Recent advances in transcriptome research in fishes: A review

Transcriptomic studies have allowed researchers to examine gene activity across the genome and gain insight into many areas of fish biology. This review, following PRISMA guidelines, synthesizes recent studies on fish development, aquaculture, physiology, immunity, nutrition, toxicology, and evolution. It also compares the species studied and the methods used and highlights the biological pathways involved. We reviewed studies that used transcriptomic profiles to trace molecular pathways involved in development, reproduction, and sex differences in farmed fish. Physiological stress studies found that temperature, low oxygen, salinity, pH, and crowding were common stressors. They also showed how these conditions changed gene activity in fish. In immunity and nutrition studies, transcriptomic analyses revealed how fish responded to bacterial challenges and how functional feed additives affected those responses. Toxicology studies linked contaminants to target organs, altered biological pathways, and biomarkers. Finally, transcriptomic data helped researchers distinguish populations, measure evolutionary distances, and identify conserved genes associated with trait differences. Together, these findings show how transcriptomics can help us understand species biology, improve aquaculture, and guide conservation. They also point to gaps that future research should address.