PDF(Pubmed)
Abstract：
Freshwater ecosystems are among the most endangered ecosystems worldwide. While numerous taxa are on the verge of extinction as a result of global changes and direct or indirect anthropogenic activity, genomic and transcriptomic resources represent a key tool for comprehending species\' adaptability and serve as the foundation for conservation initiatives. The Loire grayling, Thymallus ligericus, is a freshwater European salmonid endemic to the upper Loire River basin. The species is comprised of fragmented populations that are dispersed over a small area and it has been identified as a vulnerable species. Here, we provide a multi-tissue de novo transcriptome assembly of T. ligericus. The completeness and integrity of the transcriptome were assessed before and after redundancy removal with lineage-specific libraries from Eukaryota, Metazoa, Vertebrata, and Actinopterygii. Relative gene expression was assessed for each of the analyzed tissues, using the de novo assembled transcriptome and a genome-based analysis using the available T. thymallus genome as a reference. The final assembly, with a contig N50 of 1221 and Benchmarking Universal Single-Copy Orthologs (BUSCO) scores above 94%, is made accessible along with structural and functional annotations and relative gene expression of the five tissues (NCBI SRA and FigShare databases). This is the first transcriptomic resource for this species, which provides a foundation for future research on this and other salmonid species that are increasingly exposed to environmental stressors.
摘要：
淡水生态系统是全球最濒危的生态系统之一。尽管由于全球变化以及直接或间接的人为活动，许多分类单元濒临灭绝，基因组和转录组资源是理解物种适应性的关键工具，也是保护计划的基础。卢瓦尔河河岸，胸腺，是卢瓦尔河上游流域特有的淡水欧洲鲑鱼。该物种由分散在一小块区域的分散种群组成，已被确定为脆弱物种。这里,我们提供了一个多组织从头转录组的组装。使用来自Eukaryota的谱系特异性文库在冗余去除之前和之后评估转录组的完整性和完整性，Metazoa,脊椎动物,和Actinopterygii。评估每个分析组织的相对基因表达，使用从头组装的转录组和基于基因组的分析，使用可用的T.胸腺基因组作为参考。最后的组装，重叠群N50为1221，基准通用单拷贝正交体(BUSCO)得分高于94%，与五个组织的结构和功能注释以及相对基因表达（NCBISRA和FigShare数据库）一起变得可访问。这是该物种的第一个转录组资源，这为未来对这种和其他日益暴露于环境压力的鲑鱼物种的研究提供了基础。
