Background. Salinity stress is one of the most environmental stresses in agricultural regions worldwide. Salinity inhibits shoot and root growth of various crops, which culminate in reductions in the quality and yield. It is of crucial to understand the molecular biological mechanisms of salt stress responses and defenses in order to enhance crops salt-tolerance. Sporobolomyces pararoseus is a member of marine red yeasts. Since marine red yeast has been naturally selected for its long-term survival in high-salt marine ecosystems, some unique salt-tolerant mechanism has been developed. Little research has conducted so far by considering S. pararoseus as model microorganisms to study salt stress tolerance mechanisms. A better understanding of the mechanisms mediating salt stress of S. pararoseus NGR will provide valuable information for enhancing the crops salt-tolerant via genetic engineering. Methods. S. pararoseus NGR (CGMCC 2.5280) cultures were treated with initial NaCl concentrations of 0.75 M throughout 3 days of growth period. Transcriptome analysis was performed using RNA-seq to study the differentially expressed genes (DEGs) between the NaCl-treated cells and the control cells. Metabolome analysis was performed using the LC-MS/MS untargeted metabolic profiling to study the differentially accumulated metabolites between the NaCl-treated cells and the control cells. Co-expression network analysis was carried out using the screening parameters of correlation coefficient = 0.99 and p-value = 0.01. Transcriptome analysis results were confirmed by real-time quantitative PCR (RT-qPCR). Results. After sequencing, de novo assembly and quantitative assessment, 9,533 unigenes were finally generated with an average length of 1,538 bp. A total of 3,849 DGEs were identified in NaCl-treated cultures, including 2,019 up-regulated genes and 1,830 down-regulated genes. Screening of metabolite features with untargeted metabolic profiling of all samples in NaCl-treated and control group, we characterized 4,862 compounds from the LC–MS/MS-based dataset. An integrated analysis of transcriptome and metabolome indicated that amino acid metabolism, carbohydrate metabolism, and lipid metabolism is significantly enriched in response to salt stress. Co-expression network analysis showed that 28 genes and 8 metabolites played an important role in the response of S. pararoseus NGR and defense against salt stress, which provides valuable clues for subsequent validation. Together, our results suggested that the most primary salt-tolerant mechanism of the S. pararoseus NGR is the biosynthesis of carotenoids, and torulene showed the dominated effect among them. Moreover, amino acid metabolism, carbohydrate metabolism and lipid metabolism act as its secondary salt-tolerant mechanism.
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