title: RNA-seq-based digital gene expression analysis reveals modification of host defense responses by rice stripe virus during disease symptom development in Arabidopsis.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Sun
authors.affiliation: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China.|College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Fang
authors.affiliation: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Li
authors.affiliation: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China.
authors.forename: Linlin
authors.initials: L
authors.lastname: Du
authors.affiliation: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Lan
authors.affiliation: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China.
authors.forename: Tong
authors.initials: T
authors.lastname: Zhou
authors.affiliation: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China.
authors.forename: Yongjian
authors.initials: Y
authors.lastname: Fan
authors.affiliation: College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China. wbshenh@njau.edu.cn.
authors.forename: Wenbiao
authors.initials: W
authors.lastname: Shen
authors.affiliation: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, 210014, China. yjzhou@jaas.ac.cn.
authors.forename: Yijun
authors.initials: Y
authors.lastname: Zhou
mesh_terms: D017360:Arabidopsis / Q000821:virology*; D020869:Gene Expression Profiling / Q000379:methods*; D054884:Host-Pathogen Interactions; D010935:Plant Diseases / Q000821:virology*; D017423:Sequence Analysis, RNA / Q000379:methods*; D029364:Tenuivirus / Q000235:genetics* / Q000254:growth & development*; D013997:Time Factors
keywords: Defense response; Digital gene expression (DGE); RNA-seq; Rice stripe virus