iSB09 and iCB elicit ABA-responsive gene expression in Solanum lycopersicum seedlings

To compare the genome-wide transcriptional effect of ABA and iSB09 in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 20 uM iSB09-treated plants. Differential gene expression analysis between mock- and ABA-treated or iSB09-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. iSB09 upregulated and downregulated genes represent a subset of the ABA-responsive genes, which reflects the activation of PYL1-like and PYL4-like ABA receptors in tomato seedlings. Additionally, to compare the genome-wide transcriptional effect of ABA and iCB in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 10 uM iCB-treated plants. Differential gene expression analysis between mock- and ABA-treated or iCB-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. iCB mimics ABA transcriptional response through activation of the three subfamilies of ABA receptors. S. lycopersicum seedlings (3 d.a.g.) were transferred from plates to flashes with 3 ml of liquid Murashige and Skoog (MS medium) for 8 days in a growth chamber at 22ºC under long-day conditions (16 h light/8 h dark). Before treatment, the medium was refreshed and supplemented with either 0.1% DMSO (mock) or 10 μM ABA or 20 µM iSB09 or 10 µM iCB. Samples were collected after 3 hours of incubation, and the experiment was conducted with three independent biological replicates. We performed genome-wide expression profiling analysis using data obtained from RNA-seq of the three biological replicates. Comparative analysis of transcriptional profiles using RNA-seq data for mock, iSB09, iCB or ABA treatments (WT genotype).