title: Deep sequencing-based transcriptome profiling reveals comprehensive insights into the responses of Nicotiana benthamiana to beet necrotic yellow vein virus infections containing or lacking RNA4.
abstract: BACKGROUND
  Beet necrotic yellow vein virus (BNYVV), encodes either four or five plus-sense single stranded RNAs and is the causal agent of sugar beet rhizomania disease, which is widely distributed in most regions of the world. BNYVV can also infect Nicotiana benthamiana systemically, and causes severe curling and stunting symptoms in the presence of RNA4 or mild symptoms in the absence of RNA4.
  
  
  RESULTS
  Confocal laser scanning microscopy (CLSM) analyses showed that the RNA4-encoded p31 protein fused to the red fluorescent protein (RFP) accumulated mainly in the nuclei of N. benthamiana epidermal cells. This suggested that severe RNA4-induced symptoms might result from p31-dependent modifications of the transcriptome. Therefore, we used next-generation sequencing technologies to analyze the transcriptome profile of N. benthamiana in response to infection with different isolates of BNYVV. Comparisons of the transcriptomes of mock, BN3 (RNAs 1+2+3), and BN34 (RNAs 1+2+3+4) infected plants identified 3,016 differentially expressed transcripts, which provided a list of candidate genes that potentially are elicited in response to virus infection. Our data indicate that modifications in the expression of genes involved in RNA silencing, ubiquitin-proteasome pathway, cellulose synthesis, and metabolism of the plant hormone gibberellin may contribute to the severe symptoms induced by RNA4 from BNYVV.
  
  
  CONCLUSIONS
  These results expand our understanding of the genetic architecture of N. benthamiana as well as provide valuable clues to identify genes potentially involved in resistance to BNYVV infection. Our global survey of gene expression changes in infected plants reveals new insights into the complicated molecular mechanisms underlying symptom development, and aids research into new strategies to protect crops against viruses.
authors.affiliation: State Key Laboratory for Agrobiotechnology and Department of Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Huiyan
authors.initials: H
authors.lastname: Fan
authors.affiliation: State Key Laboratory for Agrobiotechnology and Department of Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Haiwen
authors.initials: H
authors.lastname: Sun
authors.affiliation: State Key Laboratory for Agrobiotechnology and Department of Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Agrobiotechnology and Department of Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Yongliang
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: State Key Laboratory for Agrobiotechnology and Department of Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Xianbing
authors.initials: X
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Agrobiotechnology and Department of Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Dawei
authors.initials: D
authors.lastname: Li
authors.affiliation: State Key Laboratory for Agrobiotechnology and Department of Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Jialin
authors.initials: J
authors.lastname: Yu
authors.affiliation: State Key Laboratory for Agrobiotechnology and Department of Plant Pathology, China Agricultural University, Beijing, China.
authors.forename: Chenggui
authors.initials: C
authors.lastname: Han
mesh_terms: D002482:Cellulose / Q000096:biosynthesis / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D017930:Genes, Reporter; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions; D008164:Luminescent Proteins / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation; D010935:Plant Diseases / Q000235:genetics* / Q000276:immunology / Q000821:virology; D057865:Plant Immunity / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics* / Q000276:immunology; D034622:RNA Interference; D012328:RNA Viruses / Q000472:pathogenicity / Q000502:physiology*; D012333:RNA, Messenger / Q000235:genetics / Q000276:immunology; D014026:Nicotiana / Q000235:genetics* / Q000276:immunology / Q000821:virology; D059467:Transcriptome / Q000235:genetics* / Q000276:immunology; D054875:Ubiquitination; D000097573:Red Fluorescent Protein
chemical_list: D002482:Cellulose; D008164:Luminescent Proteins; D010940:Plant Proteins; D012333:RNA, Messenger; D000097573:Red Fluorescent Protein