Shaanxi Fisheries Institute, Shaanxi, 710086, China.
Yellow River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shaanxi, 710086, China.
Genes Genomics. 2020 Jul;42(7):727-734. doi: 10.1007/s13258-020-00939-3. Epub 2020 May 24.
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.
This study was conducted to generate transcriptome assembly and annotation, as well as to develop novel microsatellite markers for B. lenok tsinlingensis.
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.
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.
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.
秦岭细鳞鲑是东北亚特有的淡水鱼类，但由于过度捕捞、栖息地恶化和全球气候变化，其种群数量急剧减少。韩国和中国分别将其列为受威胁或濒危物种。然而，野生秦岭细鳞鲑种群的保护和恢复工作需要大量的遗传和分子数据来支持遗传资源的有效管理，而相应的信息非常有限。
本研究旨在生成转录组组装和注释，并为秦岭细鳞鲑开发新的微卫星标记。
我们收集了鳃和肝脏组织，并进行了转录组测序。然后，我们对 B. lenok tsinlingensis 的第一个转录组进行了从头组装和注释。在从三个自然地点采集的 90 个个体中，在组装的转录本中搜索了微卫星标记，并对其进行了特征描述。
共组装了 110712 个编码蛋白的转录本，其中 82861 个转录本成功注释。该组装具有很高的完整性，检索到了跨脊椎动物物种保守的 94%的单拷贝直系同源物。此外，从这个转录组组装中鉴定出了 75891 个微卫星位点，并随机选择了 20 个多态性标记进行特征描述。
这些微卫星标记和第一个转录组组装将为研究野生种群的遗传多样性和系统地理结构以及分子机制对胁迫环境（如水温升高）的响应提供有价值的资源，从而指导未来的保护研究和繁殖计划。
