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Bacterial canker of tomato ( Solanum lycopersicon ) caused by the Gram-positive bacterium  Clavibacter michiganensis  subsp.  michiganensis  ( Cmm ) is an economically important disease .  To understand the host defense response to  Cmm  infection, transcriptome sequences in tomato cotyledons were analyzed by RNA-seq. Overall, 1788 and 540 genes were upregulated and downregulated upon infection, respectively. Gene Ontology enrichment analysis revealed that genes involved in the defense response, phosphorylation, and hormone signaling were over-represented by the infection. Induced expression of defense-associated genes suggested that the tomato response to  Cmm  showed similarities to common plant disease responses. After infection, many resistance gene analogs (RGAs) were transcriptionally upregulated, including the expressions of some receptor-like kinases (RLKs) involved in pattern-triggered immunity. The expressions of  WRKYs ,  NACs ,  HSFs , and  CBP60s  encoding transcription factors (TFs) reported to regulate defense-associated genes were induced after infection with  Cmm . Tomato genes orthologous to Arabidopsis  EDS1 ,  EDS5/SID1 , and  PAD4/EDS9 , which are causal genes of salicylic acid (SA)-deficient mutants, were upregulated after infection with  Cmm . Furthermore,  Cmm  infection drastically stimulated SA accumulation in tomato cotyledons. Genes involved in the phenylalanine ammonia lyase pathway were upregulated, whereas metabolic enzyme gene expression in the isochorismate synthase pathway remained unchanged. Exogenously applied SA suppressed bacterial growth and induced the expression of  WRKYs , suggesting that some  Cmm -responsive genes are regulated by SA signaling, and SA signaling activation should improve tomato immunity against  Cmm .   Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03251-8.

Transcriptome analysis of Clavibacter michiganensis subsp. michiganensis-infected tomatoes: a role of salicylic acid in the host response