Data from: De novo assembly and characterization of the Hucho taimen transcriptome

Taimen (Hucho taimen) is an important ecological and economic species that is classified as vulnerable by the IUCN Red List of Threatened Species; however, limited genomic information is available on this species. RNA-Seq is a useful tool for obtaining genetic information and developing genetic markers for non-model species in addition to its application in gene expression profiling. In this study, we performed a comprehensive RNA-Seq analysis of taimen. We obtained 157 M clean reads (14.7 Gb) and used them to de novo assemble a high-quality transcriptome with a N50 size of 1060 bp. In the assembly, 82% of the transcripts were annotated using several databases, and 14,666 of the transcripts contained a full open reading frame. The assembly covered 75% of the transcripts of Atlantic salmon and 57.3% of the protein-coding genes of rainbow trout. To learn about the genome evolution, we performed a systematic comparative analysis across 11 teleosts including 8 salmonids, and found 313 unique gene families in taimen. Using Atlantic salmon and rainbow trout transcriptomes as the background, we identified 250 positive selection transcripts. The pathway enrichment analysis revealed a unique characteristic of taimen: it possesses more immune-related genes than Atlantic salmon and rainbow trout; moreover, some genes have undergone strong positive selection. We also developed a pipeline for identifying microsatellite marker genotypes in samples, and successfully identified 24 polymorphic microsatellite markers for taimen. These data and tools are useful for studying conservation genetics, phylogenetics, evolution among salmonids and selective breeding for threatened taimen.

哲罗鲑（Taimen，学名Hucho taimen）是兼具重要生态与经济价值的物种，被世界自然保护联盟（IUCN）红色名录列为易危物种，但目前针对该物种的基因组学信息仍较为有限。RNA测序（RNA-Seq）除可用于基因表达谱分析外，亦是获取非模式物种遗传信息、开发遗传标记的有效工具。本研究对哲罗鲑开展了全面的RNA测序分析，共获得157 M条清洁读段（对应14.7 Gb数据量），并以此为基础从头组装得到高质量转录组，其N50长度为1060 bp。在该转录组组装结果中，通过多个数据库完成了82%转录本的功能注释，其中14666条转录本包含完整开放阅读框。该组装覆盖了大西洋鲑75%的转录本以及虹鳟57.3%的蛋白编码基因。为探究基因组演化特征，研究团队对包含8种鲑科鱼类在内的11种硬骨鱼开展了系统性比较分析，鉴定得到哲罗鲑特有的313个基因家族。以大西洋鲑和虹鳟的转录组作为参照背景，共筛选得到250个受正选择作用的转录本。通路富集分析揭示了哲罗鲑的一项独特特征：其免疫相关基因的数量多于大西洋鲑与虹鳟，且部分基因经历了强烈的正选择作用。本研究同时开发了一套用于样本微卫星标记基因分型的分析流程，并成功筛选得到24个哲罗鲑的多态性微卫星标记。上述数据与工具可为濒危哲罗鲑的保护遗传学、系统发育学、鲑科鱼类演化研究以及选择性育种工作提供重要支撑。