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

Abstract

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.

Soybean mosaic virus: a successful potyvirus with a wide distribution but restricted natural host range

“…It has been proposed that P3 targets eEF1A to elicit the unfolded protein response that promotes SMV accumulation. Chen et al (2016) used RNA-sequencing to investigate changes in soybean mRNA and small RNA accumulation, and the mRNA degradome, at 14 days post-inoculation in a susceptible cultivar in response to three different compatible SMV isolates. Their data suggested that SMV infection affected a variety of regulatory networks.…”

The Current Status of the Soybean-Soybean Mosaic Virus (SMV) Pathosystem

“…Chen et al (2016b) recently 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 in response to three different SMV isolates. The SMV responsive miRNAs and their potential cleavage targets were identified and subsequently validated by degradome-seq analysis, leading to the establishment of complex miRNA-mRNA regulatory networks.…”

Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

“…Therefore, we believe that the pathways controlling these processes deserve intensive research focus. The commonly used NGS technique allows for comprehensive analyses of sRNAoms, transcriptoms, and degradomes, as well as identification of sRNAs and their target genes in both model and non-model plants, for example: tomato [58], soybean [59], Arabidopsis [60,61], oilseed rape [62], Brassica juncea [63], lily [64,65], peanut [66], orchardgrass [67] or wheat [68,69].…”