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Background  Salinity is an important abiotic stress that influences the physiological and metabolic activity, reproduction, growth and development of marine fish. It has been suggested that half-smooth tongue sole ( Cynoglossus semilaevis ), a euryhaline fish species, uses a large amount of energy to maintain osmotic pressure balance when exposed to fluctuations in salinity. To delineate the molecular response of  C. semilaevis  to different levels of salinity, we performed RNA-seq analysis of the liver to identify the genes and molecular and biological processes involved in responding to salinity changes.    Results  The present study yielded 330.4 million clean reads, of which 83.9% were successfully mapped to the reference genome of  C. semilaevis . One hundred twenty-eight differentially expressed genes (DEGs), including 43 up-regulated genes and 85 down-regulated genes, were identified. These DEGs were highly represented in metabolic pathways, steroid biosynthesis, terpenoid backbone biosynthesis, butanoate metabolism, glycerolipid metabolism and the 2-oxocarboxylic acid metabolism pathway. In addition, genes involved in metabolism, osmoregulation and ion transport, signal transduction, immune response and stress response, and cytoskeleton remodeling were affected during acclimation to low salinity. Genes  acat2 ,  fdps ,  hmgcr ,  hmgcs1 ,  mvk ,  pmvk ,  ebp ,  lss ,  dhcr7 , and  dhcr24  were up-regulated and  abat ,  ddc ,  acy1  were down-regulated in metabolic pathways. Genes  aqp10  and  slc6a6  were down-regulated in osmoregulation and ion transport. Genes  abat ,  fdps ,  hmgcs1 ,  mvk ,  pmvk and dhcr7  were first reported to be associated with salinity adaptation in teleosts.    Conclusions  Our results revealed that metabolic pathways, especially lipid metabolism were important for salinity adaptation. The candidate genes identified from this study provide a basis for further studies to investigate the molecular mechanism of salinity adaptation and transcriptional plasticity in marine fish.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4825-4) contains supplementary material, which is available to authorized users.

Liver transcriptome analysis reveals extensive transcriptional plasticity during acclimation to low salinity in Cynoglossus semilaevis