Genome-wide discovery of novel and conserved microRNAs in white shrimp (Litopenaeus vannamei)

文献类型： 外文期刊

第一作者： Xi, Qian-Yun

作者： Xi, Qian-Yun;Wang, Yuan-Mei;Cheng, Xiao;Qi, Qi-En;Shu, Gang;Wang, Song-Bo;Wang, Li-Na;Gao, Ping;Zhu, Xiao-Tong;Jiang, Qing-Yan;Zhang, Yong-Liang;Liu, Li;Xiong, Yuan-Yan

作者机构：

关键词： Genome-wide;MicroRNAs;Solexa deep sequencing;Polysaccharide;White shrimp (Litopenaeus vannamei)

期刊名称：MOLECULAR BIOLOGY REPORTS （ 影响因子：2.316； 五年影响因子：2.357 ）

ISSN：

年卷期：

页码：

收录情况： SCI

摘要： Of late years, a large amount of conserved and species-specific microRNAs (miRNAs) have been performed on identification from species which are economically important but lack a full genome sequence. In this study, Solexa deep sequencing and cross-species miRNA microarray were used to detect miRNAs in white shrimp. We identified 239 conserved miRNAs, 14 miRNA* sequences and 20 novel miRNAs by bioinformatics analysis from 7,561,406 high-quality reads representing 325,370 distinct sequences. The all 20 novel miRNAs were species-specific in white shrimp and not homologous in other species. Using the conserved miRNAs from the miRBase database as a query set to search for homologs from shrimp expressed sequence tags (ESTs), 32 conserved computationally predicted miRNAs were discovered in shrimp. In addition, using microarray analysis in the shrimp fed with Panax ginseng polysaccharide complex, 151 conserved miRNAs were identified, 18 of which were significant up-expression, while 49 miRNAs were significant down-expression. In particular, qRT-PCR analysis was also performed for nine miRNAs in three shrimp tissues such as muscle, gill and hepatopancreas. Results showed that these miRNAs expression are tissue specific. Combining results of the three methods, we detected 20 novel and 394 conserved miRNAs. Verification with quantitative reverse transcription (qRT-PCR) and Northern blot showed a high confidentiality of data. The study provides the first comprehensive specific miRNA profile of white shrimp, which includes useful information for future investigations into the function of miRNAs in regulation of shrimp development and immunology.

分类号： Q7

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