RNA-Seq and gene network analysis uncover activation of an ABA-dependent signalosome during the cork oak root response to drought

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.This work was supported by FEDER through the Operational Competitiveness Program – COMPETE – and by national funds through the Foundation for Science and Technology – FCT – within the scope of projects SOBREIRO/0033/2009 “Cork oak ESTs Consortium – Abiotic stress: drought, salt and oxidative stresses” and PTDC/AGRGPL/118505/2010“An integrated approach to identify stress-related regulatory genes in cork oak (SuberStress).” PHC was supported by FEDER through COMPETE, and by national funds (FCT) within the scope of project “SUMOdulator” [Refs. FCOMP-01-0124-FEDER-028459 and PTDC/BIA-PLA/3850/2012]. HA was supported by the “Genomics and Evolutionary Biology” project, co-financed by North Portugal Regional Operational Programme 2007/2013 (ON.2 – O Novo Norte), under the National Strategic Reference Framework (NSRF), through the European Regional Development Fund (ERDF).