RNA-seq-based digital gene expression analysis reveals modification of host defense responses by rice stripe virus during disease symptom development in Arabidopsis.

Feng Sun,Peng Fang,Linlin Du,Yijun Zhou,Yongjian Fan,Ying Lan,Juan Li,Tong Zhou,Wenbiao Shen

doi:10.1186/s12985-016-0663-7

Abstract

BackgroundVirus infection induces and suppresses host gene expression on a global level. Rice stripe virus (RSV) is the type species of the genus Tenuivirus and infects rice and Arabidopsis plants. Microarray-based and next generation sequencing-based transcriptomic approaches have been used to study rice-RSV interactions. However, our knowledge of the response of Arabidopsis plants to RSV infection is limited, and it requires further investigation to determine the similarities (or differences) in virus-host interactions between monocot and dicot hosts infected with RSV.MethodsWe characterized transcriptome changes in Arabidopsis thaliana infected with rice stripe virus (RSV) with RNA-seq based digital gene expression (DGE) analysis. The transcriptomes of RSV-infected samples were compared to those of mock-treated samples at 14 and 21 days post-infection (dpi) during different stages of symptom development.ResultsWe identified 624 differentially expressed genes (DEGs) in Arabidopsis influenced by RSV at 14 dpi and 21 dpi, among which at 14 dpi, 255 transcripts were induced, and 38 were repressed; at 21 dpi, 146 were induced, and 237 were repressed. Functional annotation indicated that these DEGs were related to multiple biological functions, including defense response, secondary metabolism, protein amino acid phosphorylation and response to abiotic stress.ConclusionsImportantly, the transcription of genes related to host defense systems was activated by RSV infection at an early stage of symptom development (14 dpi), whereas over the infection period (21 dpi), the host defense response systems were suppressed. A total of 52 genes were continuously differentially expressed between the two time points, indicating that the majority of DEGs were transient and unique to a particular time point during symptom development. The DEGs, particularly the defense response genes, identified in this study are candidates suitable for further functional analysis during the RSV-Arabidopsis interaction.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-016-0663-7) contains supplementary material, which is available to authorized users.

Highlights

Virus infection induces and suppresses host gene expression on a global level
Symptom development and virus accumulation in RSVinfected Arabidopsis Four-week-old Arabidopsis plants were inoculated with Rice stripe virus (RSV) viruliferous small brown planthopper (SBPH), and mock plants were inoculated with virus-free SBPHs
We found what the RSV titer in Arabidopsis plants increased significantly over time (Fig. 1b, c, d) and was associated with plant disease symptom development

Summary

Introduction

Virus infection induces and suppresses host gene expression on a global level. Rice stripe virus (RSV) is the type species of the genus Tenuivirus and infects rice and Arabidopsis plants. Our knowledge of the response of Arabidopsis plants to RSV infection is limited, and it requires further investigation to determine the similarities (or differences) in virus-host interactions between monocot and dicot hosts infected with RSV. Rice stripe virus (RSV) is the type species of the genus Tenuivirus and primarily infects rice plants [7, 8]. The three smaller RNA segments (RNAs 2, 3 and 4) are ambisense [12, 13], each contain two ORFs which encode proteins associated with functions including virus movement, encapsidation, RNA silencing suppression, transcription, and planthopper transmission [8, 14, 15]

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Conclusion