Identification of salt-responsive genes using transcriptome analysis in Dunaliella viridis

Dunaliella viridis is one of the most salt-tolerant eukaryotes and a model organism to study plant adaptation to salinity. To explore the molecular mechanisms mediating salt stress response in D. viridis, transcriptome analysis was performed by high-throughput sequencing. A total of 2242 differentially expressed genes (DEGs) were obtained, including 1563 upregulated and 679 downregulated, in plants after 6 h of salt stress (S_6h) compared with the control (Con); 394 DEGs, including 159 upregulated and 235 downregulated, in plants after 1 h of salt stress (S_1h) compared with the control; and 1379 DEGs, including 471 upregulated and 908 downregulated, in S_6h compared with S_1h. GO and KEGG analyses revealed that these DEGs were enriched in biological processes such as metabolism, genetic information transmission, signal transduction, and material transport. Further gene expression analysis and functional annotation showed that genes involved in photosynthesis were induced under salt stress. Ornithine decarboxylase and S-adenosylmethionine decarboxylase involved in polyamine synthesis and metabolism were significantly upregulated. Synthesis of molecules involved in cell cycle regulation such as G1-S phase transition protein, cyclin, and cyclin-dependent kinase was induced under salt stress. Ubiquitin, ubiquitin conjugatase, and 26S proteasome regulatory subunit were significantly different in S_6h vs._S_1h (P < 0.01). We also found that calmodulin (CaM), calcium-calmodulin dependent protein kinase (CaMK), calcium-calmodulin dependent protein kinase kinase (CaMKK), and cGMP-dependent protein kinase genes were significantly upregulated. These results indicate that calcium messenger pathway and cGMP signaling pathway play important roles in salt stress response in D. viridis. Quantitative real-time PCR (qRT-PCR) was used to validate the high-throughput sequencing, and the expression patterns of ten randomly selected genes under salt stress at different time points were further analyzed.