De novo transcriptome sequencing, assembly, and gene expression profiling of a salt-stressed halophyte (Salsola drummondii) from a saline habitat

Salsola drummondii is a perennial habitat-indifferent halophyte growing in saline and nonsaline habitats of the Arabian hyperarid deserts. It offers an invaluable opportunity to examine the molecular mechanisms of salt tolerance. The present study was conducted to elucidate these mechanisms through transcriptome profiling of seedlings grown from seeds collected in a saline habitat. The Illumina Hiseq 2500 platform was employed to sequence cDNA libraries prepared from shoots and roots of nonsaline-treated plants (controls) and plants treated with 1200mM NaCl. Transcriptomic comparison between salt-treated and control samples resulted in 17,363 differentially expressed genes (DEGs), including 12,000 upregulated genes (7870 in roots, 4130 in shoots) and 5363 downregulated genes (4258 in roots and 1105 in shoots). The majority of identified DEGs are known to be involved in transcription regulation (79), signal transduction (82), defense metabolism (101), transportation (410), cell wall metabolism (27), regulatory processes (392), respiration (85), chaperoning (9), and ubiquitination (98) during salt tolerance. This study identified potential genes associated with the salt tolerance of S. drummondii and demonstrated that this tolerance may depend on the induction of certain genes in shoot and root tissues. These gene expressions were validated using reverse-transcription quantitative PCR, the results of which were consistent with transcriptomics results. To the best of our knowledge, this is the first study providing genetic information on salt tolerance mechanisms in S. drummondii.