Fig. 2: Exploring infection zone development at the molecular level.

a The results of sub-clustering analysis on the infection zone (clusters 5, 8, and 9). The UMAP shows the distribution of subclusters within major clusters. Bins do not belong to the infection zone are labeled as gray. Cluster 9 is circled by dotted line, illustrating its division into three subclusters. The arrowed curve indicates the developmental direction. The bar plot shows the proportion of subclusters within clusters 5, 8 and 9. The marker gene list is provided in Supplementary Data 3. b–d The pseudotime trajectories of the infection zone. The pseudotime trajectories presented in panels (b), (c), and (d) are derived using the R packages Monocle 3, Monocle 2, and Slingshot, respectively. The black lines represent the trajectories, while the arrowed black dotted lines indicate the developmental direction. The bins are color-coded to reflect the subcluster membership. The pseudotime progression obtained from Monocle 3 is displayed as an example (b). e Co-regulated modules of differentially expressed genes. The subclusters are arranged according to the developmental time. Previously investigated genes, or their orthologs, are listed on the right; genes analyzed in this study are red-colored; orthologs not assessed in this study are represented with their original names. The detailed gene list is provided in Supplementary Data 3. f The representative images of spatially visualized IZ subclusters. The main biological processes are annotated based on functional genes at each stage. g, h, n The representative images of spatially visualized LjERN1, LjEFD1 and LjNLP3. Their main expression stages are indicated by a distinct color background. i Statistics of differentially expressed genes in bulk transcriptomic analyses. ‘4 dpi’, ‘5 dpi’ and ‘6 dpi’ represent inoculated roots at indicated versus untreated roots. ‘5 vs. 4 dpi’ and ‘6 vs. 5 dpi’ represent comparison between indicated inoculated samples. The detailed gene list is provided in Supplementary Data 3. j Statistics of genes belonging to each k-means cluster in bulk transcriptomic analyses. The detailed gene list is provided in Supplementary Data 3. k Venn diagram showing the intersections of genes from indicated groups from i and j. l Line graph showing the expression of indicated genes. m Bubble plot showing the clustering expression pattern of LjLbs in the spatial transcriptomic data.