Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation

We performed a transcriptome analysis on the graft junction of tomato and pepper self grafts and heterografts. 50 Solanum lycopersicum (Var. M82) and 50 Capsicum anuum (var. Big Dipper) seedlings were wedge grafted. Graft junctions, consisting of 1 cm from the scion and 1 cm from the stock, were harvested at 1-day, 3-days, and 5-days post-grafting. Junctions were immediately flash frozen in liquid nitrogen, with 1 junction harvested per biological replicate and 4 biological replicates per time point. RNA was extracted using TRIzol reagent. The purified RNA was treated with DNAseI. RNA-seq libraries were constructed using 2.5 µg of total RNA per sample, isolated with the NEBNext® Poly(A) mRNA Magnetic Isolation Module, followed by the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® using NEBNext® Multiplex Oligos for Illumina®. Six libraries were pooled per lane and run as a single-end sequencing run with 101 cycles on an Illumina HiSeq 2500 at the University of Delaware Sequencing and Genotyping Center.