title: F118_inocul_rep3
design: RNA was extracted from asymptomatic plants of S. commersonii between three to four days after inoculation. Root samples were collected by measuring one centimeter of root from the base of the stem, of at least seven individuals per genotype per treatment (F97 and F118, inoculated and non-inoculated controls) in each of three independent biological trials.  The amount of bacteria was estimated, samples with similar bacterial amount were pooled together and flash frozen in liquid nitrogen. Pooled root tissue from each trial was ground in liquid nitrogen using a cold mortar and a pestle. Total root RNA was extracted using the NucleSpin® RNA plant extraction kit from Macherey-Nagel following manufacturer’s instructions. Samples were treated simultaneously with rRNA removal solution from Ribo-Zero(TM) magnetic kit for plant seed/root (Epicentre) and rRNA removal solution for gram-negative bacteria (Epicentre), following manufacturer´s instructions. Briefly, 2.5 µg of total RNA from each sample was treated with both the rRNA removal solution from the plant seed/root and gram-negative bacteria kits, in a 50:50 ratio. Library was pair-ended sequenced in an Illumina-Hiseq2500 apparatus using multiplexing and the kits specially adapted to obtain 100-mer reads.