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Tomato is one of the most important crops for human consumption. Its production is affected by the actinomycete  Clavibacter michiganensis  subsp.  michiganensis  ( Cmm ), one of the most devastating bacterial pathogens of this crop. Several wild tomato species represent a source of natural resistance to  Cmm . Here, we contrasted the transcriptomes of the resistant wild tomato species  Solanum arcanum  LA2157 and the susceptible species  Solanum lycopersicum  cv. Ailsa Craig, during the first 24 h of challenge with  Cmm . We used three analyses approaches which demonstrated to be complementary: mapping to  S. lycopersicum  reference genome SL3.0; semi de novo transcriptome assembly; and de novo transcriptome assembly. In a global context, transcriptional changes seem to be similar between both species, although there are some specific genes only upregulated in  S. arcanum  during  Cmm  interaction, suggesting that the resistance regulatory mechanism probably diverged during the domestication process. Although  S. lycopersicum  showed enriched functional groups related to defense,  S. arcanum  displayed a higher number of induced genes related to bacterial, oomycete, and fungal defense at the first few hours of interaction. This study revealed genes that may contribute to the resistance phenotype in the wild tomato species, such as those that encode for a polyphenol oxidase E, diacyl glycerol kinase, TOM1-like protein 6, and an ankyrin repeat-containing protein, among others. This work will contribute to a better understanding of the defense mechanism against  Cmm , and the development of new control methods.

Comparative RNA-Seq Analysis Reveals Potentially Resistance-Related Genes in Response to Bacterial Canker of Tomato