Eruca seeds of PI 426649 and PI 426652 originally from the Agricultural Research Service, USDA were germinated on filter paper immersed in liquid MS medium [87 (link)] without sugar or organic components. Seven days later the seedlings were treated for 10 h with 20% PEG-6000/liquid MS and then harvested and frozen imediately in liquid nitrogen and then stored at − 80 °C. Drought-tolerant PI 426649 is denoted as ‘DT and Drought-sensitive PI 426652 is denoted as ‘DS’. Treatment with liquid MS medium is denoted as ‘MS’ while treatment with PEG is denoted as ‘PEG’. Four samples (DT-MS, DT-PEG, DS-MS, DS-PEG) each with two biological replicates were taken for the present study. Total RNA was isolated from the whole seedlings that had been stored at − 80 °C by using TRIZOL total RNA extraction reagent (TAKARA) according to the manufacturer’s protocol. RNA integrity was verified by 1.5% Agrose gel electrophoresis and confirmed using a 2100 Bioanalyzer analyzer (Agilent, CA, USA). The mRNA enrichment, RNA fragmentation, the first and second strand cDNA synthesis and purfying, sequencing adaptors ligation and PCR amplification were performed as described [14 (link)]. The libraries were applied to Illumina sequencing platform (HiSeq 2000, SanDiego, CA, USA) for high-throughput sequencing using a paired-end read protocol with 100 bp of data collected per run.
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