Genome-Wide Investigation Using sRNA-Seq, Degradome-Seq and Transcriptome-Seq Reveals Regulatory Networks of microRNAs and Their Target Genes in Soybean during <i>Soybean mosaic virus</i> Infection

MicroRNAs (miRNAs) play key roles in a variety of cellular processes through regulation of their target gene expression. Accumulated experimental evidence has demonstrated that infections by viruses are associated with the altered expression profile of miRNAs and their mRNA targets in the host. However, the regulatory network of miRNA-mRNA interactions during viral infection remains largely unknown. In this study, we performed small RNA (sRNA)-seq, degradome-seq and as well as a genome-wide transcriptome analysis to profile the global gene and miRNA expression in soybean following infections by three different Soybean mosaic virus (SMV) isolates, L (G2 strain), LRB (G2 strain) and G7 (G7 strain). sRNA-seq analyses revealed a total of 253 soybean miRNAs with a two-fold or greater change in abundance compared with the mock-inoculated control. 125 transcripts were identified as the potential cleavage targets of 105 miRNAs and validated by degradome-seq analyses. Genome-wide transcriptome analysis showed that total 2679 genes are differentially expressed in response to SMV infection including 71 genes predicted as involved in defense response. Finally, complex miRNA-mRNA regulatory networks were derived using the RNAseq, small RNAseq and degradome data. This work represents a comprehensive, global approach to examining virus-host interactions. Genes responsive to SMV infection are identified as are their potential miRNA regulators. Additionally, regulatory changes of the miRNAs themselves are described and the regulatory relationships were supported with degradome data. Taken together these data provide new insights into molecular SMV-soybean interactions and offer candidate miRNAs and their targets for further elucidation of the SMV infection process.微小RNA（miRNAs）可通过调控靶基因的表达，在多种细胞生物学过程中发挥关键作用。已有大量实验证据表明，病毒感染会导致宿主内miRNAs及其mRNA靶标的表达谱发生改变。然而，病毒感染过程中miRNA与mRNA相互作用的调控网络仍鲜为人知。本研究针对大豆分别接种3株不同的大豆花叶病毒（Soybean mosaic virus，SMV）分离株：L（G2毒株）、LRB（G2毒株）与G7（G7毒株），通过小RNA测序（small RNA sequencing，sRNA-seq）、降解组测序（degradome sequencing，degradome-seq）以及全基因组转录组分析，对接种后大豆的全局基因与miRNA表达谱进行解析。sRNA-seq分析结果显示，相较于mock接种对照组，共有253个大豆miRNA的表达量发生了2倍及以上的变化。经降解组测序验证，共鉴定出105个miRNAs的125条潜在切割靶转录本。全基因组转录组分析显示，共有2679个基因在SMV感染后呈现差异表达，其中71个基因被预测参与防御应答过程。最终，本研究结合转录组测序、小RNA测序与降解组测序数据，构建了复杂的miRNA-mRNA调控网络。本研究采用全局综合性的研究策略，解析病毒-宿主互作机制；鉴定出响应SMV感染的宿主基因及其潜在的miRNA调控因子。此外，本研究还阐明了miRNAs自身的表达调控变化，并通过降解组测序数据验证了相关调控关系。综上，本研究的数据为解析SMV与大豆互作的分子机制提供了新视角，并为后续阐明SMV侵染过程的候选miRNAs及其靶标基因提供了依据。