基于RNA-Seq高通量测序技术的大口黑鲈转录组分析

Sequencing and bioinformatic analysis for transcriptome of Micropterus salmoides based on RNA-seq

文章以大口黑鲈(Micropterus salmoides)组织作为研究对象,利用RNA-seq技术进行转录本测序和数据分析,经拼接组装,最终获得35 659条unigenes,序列平均长度738 bp,序列长度中位数(N50)为1 052 bp。另外从长度分布与GC含量等方面对unigenes进行评估,数据显示测序质量好、可信度高。使用6大数据库(KOG、Nr、Pfam、Swiss-Prot、GO和KEGG)注释大口黑鲈转录组unigenes,分别对应有15 832、21 279、14 524、16 973、15 024和11 185条unigenes获得注释。其中,5 617条unigenes在以上所有数据库中同时注释成功,17 253条unigenes至少被一个数据库注释。KEGG分析结果显示,获得注释的11 185条unigenes被划分到267个代谢通路中,参与信号转导通路的unigenes数量最多,共有1 349条(12.06%)。另外还检测到4 030个微卫星(SSR)位点。通过对大口黑鲈转录组测序,获得了大量的转录组信息,为大口黑鲈的功能基因克隆、基因组学、遗传多样性分析、分子标记开发及遗传改良等研究奠定了基础。

The transcripts of Micropterus salmoides were obtained by RNA-seq technology to conduct a transcriptomic analysis. A total of 35 659 unigenes were generated by de novo assembly with an average length of 738 bp and N50 of 1052 bp. The unigenes were assessed for length distribution and GC content. The sequencing data were of high quality and reliability. A total of 15832, 21279, 14524, 16973, 15024 and 11185 unigenes were annotated from the KOG, Nr, Pfam, Swiss-Prot, GO and KEGG databases, respectively, among which 5617 were annotated in all the databases and 17253 were annotated in at least one database. Blasted with KEGG pathway, 11185 unigenes were annotated, belonging to 267 categories. Of all the pathways, the number of unigenes joining in the signal transduction was the most (1349, 12.06%). Finally, 4030 SSRs were identified. The results provide rich data to understand transcriptome information of M. salmoides and lay the foundation for further research on functional gene cloning, genomics, genetic diversity analysis, molecular marker exploitation and genetic improvement in M. salmoides.