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Quercus suber  (cork oak) is a West Mediterranean species of key economic interest, being extensively explored for its ability to generate cork. Like other Mediterranean plants,  Q. suber  is significantly threatened by climatic changes, imposing the need to quickly understand its physiological and molecular adaptability to drought stress imposition. In the present report, we uncovered the differential transcriptome of  Q. suber  roots exposed to long-term drought, using an RNA-Seq approach. 454-sequencing reads were used to  de novo  assemble a reference transcriptome, and mapping of reads allowed the identification of 546 differentially expressed unigenes. These were enriched in both effector genes (e.g., LEA, chaperones, transporters) as well as regulatory genes, including transcription factors (TFs) belonging to various different classes, and genes associated with protein turnover. To further extend functional characterization, we identified the orthologs of differentially expressed unigenes in the model species  Arabidopsis thaliana , which then allowed us to perform  in silico  functional inference, including gene network analysis for protein function, protein subcellular localization and gene co-expression, and  in silico  enrichment analysis for TFs and  cis -elements. Results indicated the existence of extensive transcriptional regulatory events, including activation of ABA-responsive genes and  ABF -dependent signaling. We were then able to establish that a core ABA-signaling pathway involving  PP2C - SnRK2 - ABF  components was induced in stressed  Q. suber  roots, identifying a key mechanism in this species’ response to drought.

RNA-Seq and Gene Network Analysis Uncover Activation of an ABA-Dependent Signalosome During the Cork Oak Root Response to Drought