School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, PR China.
School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, PR China.
Fish Shellfish Immunol. 2014 Mar;37(1):75-86. doi: 10.1016/j.fsi.2014.01.002. Epub 2014 Jan 21.
The sustainable development of the scallop Chlamys farreri industry in China is hindered by mass mortality mainly caused by a novel pathogen known as acute viral necrosis virus (AVNV). A better understanding of host-virus interactions, especially those at the molecular level, may facilitate the prevention and cure of AVNV infections. MicroRNAs (miRNAs) represent a class of small RNA molecules involved in several biological processes, including mediating host-pathogen responses. In this study, two hemocyte small RNA libraries were constructed from control (control library, CL) and AVNV-infected (infection library, IL) C. farreri for high throughput sequencing using Solexa technology. Acquired data were further used to identify conserved and novel miRNAs, screen differentially expressed miRNAs, and predict their target genes through bioinformatics analysis. Solexa sequencing produced 19,485,719 and 20,594,513 clean reads representing 2,248,814 and 1,510,256 unique small RNAs from CL and IL, respectively. A total of 57 conserved miRNAs were identified in both libraries, among which only two were unique to IL. Novel miRNA prediction using the Crassostrea gigas genome as a reference revealed 11 candidate miRNAs, 10 of which were validated by RT-PCR. Differential expression (p < 0.001) between libraries was observed in 37 miRNAs, among which 30 and 7 miRNAs were up- and downregulated, respectively. Expression differences were further confirmed by qRT-PCR. A sequence homology search against available C. farreri ESTs showed that these differentially expressed miRNAs may target 177 genes involved in a broad range of biological processes including immune defense and stress response. This study is the first to characterize C. farreri miRNAs and miRNA expression profiles in response to AVNV infection by deep sequencing. The results presented here will deepen our understanding of the pathogenesis of AVNV at the molecular level and provide new insights into the molecular basis of host-pathogen interactions in C. farreri.
中国扇贝养殖业的可持续发展受到大规模死亡的阻碍，主要是由一种新型病原体引起的，这种病原体被称为急性病毒性坏死病毒（AVNV）。更好地了解宿主-病毒相互作用，特别是在分子水平上，可能有助于预防和治疗 AVNV 感染。microRNAs（miRNAs）是一类参与多种生物学过程的小 RNA 分子，包括介导宿主-病原体反应。在这项研究中，我们从对照组（对照组文库，CL）和 AVNV 感染组（感染组文库，IL）的中国扇贝中构建了两个血细胞小 RNA 文库，用于高通量测序，使用 Solexa 技术。通过生物信息学分析，进一步利用获得的数据鉴定保守和新型 miRNAs，筛选差异表达的 miRNAs，并预测其靶基因。Solexa 测序分别产生了 19,485,719 和 20,594,513 条清洁读数，分别代表 2,248,814 和 1,510,256 个独特的小 RNA。在两个文库中均鉴定出 57 个保守 miRNAs，其中仅 2 个是 IL 所特有的。利用中国毛蚶基因组作为参考预测新型 miRNA 显示出 11 个候选 miRNA，其中 10 个通过 RT-PCR 得到验证。文库间差异表达（p < 0.001）观察到 37 个 miRNAs，其中 30 个上调，7 个下调。qRT-PCR 进一步证实了表达差异。与现有 C. farreri ESTs 的序列同源性搜索表明，这些差异表达的 miRNAs 可能靶向 177 个参与广泛生物学过程的基因，包括免疫防御和应激反应。本研究首次通过深度测序对中国扇贝的 C. farreri miRNAs 和 miRNA 表达谱进行了表征，对 AVNV 感染的响应。这里呈现的结果将加深我们对 AVNV 分子水平发病机制的理解，并为 C. farreri 中宿主-病原体相互作用的分子基础提供新的见解。
