Bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), is the most dangerous bacterial disease for Prunus. 'Redkist' peach variety is spot resistant whereas 'J.H. Hale' is susceptible. In order to characterize the molecular mechanisms underlying the incompatible and the compatible interaction between peach and Xap, we performed RNA sequencing for differential gene expression profiling on both varieties during very-early phases of interaction: 30 min, 1 h, 3h post-infection (hpi). Over 550 million reads provided an extensive view on the defense responses in both genotypes. RNA-Seq analysis detected 20,837 expressed genes in leaf, representing 75% of peach predicted genes. A total of 803 and 838 differentially expressed genes (DEGs) were identified as spot responsive genes in 'Redkist' and 'J.H. Hale' respectively during all the time points. The former regulated 88.9% of DEGs at 3 hpi while the latter only 53.4%. Both varieties induced genes involved in signal transduction, hormone biosynthesis, secondary metabolism, ROS burst, defense proteins, transcription factors. Also, GO term enrichment analysis resulted in terms including ‘immune system process’, ‘defense response’, ‘cell death’. Finally, the validation by Q-PCR confirmed the relative gene expression to be consistent with RNA-Seq data analysis. This study revealed very similar molecular responses to Xap in 'Redkist' and 'J.H. Hale' after bacterial infection and are consistent with previous studies. Between the two, crucial differences were detected in the expression of transcription factors, salicylic acid biosynthetic genes, and ROS burst, shedding light on the effective disease response exerted by a resistant host relative to a susceptible
