Infected stem 7 dpi (replicate 2)
The sample was frozen with liquid nitrogen and then pulverized using a mortar and a pestle. Total RNA was isolated from each sample using PureLink Plant RNA Reagent (Thermo Fisher Scientific) following the manufacturers protocol. RNA concentration was measured on a NanoDrop 2000c spectrophotometer (Thermo Scientific) and RNA integrity (RIN  8.5) was evaluated on an Agilent 2100 Bioanalyzer using RNA 6000 Nano-kit (Agilent Technologies). 200 ng of total RNA from each selected sample were used to generate their corresponding sequencing libraries. We used the RNA-seq method based on poly(A) selection. Using TruSeq RNA Sample Preparation Kit (Illumina) and index codes to identify each sample independently, RNA-sequencing libraries were generated in the Massive Sequencing Unit from Ecology Institute (INECOL) which offers next-generation sequencing services using Illumina Sequencing instrumentation (MiSeq FGx and NextSeq500). Multiplexed libraries were sequenced on a single flow cell of the NexSeq500 platform (Illumina) to generate 150bp paired-end reads.