Genome-wide identification and expression profiling of Na-K-Cl cotransporter 1 gene (Slc12a2) in Hilsa Shad across marine-freshwater transition.

The Hilsa Shad is an anadromous fish of major ecological and economic importance in Bangladesh. It migrates between marine and freshwater environments and faces substantial osmotic challenges. There is limited research on osmoregulatory gene expression during migration across diverse habitats. This study provides the first genome-wide identification of the Slc12a2 gene in Hilsa Shad and confirms the existence of two Slc12a2 gene paralogs. To evaluate their potential role in salinity adaptation, we further examined their expression across contrasting habitats. The Bay of Bengal where the fish originates, the genome-wide expression of Slc12a2 has not yet been investigated. The Surma River has been identified as a significant freshwater habitat for Hilsa Shad. However, the molecular information including gene expression data has not yet been reported for this population. In this study, RT-qPCR was used to analyze gill, kidney, liver, and muscle tissues of Hilsa Shad. The results showed that both Slc12a2 paralogs were significantly down-regulated during upstream migration from the Bay to Bengal to the Surma River. These findings demonstrate the essential role of Slc12a2 in maintaining osmotic balance during habitat transition. This genome-wide approach also gives an overall picture of how multiple Slc12a2 gene copies respond to environmental salinity changes and regulate homeostasis.