RNA-seq-based digital gene expression analysis reveals modification of host defense responses by rice stripe virus during disease symptom development in Arabidopsis
Autor: | Wenbiao Shen, Fang Peng, Lan Ying, Yijun Zhou, Zhou Tong, Juan Li, Linlin Du, Feng Sun, Yongjian Fan |
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Rok vydání: | 2016 |
Předmět: |
0106 biological sciences
0301 basic medicine Time Factors Digital gene expression (DGE) viruses Arabidopsis Rice stripe virus RNA-Seq 01 natural sciences Defense response Transcriptome 03 medical and health sciences Virology Gene expression Arabidopsis thaliana Gene Tenuivirus Plant Diseases Genetics biology Sequence Analysis RNA Research Gene Expression Profiling food and beverages virus diseases biology.organism_classification 030104 developmental biology Infectious Diseases Host-Pathogen Interactions RNA-seq 010606 plant biology & botany |
Zdroj: | Virology Journal |
ISSN: | 1743-422X |
Popis: | Background 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. 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. Methods We 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. Results We 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. Conclusions Importantly, 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 material The online version of this article (doi:10.1186/s12985-016-0663-7) contains supplementary material, which is available to authorized users. |
Databáze: | OpenAIRE |
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