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/).

Keywords: Abscisic acid (ABA) signaling; Arundo donax; Conserved drought-responsive genes; Osmoregulatory proline metabolism; Poaceae; RNA-Seq; Transcription factors; Water stress.

Fig. 1

Summary of DEGs in shoots and roots of A. donax upon drought stress. a Number of genes up-/down-regulated by drought stress under different conditions (MC mild water stress vs. control, SC severe water stress vs. control, SM severe water stress vs. mild water stress.) in root and shoot. b Total number of DEGs in common between root and shoot. c Number of regulated genes between different conditions. Gray bar down-regulated genes; black bar up-regulated genes

Fig. 2

Distribution of stress-related functional categories of DEGs. Stress-related functional categories are identified by annotation of A. donax putative homologs in of Arabidopsis genes from ASPRGDB. Data are sorted by number of shoot DEGs. Black bar root DEGs; gray bar shoot DEGs

Fig. 3

Venn diagram of significantly enriched GOs. The GO terms which were overrepresented under different conditions have been slimmed by REVIGO, and compared by category: a molecular function; b biological process. MC mild water stress vs. control, SC severe water stress vs control; SM severe water stress vs. mild water stress

Fig. 4

Distribution KEGG Pathways for DEGs in shoot and root. Data are sorted by number of root DEGs mapping to KEGG pathways. Black bar root DEGs; gray bar shoot DEGs

Fig. 5

Distribution of transcription factors responsive to water stress in A. donax. Data are sorted by number of root DEGs. Only categories with more than 3 DEGs identified as transcription factors are shown. Black bar root DEGs; gray bar shoot DEGs

Fig. 6

Drought response genes comparison across A. donax, rice, foxtail, and sorghum. The Venn diagram represents putative orthologs of A. donax stress-responsive genes identified by OrthoMCL in at least two species