Counts of Illumina mRNA-seq reads from susceptible (S) and Ty-1 resistant (R) tomato plants mock-inoculated or infected with TYLCV-IL, its recombinant derivative TYLCV-IS76 or their combination (IL+IS76) at 10 and 30 days post inoculation (dpi).

The Illumina 100 nt paired-end reads from each library (two biological replicates per condition: pool 1 and pool 2) were mapped without (A) or with (B) mismatches to the reference sequences of the Solanum lycopersicum genome (nuclear, chloroplast and mitochondrion) and the viral genomes (IL and IS76), sorted by polarity (forward, reverse, total) and counted. The counts of plant and viral reads mapped without mismatches were then normalized per million of total reads (RPM) in each library (C).
(XLSX)