Identification and comparative analysis of the Eriocheir sinensis microRNA transcriptome response to Spiroplasma eriocheiris infection using a deep sequencing approach
Identification and comparative analysis of the Eriocheir sinensis microRNA transcriptome response to Spiroplasma eriocheiris infection using a deep sequencing approach
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利用深度测序方法鉴定和比较分析中华绒螯蟹对绒毛虫感染的 microRNA 转录组反应
DOI：
10.1016/j.fsi.2011.11.027
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发表时间：
2012-02-01
影响因子：
4.7
通讯作者：
Wang, Wen
中科院分区：
文献类型：
--
作者：
Ou, Jiangtao;Meng, Qingguo;Wang, Wen
中华绒螯蟹是我国最重要的淡水养殖甲壳类动物之一。微小RNA（microRNAs，miRNAs）是一类小分子非编码RNA，在复杂的宿主-病原体相互作用网络中起重要作用。为了增加甲壳类动物中特有的miRNA库并研究宿主miRNA表达与病原体感染之间的关系，我们使用Illumina/Solexa深度测序技术对从E.中华绒螯蟹在正常条件下和感染绒螯蟹螺原体期间。高通量测序产生约30，975，151和30，826，277个原始读段，分别对应于正常和感染血细胞样品的12，077，088和16，271，545个高质量可映射读段。生物信息学分析确定了735个独特的miRNA，包括36个在甲壳类动物中保守的，134个对螃蟹来说是新的，但存在于其他节肢动物中（PN型），565个是全新的（PC型）。228个独特的miRNA在正常和感染的血细胞样品之间显示出显著的差异表达（p < 0.0001）。其中，133个（58%）在S.绒螯蟹对两个样本的10种miRNA进行了实时定量PCR（RT-qPCR）实验，测序结果与RT-qPCR数据一致。据我们所知，这是首次对E.中国大肠杆菌miRNAs的表达分析。中华绒螯蟹暴露于S.绒螯蟹当暴露于病原体时，许多miRNAs受到差异调节，这些发现支持某些miRNAs可能在宿主病原体相互作用中必不可少的假设。我们的研究结果表明，阐明负责miRNA调节宿主先天免疫系统的分子机制将有助于开发新的控制策略来预防或治疗S。甲壳类动物的绒螯蟹感染。皇冠版权所有（C）2011由爱思唯尔有限公司出版。保留所有权利。
The Chinese mitten crab Eriocheir sinensis is one of the most important freshwater aquaculture crustacean species in China. MicroRNAs (miRNAs) are small non-coding RNAs that are important effectors in the intricate host pathogen interaction network. To increase the repertoire of miRNAs characterized in crustaceans and to examine the relationship between host miRNA expression and pathogen infection, we used the Illumina/Solexa deep sequencing technology to sequence two small RNA libraries prepared from haemocytes of E. sinensis under normal conditions and during infection with Spiroplasma eriocheiris. The high-throughput sequencing resulted in approximately 30,975,151 and 30,826,277 raw reads corresponding to 12,077,088 and 16,271,545 high-quality mappable reads for the normal and infected haemocyte samples, respectively. Bioinformatic analyses identified 735 unique miRNAs, including 36 that are conserved in crustaceans, 134 that are novel to crabs but are present in other arthropods (PN-type), and 565 that are completely new (PC-type). Two hundred twenty-eight unique miRNAs displayed significant differential expression between the normal and infected haemocyte samples (p < 0.0001). Of these, 133 (58%) were significantly up-regulated and 95 (42%) were significantly down-regulated upon challenge with S. eriocheiris. Real-time quantitative PCR (RT-qPCR) experiments were preformed for 10 miRNAs of the two samples, and agreement was found between the sequencing and RT-qPCR data. To our knowledge, this is the first report of comprehensive identification of E. sinensis miRNAs and of expression analysis of E. sinensis miRNAs after exposure to S. eriocheiris. Many miRNAs were differentially regulated when exposed to the pathogen, and these findings support the hypothesis that certain miRNAs might be essential in host pathogen interactions. Our results suggest that elucidation of the molecular mechanisms responsible for miRNA regulation of the host's innate immune system should help with the development of new control strategies to prevent or treat S. eriocheiris infections in crustaceans. Crown Copyright (C) 2011 Published by Elsevier Ltd. All rights reserved.