De novo assembly and microsatellite marker development of the transcriptome of the endangered Brachymystax lenok tsinlingensis

Background Brachymystax lenok tsinlingensis is an endemic freshwater fish in Northeast Asia, but experienced a dramatic population decline due to over-exploitation, deteriorated habitats and global climate change. It has been listed as a threatened or endangered species in South Korea and China, respectively. However, the conservation and restoration work in wild B. lenok tsinlingensis populations require large amount of genetic and molecular data to support effective management of genetic resources, while the corresponding information is very limited. Objective This study was conducted to generate transcriptome assembly and annotation, as well as to develop novel microsatellite markers for B. lenok tsinlingensis. Methods We collected gill and liver tissues and performed transcriptome sequencing. Then the first transcriptome for B. lenok tsinlingensis was de novo assembled and annotated. Microsatellite markers were searched in the assembled transcripts and characterized within ninety individuals collected from three natural sites. Results A total of 110,712 protein-coding transcripts were assembled, of which 82,861 transcripts were successfully annotated. This assembly displayed a high level of completeness with retrieving 94% of the single-copy orthologs conserved across vertebrate species. Furthermore, 75,891 microsatellite loci were identified from this transcriptome assembly and 20 polymorphic markers were randomly selected for characterization. Conclusions The microsatellite markers and the first transcriptome assembly would provide valuable resources for investigating genetic diversity and phylogeographic structure of wild populations and molecular mechanisms responding to stressful environments (e.g. increased water temperature) to guide future conservation studies and breeding programs.