De novo transcriptome assembly and variable salinity induced differential biochemical and transcript responses in Kappaphycus alvarezii, a red carrageenophyte

Kappaphycus alvarezii is an important kappa-carrageenan producer. Fluctuating environmental conditions, especially seawater salinity, significantly affect the cultivation of K. alvarezii. To assess the variable salinity-induced responses, biochemical responses and gene expressions via high throughput RNA sequencing were studied in K. alvarezii under hypo- [3.25 practical salinity units (psu)] and hyper- (65 psu) salinity conditions. Under variable salinity, the influx of Na⁺ and efflux of K⁺ ions resulted in a lower K⁺/Na⁺ ratio. Both salinity levels had differential effect on accumulation of different solutes and photosynthetic pigments. Superoxide dismutase, ascorbate peroxidase and glutathione peroxidase exhibited higher activity under stress. The RNA sequencing revealed the differential gene expression in K. alvarezii at variable salinity. In this study, 52,875 CDS were predicted, and most of these showed a match with Chondrus crispus. At hypo-salinity, 246 and 171 genes exhibited up- and down-regulation, respectively. At hyper-salinity, 457 and 1,008 exhibited up- and down-regulation, respectively. Transcriptome data revealed differential expression of genes encoding components of photosynthetic, signal transduction, fatty acid and amino acid metabolism, energy metabolism and redox homeostasis machineries under stress. Differential expression of ubiquitin-mediated proteolytic genes and heat shock proteins indicated the important role of these genes under studied strengths of salinity. The differentially expressed genes showed a correlation with biochemical responses and ion accumulation. The study identified numerous key genes regulating different metabolic pathways and antioxidant machinery. The results would facilitate insights into the molecular mechanism underlying the salinity stress adaptation in K. alvarezii and studies on the gene discoveries for subsequent strain improvement.