Comprehensive transcriptional profiling of NaHCO3-stressed Tamarix hispida roots reveals networks of responsive genes.

Root tissue is the primary site of perception for stress from soil, and is the main tissue involved in stress response. Tamarix hispida is a woody halophyte that is highly tolerant to salt and drought stress, but little information available about gene expression in roots in response to abiotic stress. In this study, eight transcriptomes from roots of T. hispida treated with NaHCO3 for 0, 12, 24 and 48 h (two biological replicates were set at each time point) were built. In total, 47,324 unigenes were generated, and 6,267 differentially expressed genes (DEGs) were identified. There were 2,510, 3,690, and 2,636 genes significantly differentially expressed after stress for 12, 24 and 48 h, respectively. Co-expressed DEGs were clustered into ten classes (P < 0.001). Gene ontology enrichment analysis showed that 13 pathways were highly enriched, such as signal transduction, cell wall, phosphatase activity, and lipid kinase activity, suggesting that these pathways play important roles in the saline-alkaline response. Furthermore, the genes involved in lignin metabolic processes and biosynthesis of proline and trehalose are found closely involved in NaHCO3 stress response. This systematic analysis may provide an in-depth view of stress tolerance mechanisms in T. hispida.