Fig. 1

Expression patterns of genes upregulated in tomato cotyledon after infection with Cmm (upregulated differentially expressed genes (DEGs)). a Disease symptom of the tomato cotyledons after infection with Cmm. The values represent the number of days after inoculation. b Quantification of the bacterial biomass by measuring the amount of genomic DNA in tomato cotyledons. The amount of Cmm ptssk DNA relative to tomato COX DNA was determined by qPCR analysis. A represents cotyledons immediately after inoculation. Values are represented as means ± standard deviation for six seedlings. c Cluster analysis of upregulated DEGs; 0 dpi refers to uninoculated cotyledons. The phylogenetic tree was constructed by the unweighted pair group method with arithmetic mean analysis. Z-score-transformed relative gene expressions were visualized with a heatmap. Genes were divided into the following five clusters: low expression until 3 dpi then greatly increasing at 6 dpi (cluster 1); increased expression at 3 dpi then maintaining a high level until 6 dpi (cluster 2); increased expression at 1 dpi then maintaining a high level until 6 dpi (cluster 3), increased expression until 3 dpi then deceasing at 6 dpi (cluster 4), and increased expression at 1 dpi then decreasing at 3 dpi (cluster 5). d Time-series expression levels of genes in each cluster. Z-scored expression data are shown as gray lines. In clusters 1 and 2, the data of 50 genes were randomly selected and are shown. The average of each expression level is shown as a red line