RNA-seq analysis of ABA-treated Nicotiana benthamiana seedlings
Analysis of abscisic acid (ABA) perception and signaling in crops is complicated by the multigenic nature of the PYR/PYL/RCAR ABA receptor family and the reported functional redundancy, which is a formidable challenge, particularly in polyploid plants. Therefore, few molecular genetics studies have been performed in crop species to study the contribution of ABA signaling to balance plant growth and adaptation to the environment. Our data reveal ABA-responsive genes in Nicotiana benthamiana, an allotetraploid biotech crop, and provide a molecular framework  for gene expression analyses aimed at optimizing plant growth and environmental adaptation in agriculture.  To obtain the genome-wide transcriptional effect of ABA in Nb WT plants, we performed RNA-seq studies as described in experimental procedures. Differential gene expression analysis between mock- and ABA-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 Overall design: N. benthamiana seedlings (10 d.a.g.) were transferred from plates to flashes with 2 ml of liquid Murashige and Skoog (MS medium) for ten 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. 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 and ABA treatments (WT genotype and pent1, LAB strain)