Fig. 2

KEGG pathway enrichment analysis of differentially expressed genes (DEGs) in the lettuce cultivars Green Towers (GT) and Lollo Rossa (LR) at 1- and 7-days post inoculation (DPI) with Salmonella enterica ser. Typhimurium 14028s or Escherichia coli O157:H7. Pathway coverage ratio corresponds to the number of DEGs mapped to a KEGG pathway divided by the total number of genes comprising that KEGG pathway. To map the genes to the metabolic pathways, the protein sequences of the corresponding annotated genome were used to obtain the KEGG protein IDs using the KofamKOALA BLAST tool (https://www.genome.jp/tools/kofamkoala/). Protein sequences with an E-value < 1 × 10^− 5 (Dataset S1) were used as input for the KEGG Mapper Reconstruct Pathway tool (https://www.kegg.jp/kegg/tool/map_pathway.html). Mapped KEGG metabolic categories are listed on the right. Enrichment analysis was conducted with the hypergeometric test and significantly enriched pathways are marked with *, where * = p < 0.5; ** = p < 0.01; *** = p < 0.001