Bulk RNA-seq datasets analysis integration identifies robust drought-responsive genes and functional networks in Eucalyptus grandis

Eucalyptus grandis is a cornerstone of global forestry, yet its productivity is increasingly threatened by drought. To elucidate the core molecular mechanisms of its drought response, we conducted a meta-analysis of three independent RNA-Seq datasets. Using a rigorous bioinformatic pipeline that included a leave-one-out Jackknife validation to ensure robustness and mitigate single-study bias, we identified a high-confidence set of drought-responsive genes. Our analysis pinpointed a core set of 472 robust differentially expressed genes (DEGs), with 274 being consistently upregulated and 198 downregulated. Functional analysis revealed a clear “growth-defense” tradeoff, considering that upregulated genes were predominantly involved in protective functions, including protein folding (heat shock proteins), the synthesis of osmolytes like inositol and trehalose, and abscisic acid (ABA) signaling, while genes related to cell division, DNA replication, and cell wall biosynthesis were significantly repressed, indicating a strategic diversion of resources away from growth. Also, protein-protein interaction network analysis provided a systems-level view of this strategy, visualizing a highly interconnected module where the induction of protein repair enzymes was linked to the coordinated shutdown of the DNA replication machinery. Finally, this work provides a reliable catalog of high-priority candidate genes, including many previously uncharacterized proteins, for future functional studies and for the development of molecular markers. Specially, these findings are crucial for breeding programs aimed at enhancing drought resilience, thereby supporting the sustainability of eucalyptus forestry under climate change.