Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Digital gene expression (DGE) of CMV-infected tobacco leaves

ABSTRACT: Here we performed a transcriptomic study on complete symptom development process of CMV-infected Nicotiana tabacum using Solexa/Illumina's high-throughput digital gene expression (DGE) system. 12 DGE libraries (from six virus-infected samples and six corresponding mock-inoculated samples) were constructed, and the gene expression variations between the virus-infected sample and the mock-inoculated sample in each symptom stage were compared. Thousands of differentially expressed genes were obtained by the comparison, and KEGG pathway analysis of these genes suggested that many biological processes (such as phtosynthesis, pigment metabolism and plant-pathogen interaction) were related to the symptom development. The authenticity of the DGE data was further confirmed by analyzing real-time RT-PCR using several random-selected genes. We sequenced a cDNA library constructed from mixture of total RNA from six virus-infected samples and six mock-inoculated samples to get gene information for tobacco leaves in different symptom stages, including vein clearing, mosaic, severe chlorosis, partial recovery, total recovery and re-mosaic, and 95,916 Unigenes were obtained Tobacco leaves were inoculated by CMV-infected leaf homogenate and healthy leaf homogenate, respectivley. Six time points with different symptom stage were selected, and one virus-infect sample and one mock-inoculated sample were collected at each time. In order to average out variation of different plants, five leaves from five different plants were mixed to prepare every RNA sample. Twelve individual tag libraries of samples (six infected samples and six mock-inoculated samples) were constructed in parallel. For the gene expression analysis, the twelve samples were grouped into six groups, and each group contained a virus-infected sample and a mock-inoculated sample collected at the same time. In each group, the DGE data of virus-infected sample were compared to that of mock-inoculated sample to obtain the gene expression variations. Illumina sequencing of transcripts from virus-infected and mock-inoculated samples to get gene information for tobacco leaves in different symptom stages. In order to get more gene information, the systemically infected leaves and mock-inoculated leaves were harvested at six time points and five leaves from five different plants were collected at each time point. The RNA-Seq analysis provided gene information for mock-inoculated and virus-infected tobacco leaves in different symptom stages.

ORGANISM(S): Nicotiana tabacum

SUBMITTER: Jie Lu

PROVIDER: E-GEOD-30162 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptome analysis of Nicotiana tabacum infected by Cucumber mosaic virus during systemic symptom development.

Lu Jie J Du Zhi-Xin ZX Kong Jun J Chen Ling-Na LN Qiu Yan-Hong YH Li Gui-Fen GF Meng Xiao-Hua XH Zhu Shui-Fang SF

PloS one 20120828 8

Virus infection of plants may induce a variety of disease symptoms. However, little is known about the molecular mechanism of systemic symptom development in infected plants. Here we performed the first next-generation sequencing study to identify gene expression changes associated with disease development in tobacco plants (Nicotiana tabacum cv. Xanthi nc) induced by infection with the M strain of Cucumber mosaic virus (M-CMV). Analysis of the tobacco transcriptome by RNA-Seq identified 95,916 ...[more]

PMID: 22952684

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Project description:Objectives: Our work focuses on the responses of Solanaceous plants to viruses that cause economically important diseases in tree fruits. Using mock inoculated leaf tissue as a reference, we plan to compare the gene expression profiles of Nicotiana Benthamiana plants infected with one of three viruses; Plum Pox Potyvirus (PPV), Tomato Ringspot Nepovirus (ToRSV), and Prunus Nectrotic Ringspot Nepovirus (PNRSV). Our goals are as follows: (1) Identify genes that are induced/repressed in response to individual viruses. (2) Identify genes that are induced/repressed in response to all 3 viruses. (3) Compare results to existing potato array data to look for similarities in responses to other pathogens. Experimental Design: Nicotiana benthamiana plants were inoculated with one of three viruses: PPV, ToRSV, or PNRSV. 3 week old plants were inoculated by rubbing virus infected plant sap onto leaves dusted with carborundum. Control plants were mock inoculated using sap from healthy plants. All plants were maintained in a growth chamber at 22C for 18 days. 8 plants were inoculated with each virus or mock inoculated. This experiment was repeated twice. 4 biological replicates derived from 2 virus infected plants from each replica experiment (4 plants) are to be used for hybridizations. RNA from all mock inoculated plants was similarly pooled to create 4 biological replicates. Each replicate control will serve as a universal reference sample that is to be hybridized pair wise with each of the three virus infected samples. RNA extraction: After 18 days, un-inoculated leaves displaying clear symptoms were harvested and immediately frozen in liquid N2. Total RNA was purified using Trizol according to TIGRs listed protocol. RNA was subsequently treated with Turbo DNA-free RNase (Ambion cat#1907). Finally, total RNA was further purified on RNeasy columns (Qiagen) according to manufacturer’s instructions and quantified using a Nanodrop spectrophotometer. Keywords: Reference design 23 hybs total

Project description:Virus resistances that are recessively inherited are associated with loss-of-susceptibility resistance alleles. Resistance to Watermelon mosaic virus (WMV) of melon accession TGR-1551 is expressed as a drastic reduction of the virus titer, and is recessively inherited. In this work, viral RNA accumulation was measured in TGR-1551 and in susceptible WMV-infected melon plants by real time quantitative PCR (qPCR), and gene expression of 17,443 unigenes represented in a melon microarray was monitored in a time-course experiment. Virus accumulation was higher in inoculated cotyledons of the resistant genotype up to 7 days post-inoculation; from this time on, virus accumulation was much higher in plants of the susceptible genotype. Microarray experiments were carried with samples from inoculated cotyledons at 1 and 3 dpi to monitor early changes in response to virus infection, and at 7 dpi. Samples from systemically infected leaves harvested at 15 dpi were also included in the analysis. Results showed much more profound transcriptomic alterations in resistant plants compared to susceptible ones. Analyses of gene expression profiles reveal deep and extensive transcriptomic alterations in TGR-1551 plants, many of them involving pathogen response-related genes. Overall, data suggested that resistance to WMV in TGR-1551 is associated with a defense response, contrasting with its recessive nature. Two melon genotypes have been used to analyse transcriptomic responses to infection by Watermelon mosaic virus: Tendral (susceptibel to WMV) and TGR-1551 (resistant to WMV). For each genotype, 60 melon seedlings were inoculated with WMV-M116 and another 60 were mock-inoculated. Cotyledons of 10 plants were harvested at 1, 3, 5, 7, 9 and 15 dpi. At 15 dpi, the systemically infected second true leaf was also harvested. To reduce variability, each biological replicate used in this study was prepared by mixing the RNA extracts from 2 or 4 mock or WMV-inoculated cotyledons, respectively, or from 3 melon leaves. Samples (WMV infected and mock inoculated) corresponding to cotyledons at 1, 3 and 7 dpi, and leaves at 15 dpi were used for microarray hybridisations, three biological replicates for each one, leading to a total of 48 samples.

Dataset Information

Digital gene expression (DGE) of CMV-infected tobacco leaves

Publications

Transcriptome analysis of Nicotiana tabacum infected by Cucumber mosaic virus during systemic symptom development.

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