Dataset for transcriptional response of barley (Hordeum vulgare) exposed to drought and subsequent re-watering

Barley (Hordeum vulgare) is an economically important species, which can be cultivated in environmentally adverse conditions due to its higher tolerance in contrast to other cereal crops. The draft of H. vulgare genome is available already for couple of years; however its functional annotation is still incomplete. All available databases were searched to expand current annotation. The improved annotation was used to describe processes and genes regulated in transgenic lines showing higher tolerance to drought in our associated article, doi:10.1016/j.nbt.2016.01.010 (Vojta et al., 2016) [1]. Here we present whole transcriptome response, using extended annotation, to severe drought stress and subsequent re-watering in wild-type barley plants in stem elongation phase of growth. Up- and down-regulated genes fall into distinct GO categories and these enriched by stress and revitalization are highlighted. Transcriptomic data were evaluated separately for root and aerial tissues.


Specifications
Enriched gene ontology (GO) term analysis highlights processes targeted by above mentioned conditions.
The dataset can serve as a source of candidate genes for markers used for drought associated studies.

Data
This data consist of five high-throughput sequenced samples of barley roots (Supplementary  Table 1, n¼ 2) and upper part (Supplementary Table 2, n ¼3), exposed to optimal or drought conditions and subsequent re-watering, generated from an Illumina HiSeq 2500, together with GO term analysis of the most affected Biological Processes (Tables 1-3). Predicted genes from the latest genome version (082214v1.25) have been annotated based on three various databases ( Fig. 1) and associated to GO term categories (Fig. 2). Several GO terms have been assigned to each predicted sequence (Fig. 3).

Plant material
Spring barley plants, cultivar Golden Promise, were grown in a phytotron with a photoperiod of 15°C/16 h light and 12°C/8 h dark in soil or in hydroponic tanks containing aerated Hoagland nutrient solution. Samples of root tissue 4 weeks after germination were collected from hydroponically grown plants due to the inability to collect root tissues from soil without initiation of mechanical stress. The stress was applied by removing the nutrient solution off the tank. Control samples were collected just before stress induction; stressed root samples were collected 24 h later. Aerial part samples were collected from 4 week old plants cultivated in the shallow soil. Watering on daily basis was interrupted for four days and stressed samples were collected in the end of the drought period. Revitalization samples were collected 12 h after re-watering. Each sequencing library was prepared from pool of 3 individual plants.

Annotation
Additional annotation of predicted genes was mined using Blast2GO version 3.0 program to improve raw reference genome available at Ensembl (http://plants.ensembl.org/index.html, version 082214v1.25). Gene description from the National Center for Biotechnology Information database (NCBI; version b2g_Jan15) were mined using the BLAST module from program Blast2GO with parameters blastn and e-value r10 À 5 . The other step in annotation process was mapping predicted genes to other databases using Blast2GO with default parameters. Additional annotation of other predicted genes was extracted from The UniProt Knowledgebase database (http://www.uniprot.org/, version 2015_02) and the Plant Genome and Systems Biology database (PGSB; http://pgsb.helmholtzmuenchen.de/plant/, version 2014_07_31) for hits with blastn stringency of e-value r10 À 5 . Finally, annotation information was obtained for 17,885 genes from a total number of 26,072 predicted genes in Hordeum vulgare genome (Fig. 1). Gene ontology analysis was performed using the Blast2GO v.3.0 [2], firstly for all predicted genes and then specifically for significantly up-regulated and down-regulated genes with adjusted p-value (padj) r0.05. Total number of 70,719 GO terms was assigned to 20,991 predicted genes. Out of these 40.87%, 42.12% and 17.01% were assigned to Biological Processes, Molecular Function and Cellular Component GO categories, respectively (Fig. 2). Number of GO terms assigned to one predicted sequence was in range from 1 to 35 (Fig. 3). Differentially expressed genes were categorized to Biological Processes (BP), Cellular Components (CC) and Molecular Functions (MF) on the level 6. Number of differentially expressed genes for particular GO terms was compared with total number of genes assigned to the term and enriched GO terms were highlighted (Tables 1-3). Supplementary Table 2 The most affected GO terms from Biological Processes in the stressed aerial part and percentage of differentially expressed genes (adjusted p-value r 0.05) at the GO level 6.  Tables 3 and 4 contains GO terms at the level 6 with associated 10 or more genes in roots and aerial part, respectively. GO terms with associated 9 or less genes were filtered out and are not listed. GO terms are sorted due to increased percentage in category of differentially expressed genes with adjusted p-value r0.05 from total number of genes with the same assigned GO term. The 30 most affected Biological Processes are shown for stressed root (Table 1), stressed aerial part (Table 2) and the aerial part after re-watering (Table 3).

RNA-extraction and sequencing
Total RNA was extracted and cDNA sequencing library was prepared and sequenced as described elsewhere [1,3].