title: Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq.
abstract: BACKGROUND
  Arundo donax L. (Poaceae) is considered one of the most promising energy crops in the Mediterranean region because of its high biomass yield and low input requirements, but to date no information on its transcriptional responses to water stress is available.
  
  
  RESULTS
  We obtained by Illumina-based RNA-seq the whole root and shoot transcriptomes of young A. donax plants subjected to osmotic/water stress with 10 and 20 % polyethylene glycol (PEG; 3 biological replicates/organ/condition corresponding to 18 RNA-Seq libraries), and identified a total of 3034 differentially expressed genes. Blast-based mining of stress-related genes indicated the higher responsivity of roots compared to shoots at the early stages of water stress especially under the milder PEG treatment, with a majority of genes responsive to salt, oxidative, and dehydration stress. Analysis of gene ontology terms underlined the qualitatively different responses between root and shoot tissues. Among the most significantly enriched metabolic pathways identified using a Fisher's exact test with FDR correction, a crucial role was played in both shoots and roots by genes involved in the signaling cascade of abscisic acid. We further identified relatively large organ-specific differences in the patterns of drought-related transcription factor AP2-EREBP, AUX/IAA, MYB, bZIP, C2H2, and GRAS families, which may underlie the transcriptional reprogramming differences between organs. Through comparative analyses with major Poaceae species based on Blast, we finally identified a set of 53 orthologs that can be considered as a core of evolutionary conserved genes important to mediate water stress responses in the family.
  
  
  CONCLUSIONS
  This study provides the first characterization of A. donax transcriptome in response to water stress, thus shedding novel light at the molecular level on the mechanisms of stress response and adaptation in this emerging bioenergy species. The inventory of early-responsive genes to water stress identified could constitute useful markers of the physiological status of A. donax and be a basis for the improvement of its productivity under water limitation. The full water-stressed A. donax transcriptome is available for Blast-based homology searches through a dedicated web server (http://ecogenomics.fmach.it/arundo/).
authors.affiliation: Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Trento Italy.|Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona, Italy.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Fu
authors.affiliation: Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Trento Italy.|Dipartimento di Scienze Agrarie, Università di Bologna, Bologna, Italy.
authors.forename: Michele
authors.initials: M
authors.lastname: Poli
authors.affiliation: Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Trento Italy.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Sablok
authors.affiliation: Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Trento Italy.|Centro di Biologia Integrata (CIBIO), University of Trento, Trento, Italy.
authors.forename: Bo
authors.initials: B
authors.lastname: Wang
authors.affiliation: College of Computer Science and Technology, Jilin University, Changchun, China.
authors.forename: Yanchun
authors.initials: Y
authors.lastname: Liang
authors.affiliation: Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Trento Italy.|MOUNTFOR Project Centre, European Forest Institute, Via E. Mach 1, 38010 San Michele all'Adige, Trento Italy.
authors.forename: Nicola
authors.initials: N
authors.lastname: La Porta
authors.affiliation: Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Trento Italy.|Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria.
authors.forename: Violeta
authors.initials: V
authors.lastname: Velikova
authors.affiliation: The National Research Council of Italy (CNR), Department of Biology, Agriculture and Food Sciences, Rome, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Loreto
authors.affiliation: Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Trento Italy.
authors.forename: Mingai
authors.initials: M
authors.lastname: Li
authors.affiliation: Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Trento Italy.
authors.forename: Claudio
authors.initials: C
authors.lastname: Varotto
keywords: Abscisic acid (ABA) signaling; Arundo donax; Conserved drought-responsive genes; Osmoregulatory proline metabolism; Poaceae; RNA-Seq; Transcription factors; Water stress