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. Overall design: 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.