基于RNA-seq 的黄尾鲴肝脏转录组测序与分析

为了发掘黄尾鲴（Xenocypris davidi）功能基因特别是免疫相关基因,为其种质资源评价、群体遗传学多样性分析、基因连锁图谱构建、免疫相关功能基因地位以及分子标记辅助育种提供基础信息,采用Illumina HiSeq 2500 高通量技术平台对黄尾鲴肝脏进行转录组测序。通过去除低质量的raw reads,共获得了50 702 046条clean reads,组装得到53 527 条Unigenes。采用BLAST 相似性比对方法,把这些序列比对NR、String、Swissprot、KEGG和Pfam数据库,共有26 613条Unigenes得到了注释。有15 532条Unigenes获得了GO注释并分类到64个功能类别中,有7 737条Unigenes被归纳到COG的26个功能分类,共有14 642条获得了KEGG注释,共参与33条代谢通路中。根据免疫系统分类,共有1 299条Unigenes参与了16条代谢通路。从 53 527 个 Unigenes 中共找到 98 826个单核苷酸多态性位点（SNP）（转换 64 396 个,颠换 34 430个）和18 119 个 SSR 位点。研究结果为黄尾鲴免疫学、基因组学、基因克隆以及分子标记辅助育种提供了重要依据。

Transcriptome Analysis of Xenocypris davidi Bleeker Based on RNA sequencing

Xenocypris davidi Bleeker is a species considered excellent for aquaculture because of its high nutritional quality, delicious taste and good adaptability. While there is a high market demand for X. davidi, wild populations have rapidly declined because of over fishing and led to rapid development of artificial culturing. However, disease outbreaks in intensive aquaculture ponds and loss of genetic diversity are problematic. In this research, the total RNA of Xenocypris davidi Bleeker was extracted and a genetic library was established for the species. The transcriptome of X. davidi was developed and functional genes, particularly those related to the immune system, were identified to lay a solid foundation for molecular biology research. The X. davidi transcriptome was sequenced de novo on the Illumina platform. After data cleaning and testing, 50,702,046 high-quality reads were obtained and 53,527 unigenes were assembled. After searching against NR, String, Swissprot, KEGG and Pfam databases, 26,613 unigenes were successfully annotated: 15,532 unigenes were classified into 64 functional categories under three GO ontologies; 7,737 unigenes were assigned to COG, grouped into 26 functional categories; and 14,642 unigenes with significant matches in the database were assigned to 33 KEGG pathways. According to an immune system classification, 1,299 unigenes are involved in 16 metabolic pathways. A total of 98,826 SNPs (64,396 transitions and 34,430 transversions) and 18,119 SSRs were detected in the 53,527 unigenes. This study provides a foundation for future genetic research and molecular marker-assisted breeding of X. davidi.