysis between PTCs and cell clusters in spatial coordinates. Colors indicated the enrich scores. b, Heat map showing Pearson correlation coefficients between PTCs and cell clusters. The hierarchical clustering results shows in the top. c, Slingshot showing the pseudotime trajectories of the representative clusters. Each dot represented a segmented cell and colored based on clusters. d, Pseudotime trajectory analysis of representative clusters at 6 hpi. Cells are colored by pseudotime or cell type. UEC, upper epidermal cell; SMC, spongy mesophyll cell; PMC, palisade mesophyll cell; LEC, lower epidermal cell; GC, guard cell. e, Box plot showing immune scores of all major cell clusters. Colors of the box indicate the different cell clusters. 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.

Extended Data Fig. 9 Dynamic changes of gene expression pattern across potato leaves.

a, Scatter plot showing the expression patterns of StPR1, StBCB, StWRKY41, StWRKY70, StLHCA, and StLHCB at 6hpi. b, Upset plot showing a comparison of genes in two adjacent gene clusters at 6hpi related to (Fig. 5e). c, Venn diagram showing overlapping DEGs between induced expressed genes and TFs in the middle stage of the pseudotime trajectory at 6hpi. d, Scatter plot displaying the correlated expression of StWRKY75 with representative regulated genes. Cells are colored based on clusters.

Extended Data Fig. 10 StWRKY75 is induced in host microenvironment of potato leaves and contributes to resistance by modulating multi-layered pathway.

a, The representative images showing spatial visualization of StWRKY75. The white dotted lines represent the boundary between the inoculated and the non-inoculated regions as defined by the spatial distribution of zoospore droplets. Scale bar, 100 μm. b, Box plot showing the expression level of StWRKY75 in Mock, PTCs and SPCs. Pairwise comparisons within each time point were performed using two-tailed Mann-Whitney U test (ns: not significant, *P < 0.05, **P < 0.01, ***P < 0.001). c, d, Transcript levels of StWRKY75-RNAi (c) and overexpression plants (d) were measured by RT-qPCR and normalized with endogenous StELF1. Bars represent the mean ± s.d. (n = 3 biological replicates). The asterisks indicate significant differences as assessed by one-way ANOVA (with Tukey’s test) (****P < 0.0001). e, f, Relative biomass of P. infestans was determined by qPCR of P. infestans genomic DNA normalized to potato genomic DNA at 4 dpi. Bars represent the mean ± s.d. (n = 3 biological replicates). The asterisks indicate significant differences as assessed by one-way ANOVA (with Tukey’s test) (***P < 0.001, ****P < 0.0001). This experiment was repeated three times with similar results. g, h, P. infestans infection assay on StWRKY75-RNAi (g) and overexpression plants (h). Plants were photographed at 4 dpi. Scale bar, 1.5 cm. i, Volcano plot depicting the DEGs resulting from the overexpression of StWRKY75 compared with WT. j, Bulk RNA-seq of Desiree WT and StWRKY75 overexpression plants treated with water (Mock) or P. infestans strain 88069 at 12 hpi. DEGs (adjusted P < 0.05, |log2-adjusted fold change| > 1) between Desiree WT and StWRKY75 overexpression after infection are shown. k, Transcript levels of indicate genes were measured by RT-qPCR and normalized with endogenous StELF1. Bars represent the mean ± s.d. (n = 3 biological replicates). The asterisks indicate significant differences as assessed by one-way ANOVA (with Tukey’s test) (*P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001). In b–f and k, exact P values are shown in source data with 95% confidence intervals. In i and j, Adjusted P value (Benjamini-Hochberg method) was calculated with two-tailed Wald test implement in DESeq2 package.

Source data

Supplementary information

Supplementary Information

Supplementary Figs. 1–7.

Reporting Summary

Supplementary Table 1

Lists of cell type-specific expressed marker genes or cluster-specific expressed marker genes.

Supplementary Table 2

Gene lists and GO term analysis for coordinated and heterogeneous cell-type expression patterns.

Supplementary Table 3

Lists of genes for dynamic expression of P. infestans or host vesicle trafficking and CME.

Supplementary Table 4

Lists of genes for dynamic expression in PTCs and SPCs.

Supplementary Table 5

Lists of genes for intercellular spatial expression patterns across leaf tissue.

Supplementary Table 6

The cell counting used in this study.

Supplementary Table 7

Primers used in this study.

Source data

Source Data Fig. 5

Statistical source data.

Source Data Extended Data Fig. 10

Statistical source data.

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Li, Y., Dai, J., Dong, Z. et al. Host microenvironment in potato–Phytophthora infestans interaction revealed by single-cell spatiotemporal transcriptome. Nat. Plants 12, 241–257 (2026). https://doi.org/10.1038/s41477-025-02181-9

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