Genome-wide characterization of the Triplophysa dalaica slc4 gene family and expression profiles in response to salinity changes

BACKGROUND: The solute carrier 4 (SLC4) gene family is involved in a variety of physiological processes in organisms and is essential for maintaining acid-base balance in the body. The slc4 genes have been extensively studied in mammals, and they play important roles in intracellular and extracellular pH regulation and in the secretion and uptake of HCO(3)(−) and other ions (Na(+) and Cl(−)) between transepithelial cells in different tissues. This study identified and characterized the entire slc4 gene family of Triplophysa dalaica. RESULTS: Fifteen slc4 genes were identified in the whole genome of Triplophysa dalaica in this study, including five copies of Na(+)-independent Cl(−)/HCO(3)(−) transporters, eight members of Na(+)-dependent HCO(3)(−) transporters, and two genes coding Na(+)-coupled borate transporters. The chromosomal location information, isoelectric points, and molecular weights of the 15 slc4 genes were analyzed. The results for gene structure, domain analysis, and phylogenetic relationships of this gene family showed that the slc4 genes (except for slc4a9, which is missing in teleosts) are significantly expanded in teleosts compared to higher vertebrates. This phenomenon suggests that the slc4 gene family played an important role in the transition from aquatic to terrestrial animals. RT-PCR results showed that different slc4 genes showed diversified expression patterns in the tissues of T. dalaica. For osmotic pressure regulating organs, slc4a1b, slc4a4b, slc4a7, and slc4a11a were highly expressed in gills. In the kidney, slc4a1a, slc4a3, and slc4a10b were highly expressed, suggesting that the slc4 genes play a specific role in the salinity adaptation of T. dalaica. Our study has deciphered the biological roles of the slc4 genes in maintaining ionic and acid-base homeostasis in teleost fishes and provides a foundation for future exploration of the highly differentiated gene family in Triplophysa. CONCLUSIONS: The results are relevant for the breeding of alkali-tolerant varieties in saline-alkali areas for aquaculture. Our findings have important implications for the adaptation process of freshwater species to saline-alkali water. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-09057-8.