Differences in gene expression were studied after Plum pox virus (PPV, sharka disease) infection in peach GF305 leaves with and without sharka symptoms using RNA-Seq. For each sample, >80% of 100 nt paired-end (PE) Illumina reads were aligned on the peach reference genome. In the symptomatic sample, a significant proportion of reads were mapped to PPV reference genomes (1.04% compared to 0.00002% in non-symptomatic leaves), allowing for the ultra deep assembly of the complete genome of the PPV isolate used (9775 nt, missing only 11 nt at the 5' genome end). In addition, significant alternative splicing events were detected in 359 genes and a total of 12,990 single nucleotide polymorphisms (SNPs) were identified, of which 425 could be annotated. Gene ontology annotation revealed that high-ranking mRNA target genes associated with the expression of sharka symptoms are mainly related to the response to biotic stimuli, to lipid and carbohydrate metabolism and to the negative regulation of catalytic activity. A higher number of differentially expressed genes was observed in the early asymptomatic phase of PPV infection in comparison with the symptomatic phase. These early infection events were associated with an induction of genes related to pathogen resistance such as jasmonic acid, chitinases, cytokinin glucosyl transferases or Lys-M proteins. Once the virus had accumulated, the overexpression of Dicer protein 2a genes could suggest a gene silencing plant response that is suppressed by the virus HCPro and P1 proteins. These results illustrate the dynamic nature of the peach-PPV interaction at the transcriptome level and confirm that sharka symptom expression is a complex process that can be understood on the basis of changes in plant gene expression.Read less <