Deciphering transcriptomic insights into climate adaptation in Etroplus suratensis (pearl spot) under combined thermal-saline stress.

Climate change poses significant challenges to aquaculture through rising temperatures and salinity fluctuations, necessitating insights into molecular adaptation mechanisms in resilient species like pearl spot (Etroplus suratensis) which is an euryhaline fish. This study performed de novo transcriptomic profiling of gill, liver, and kidney tissues from juvenile pearl spot exposed to combined temperature (28 °C control, 31 °C intermediate, 34 °C stress) and salinity (0 ppt freshwater, 15 ppt brackishwater) treatments over 90 days in triplicate setups. Illumina NovaSeq 6000 sequencing generated 1634 million raw reads, yielding 1613 million high-quality paired-end reads post-filtering. De novo assembly produced 876,873 contigs enabling identification of 23,204 differentially expressed genes in liver, 11,190 in gill, and 8005 in kidney, revealing tissue-specific responses dominated by temperature with synergistic salinity effects. Liver exhibited robust metabolic remodelling (upregulated FASN, ACC, HK4 for lipid/glucose pathways), proteostasis (HSP70/90, HYOU1), balanced immunity (C3 downregulation, dcst1/hells upregulation), and transcription/apoptosis regulation (MafA-like, RNF2). Gill DEGs emphasized osmoregulation (Na+/K+-ATPase downregulation, Piezo2 upregulation), oxygen transport (hemoglobin subunits), and ECM remodelling. Kidney highlighted ion homeostasis (STC, CEBPD) and DNA repair. Gene Set Enrichment Analysis revealed enriched pathways including fatty acid biosynthesis (27-fold at T3L), steroid biosynthesis, arginine metabolism, and oxidative phosphorylation. Quantitative RT-PCR validation of six key DEGs confirmed RNA-seq results (R² = 0.9). These findings elucidate tissue-specific molecular signatures characterising pearl spot resilience, identifying biomarkers (HSPs, STC) for breeding climate-resilience aquaculture strains in response to environmental shifts.