Transcriptome and expression profiling analysis of Leuciscus waleckii: an exploration of the alkali-adapted mechanisms of a freshwater teleost

Abstract

The strategies by which freshwater teleosts maintain acid–base homeostasis under alkaline stress are attractive and have been explored for a long time. In this study, a cyprinid fish that tolerates extremely alkaline environments (pH 9.6), Leuciscus waleckii, was used as a model to explore the molecular mechanisms of acid–base regulation. Using a lab-controlled alkaline challenge test and 454 sequencing, the transcriptomes of their gills and kidney were profiled and compared. mRNA profiling produced 1 826 022 reads, generated 30 606 contigs with an average length of 1022 bp, of which 19 196 were annotated successfully. Comparative analysis of the expression profiles between alkaline and freshwater L. waleckii habitats revealed approximately 4647 and 7184 genes that were differentially expressed (p < 0.05) in gills and kidney, respectively, of which 2398 and 5127 had more than twofold changes in expression. Gene ontology analysis and KEGG enrichment analysis were conducted. Comprehensive analysis found that genes involved in ion transportation, ammonia transportation, and arachidonic acid metabolism pathways changed dramatically and played important roles in acid–base homeostasis in fish under alkaline stress. These results support the existing hypotheses about candidate genes involved in acid–base regulation under alkaline stress and prompt several new hypotheses. The large transcriptome dataset collected in this study is a useful resource for the exploration of homeostasis modulation in other fish species.