comparative transcriptomics of two temperate C3 bioenergy and forage grasses under water stress

Uniform potted plants of C3 bioenergy and forage grasses Dactylis glomerata and Phalaris arundinacea were grown under glasshouse conditions and subjected to drought and waterlogging stress. Over two weeks of treatment, leaf samples of treated and control plants were flash frozen in liquid nitrogen for the investigation of differentially expressed sequences involved in water stress response. Simultaneously, measurements of soil moisture, chlorophyll content, relative water content of leaves, electrolyte leakage, and biomass accumulation were taken to assess the success of the treatment regime and the physiological state of the plants. From the frozen samples, total RNA was extracted, converted into sequencing libraries using the Illumina TruSeq RNA sample preparation kit, and sequenced on an Illumina HiSeq 2000 platform. For both species, reference transcriptomes were assembled using all reads generated from treatment and control plants (Dactylis: 1 billion reads; Phalaris: 800 million reads), resulting in transcriptomes of 69274 and 60813 transcripts for Dactylis and Phalaris, respectively. The translated transcripts were annotated by a BLASTx search against the non-redundant NCBI protein database, adopting existing annotations. Differential gene expression was investigated by modified application of RoDEO the software, first described in Haiminen et al. (2014).