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Transcriptome analysis of rice infected with Rice black streak dwarf virus

ABSTRACT: Rice black streak dwarf virus (RBSDV) is the causal agent of rice black streak dwarf disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RBSDV infection.

ORGANISM(S): Oryza sativa Oryza sativa Japonica Group

PROVIDER: GSE34263 | GEO | 2012/12/01

SECONDARY ACCESSION(S): PRJNA149729

REPOSITORIES: GEO

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Transcriptome analysis of rice infected with Rice black streak dwarf virus

Project description:Rice black streak dwarf virus (RBSDV) is the causal agent of rice black streak dwarf disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RBSDV infection. Comparison between RBSDV and mock infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested. 1 samples derived from 5 plants grown under same conditons

2012-12-01 | E-GEOD-34263 | biostudies-arrayexpress

Transcriptome analysis of rice reveals the lncRNA-mRNA regulatory network in response to Rice black-streaked dwarf virus infection

Project description:To better understand the response mechanism of rice plants to Rice black-streaked dwarf virus (RBSDV) infection, we performed a comparative transcriptome analysis between the RBSDV-infected and non-infected rice plants. A total of 1342 mRNAs and 22 lncRNAs were identified to be differentially expressed after RBSDV infection. Most differentially expressed transcripts involved in the plant-pathogen interaction pathway were upregulated after RBSDV infection, indicating the activation of rice defense response by RBSDV. A network of differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) was then constructed. In this network, there are 56 plant-pathogen interaction-related DEmRNAs co-expressing with 20 DElncRNAs, suggesting these DElncRNAs and DEmRNAs may play essential roles in rice innate immunity against RBSDV.

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Comparative proteomic analysis of maize (Zea may L.) seedlings under rice black-streaked dwarf virus infection

Project description:Maize rough dwarf disease (MRDD) is a severe disease that has been occurring frequently in southern China and many other Asian countries. MRDD is caused by the infection of Rice black streaked dwarf virus (RBSDV) and leads to significant economic losses in maize production. To well understand the destructive effects of RBSDV infection on maize growth, comparative proteomic analysis of maize seedlings under RBSDV infection was performed using an integrated approach involving LC-MS/MS and TMT labeling. Our study identified 7615 maize proteins, of which 6319 proteins were quantified. A total of 116 differentially expressed proteins (DEPs) were identified, including 35 up- and 81 down-regulated proteins under RBSDV infection. Enrichment analysis showed that the DEPs were most strongly associated with Cyanoamino acid metabolism, protein processing in ER, and ribosome-related pathways. Two sulfur metabolism-related proteins were significantly reduced, indicating that sulfur may participate in the resistance against RBSDV infection. Furthermore, 15 DEPs involved in six metabolic pathways were identified in maize under RBSDV infection. Our data revealed that the responses of maize to RBSDV infection were controlled by various metabolic pathways.

2017-12-18 | PXD008186 | Pride

Transcriptome analysis of rice infected with Rice gall dwarf virus

2012-12-01 | GSE34264 | GEO

Transcriptome analysis of rice infected with Rice gall dwarf virus

Project description:Rice gall dwarf virus (RGDV) is the causal agent of rice gall dwarf disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RGDV infection. Comparison between RGDV and mock infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested. 1 samples derived from 5 plants grown under same conditons

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iTRAQ-based quantitative proteomics suggests mitophagy involvement after Rice black-streaked dwarf virus acquisition in insect vector small brown planthopper Laodelphax striatellus Fallén

Project description:Plant virus triggers numerous responses in its insect vectors. Using the iTRAQ-based quantitative proteomics analysis. Early responses of the insect vector small brown planthopper (Laodelphax striatellus Fallén, SBPH) after acquiring Rice black-streaked dwarf virus (RBSDV) at 3 days and 5 days post first access to disease plants (padp), respectively, were revealed. A total of 582 differentially abundant proteins (DAPs) in SBPH with a fold change > 1.500 or <0.667 (p-value<0.05) were identified. The proteomic analysis in SBPH at 3 days padp revealed 106 high abundant proteins and 193 low abundant proteins, while 5 days padp revealed 214 high abundant proteins and 182 low abundant proteins. Among them, 51 high abundant proteins and 42 low abundant proteins were consistently differentially abundant at both 3 days and 5 days padp.

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Alterations of rice (Oryza sativa L.) DNA methylation patterns associated with gene expression in response to Rice black-streaked dwarf virus

Project description:High-throughput single-base resolution bisulfite sequencing (BS-Seq) was carried out to analyze the distribution pattern and characteristics of cytosine methylation in RBSDV-infected rice. Widespread differences were identified at CG and non-CG contexts between the RBSDV-infected and RBSDV-free rice. We identified a large number of differentially methylated regions (DMRs) along the genome of RBSDV-infected rice. And meanwhile, the transcriptome sequencing analysis obtained 1119 differentially expressed genes (DEGs). Correlation analysis of DMRs-related genes (DMGs) and DEGs filtered 71 genes with negative relationship between methylation level at promoter regions and gene expression. Many of them were significantly enriched in the KEGG pathways of biosynthesis of amino acids, plant-pathogen interaction and plant hormone signal transduction.

2020-10-28 | GSE150378 | GEO

Rice plants infected by Rice dwarf virus

Project description:We investigated changes in gene expression in rice plants exposed to RDV to gain some insight into the fundamental physiological and biochemical changes that are induced by viral infection, in the hope of finding clues that might help to control the viral disease. An analysis, using microarrays, of gene expression in rice plants infected with Rice dwarf virus revealed significant decreases in levels of expression of genes that are involved in the formation of cell walls, reflecting the stunted growth of diseased plants. The expression of plastid-related genes was also suppressed, as anticipated from the white chlorotic appearance of infected leaves. By contrast, the expression of defense- and stress-related genes was enhanced after viral infection. Keywords: disease state analysis

2007-03-14 | GSE5286 | GEO

Oryza sativa strain:Black Rice | cultivar:Black Rice

Project description:Oryza sativa strain:Black Rice | cultivar:Black Rice Raw sequence reads

| PRJNA681071 | ENA

Transcriptome analysis of rice infected with three RDV strains

Project description:Rice dwarf virus (RDV) is the causal agent of rice dwarf disease which causes severe loss of rice yield in northern Asia countries. The disease symptoms are stunting of plant growth, chlorosis specks on leaves, and delayed and incomplete panicle exertion. Symptom severity was different among three strains (RDV-O, –D84, and -S), and was in the rank order RDV-O < -D84, < -S. In this study, we have analyzed the relationship between symptom severity and host gene responses by the gene expression analysis through the 60-mer oligo microarray. Keywords: virus infection, disease response

2011-07-02 | GSE24937 | GEO

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