The use of transcriptomics in situ study through fish: a systematic review on pollution

Abstract Aquatic systems are the first environment to show signs of vulnerability due to the presence of pollutants presenting changes in water quality. These changes are a source of stress for aquatic organisms, including fish, which can bioaccumulate and biomagnify the substances found in their environment. In this sense, fish become the main axis to evaluate the quality of ecosystems through increasingly detailed tools such as RNA sequencing (RNA-seq) to identify metabolic pathways and genes. The objective of this systematic review was to determine the pathways and genes involved in transcriptomics studies performed in situ using fish to assess environmental contamination. It was found that contaminants can be differentiated into point or diffuse, ranging from heavy metals, endocrine disruptors, and organic compounds to those that seek to identify biomarkers by assessing the health of fish. We found 38 differentially expressed genes in common that are related to lipid and xenobiotic metabolism pathways, cell death, immune and inflammatory response, oxidative stress and hormonal signalling. In addition, we highlight the need to perform these studies in regions with a high number of fish species, such as Africa and South America, where studies are scarce or non-existent at the time of this review.