Comparative transcriptome analysis of Triplophysa yarkandensis in response to salinity and alkalinity stress

Triplophysa yarkandensis, a fish belonging to the family Nemacheilidae, is distributed in the Tarim River, China, immediately north of the Qinghai-Tibet Plateau. Due to increasing salinity and alkalinity in the Tarim River, the habitats of T. yarkandensis have been seriously altered. To identify the genes and pathways that are important for responding to salinity and alkalinity stress, the gill transcriptomes of fish living under different salinity and alkalinity conditions were obtained using RNA sequencing. A total of 1,123,448,964 clean reads were obtained and assembled into 177,271 unigenes, with an average length of 1703 bp. Around 13,526 unigenes showed differential expression when comparing different salinity concentrations with the controls, 6967 of which were upregulated and 6559 were downregulated. When comparing different alkalinity concentrations with the controls, there were 17,475 unigenes that showed differential expression, of which 10,457 were upregulated and 7018 were downregulated. Only 146 unigenes were both differentially expressed in salinity and alkalinity groups compared to the control. The results of KEGG enrichment showed that there were five upregulated and 12 downregulated pathways in fish subject to salinity treatment. For fish exposed to alkalinity treatment, 15 pathways were upregulated and 13 downregulated. There were four upregulated and four downregulated pathways that were shared by fish subject to salinity and alkalinity treatments. To our knowledge, this is the first study on the T. yarkandensis transcriptome; the information presented here will provide further understanding of the fish's response to salinity and alkalinity stress, as well as further insight into the T. yarkandensis genome.