title: V. macrocarpon healthy
design: RNA was sent to the Novogene Corporation (Sacramento, CA) for library construction and sequencing. Three independent cDNA libraries were constructed for each treatment (uninfected and infected). Prior to library construction, all samples were tested for RNA integrity and determined to be of sufficient quality, as determined by Novogene by using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). After passing the quality-control procedures, mRNA was enriched using oligo(dT) beads. The mRNA was randomly fragmented, and the first-strand cDNA was synthesized using random hexamers and reverse transcriptase. Then, the second strand was synthesized with a custom Illumina second-strand synthesis buffer (Illumina Inc, San Diego, CA) with DNA polymerase I, dNTPs, and RNase H. The double-stranded cDNA fragments were purified, end repaired, poly-A tailed, adapter ligated, size selected, and PCR enriched. Library concentration was quantified using a Qubit 2.0 fluorometer (Invitrogen, Carlsbad, CA), then diluted to 1 ng/L before checking insert size on an Agilent 2100, and quantified to greater accuracy by quantitative PCR. Libraries were sequenced using the Illumina HiSeq platform.