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Background  Leaf mold disease caused by  Cladosporium fulvum  is a serious threat affecting the global production of tomato. Cf genes are associated with leaf mold resistance, including Cf -16 , which confers effective resistance to leaf mold in tomato. However, the molecular mechanism of the Cf -16 -mediated resistance response is largely unknown.    Results  We performed a comparative transcriptome analysis of  C. fulvum -resistant (cv. Ontario7816) and  C. fulvum -susceptible (cv. Moneymaker) tomato cultivars to identify differentially expressed genes (DEGs) at 4 and 8 days post inoculation (dpi) with  C. fulvum . In total, 1588 and 939 more DEGs were found in Cf -16  tomato than in Moneymaker at 4 and 8 dpi, respectively. Additionally, 1350 DEGs were shared between the 4- and 8-dpi Cf -16  groups, suggesting the existence of common core DEGs in response to  C. fulvum  infection. The up-regulated DEGs in Cf -16  tomato were primarily associated with defense processes and phytohormone signaling, including salicylic acid (SA) and jasmonic acid (JA). Moreover, SA and JA levels were significantly increased in Cf -16  tomato at the early stages of  C. fulvum  infection. Contrary to the previous study, the number of up-regulated genes in Cf -16  compared to Cf -10  and Cf -12  tomatoes was significantly higher at the early stages of  C. fulvum  infection.    Conclusion  Our results provide new insight into the Cf-mediated mechanism of resistance to  C. fulvum , especially the unique characteristics of Cf -16  tomato in response to this fungus.

Comparative transcriptome analysis reveals the response mechanism of Cf-16-mediated resistance to Cladosporium fulvum infection in tomato