The Tibetan Plateau is the world's largest plateau that is characterized by low temperature, low oxygen, and strong ultraviolet radiation. Colonized species that invade the plateau must change their characteristics to adapt to the harsh environment. However, research on the adaptation of introduced species on plateaus is limited. In this study, brown trout (Salmo trutta fario) was studied as a colonized species of the Tibetan Plateau, and a de novo transcriptome assembly was conducted to explore the genetic basis of plateau adaptation. A total of 38,606 unigenes were assembled, with over 90% of the unigenes annotated. Using comparative transcriptomics analysis, we identified 129 positively selected genes and 126 species‐specific gene families in colonized brown trout that were associated with energy metabolism, angiogenesis, heart development, ammonium transport, and DNA damage and repair, which may play essential roles in the adaptation to high altitude of colonized brown trout compared to other inland Salmonidae species. Our results provide an integrated and comprehensive transcriptomic resource for brown trout colonized in Tibet. These results potentially contribute to future studies aiming to identify candidate genes and pathways underlying the genetic basis of adaptation in the Tibetan plateau and assist in the population protection and aquaculture of brown trout in Tibet.

Topmouth culter (Culter alburnus) is an important freshwater species in China. In recent years, the population of topmouth culter has declined sharply due to the increasing pollution, overfishing and habitat destruction. It may lead to adverse effects, including weakening health, causing disease, and reducing the quality of topmouth culter. It is urgent to conduct resource management, protection and genetic improvement strategies in topmouth culter, especially develop genetic breeding program with disease resistance. In this study, we applied RNA‐seq technology to de novo assemble a comprehensive transcriptome, and to discover immune‐related genes and pathways in topmouth culter. A total of 102 017 transcripts were assembled with an average length of 945 bp, of which 45 482 protein coding sequences were predicted. BLAST search resulted in 53 575 and 45 602 transcripts with homologous sequences in NCBI‐NR and UniProt respectively. Further functional analysis identified 24 052 transcripts in Gene Ontology (GO) categories and 19 260 transcripts in KEGG pathways. Significantly, 13 immune‐related pathways with 524 immune‐related genes were identified. Our data provided an integrated and comprehensive transcriptome resource for topmouth culter, which could be essential for further research in selective breeding of disease resistance, functional genomics, and genome editing of topmouth culter.