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De novo assembly and characterization of the Hucho taimen transcriptome

文献类型： 外文期刊

作者： Tong, Guang-Xiang 1 ; Xu, Wei 1 ; Zhang, Yong-Quan 1 ; Zhang, Qing-Yu 1 ; Yin, Jia-Sheng 1 ; Kuang, You-Yi 1 ;

作者机构： 1.Chinese Acad Fishery Sci, Heilongjiang River Fisheries Res Inst, Harbin, Heilongjiang, Peoples R China

关键词： comparative transcript analysis;Hucho taimen;microsatellite markers;positive selection;RNA-Seq

期刊名称：ECOLOGY AND EVOLUTION （ 影响因子：2.912； 五年影响因子：3.271 ）

ISSN： 2045-7758

年卷期： 2018 年 8 卷 2 期

页码：

收录情况： SCI

摘要： 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 nonmodel species in addition to its application in gene expression profiling. In this study, we performed a comprehensive RNA-Seq analysis of taimen. We obtained 157M clean reads (14.7Gb) and used them to de novo assemble a high-quality transcriptome with a N50 size of 1,060bp. 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 eight 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.

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