Transcriptome-based meta-analysis of drought stress regulatory genes in tomato

Plants possess various molecular defense systems to ward off biotic and abiotic stresses and adjust to environmental changes. The RNA-seq technology assists biologists in quickly identifying genes responding to abiotic stresses. Thereby, using meta-transcriptomic data from the GEO NCBI public database, we have attempted to reach a consensus on gene variations. This approach identified a global set of 18 drought-responsive genes by Bonferroni-adjusted proportional test on one sample, p < 0.05, and extensive meta-transcriptome analytics. The annotation of these differentially expressed genes identified the biological process, molecular function, cellular component, KEGG, and plant ontology terms. The terms that were found to be top-enriched (with P and Q adjusted to be < 0.05) were intracellular signal transduction (Solyc04g076810 and Solyc10g076710), ribonuclease P activity (Solyc05g054420), nucleolar ribonuclease P complex (Solyc05g054420), Glycosphingolipid biosynthesis and lateral root apical meristem (Solyc03g005227), respectively. These meta-DEGs description include CBL-interacting protein kinase 8 (biological process), phospholipase C₂ (biological process), XH/XS domain-containing protein (molecular function & cellular component), alpha 1,4-glycosyltransferase family protein (KEGG) and Histone superfamily protein (plant ontology). qRT-PCR-based gene expression analyses elaborated the similar trends in gene expression in both local genotypes under drought stress conditions covering the ratio of six to four as per down and upregulated meta-genes, respectively. This could indicate that these genes are part of a putative set of stress-responsive genes that are crucial for survival and adaptation under drought conditions thereby, they may serve as potential targets for future functional studies and breeding applications that will be helpful to enhance tomato production in the future.