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Host-based markers for the early stage of infection by the grapevine trunk pathogen Neofusicoccum parvum

ABSTRACT: In the vineyard, symptoms of the grapevine trunk disease Botryosphaeria dieback do not appear until 1 or 2 years after the causal fungus Neofusicoccum parvum establishes a necrotic canker in the permanent woody structure of the vine. There are preventative management practices, but growers tend to wait until symptoms are widespread, at which point prevention has limited efficacy. Toward development of an early detection tool, we examined the leaves of inoculated vs. non-inoculated plants for differential gene expression via RNASeq. Stems were examined to monitor spread of the infection, and its spatial and temporal relationship to anatomical changes via light microscopy and high resolution computed tomography (HRCT). The early stage of infection occurred prior to 2 months post-inoculation (MPI), at which point spread of the pathogen beyond the inoculation site was greatest. This incubation period was also characterized by the largest stem lesions, the highest levels of fungal colonization and xylem vessels fully-occluded by gels, and the lowest starch content of xylem fibers and rays. Prior to 2 MPI, RNASeq and validative qPCR analysis identified eight candidate markers, which are transcriptionally activated by infection, but not by wounding alone. Our best marker genes, a dehydrin, a BURP domain containing protein and an abscissic acid-induced wheat plasma membrane polypeptide 19 (AWPM-19), identified the pathogen’s presence with high specificity. Screening of genome-wide expression data revealed that this signature is not affected by many abiotic and biotic stresses.

ORGANISM(S): Vitis vinifera

PROVIDER: GSE58653 | GEO | 2015/03/24

SECONDARY ACCESSION(S): PRJNA253108

REPOSITORIES: GEO

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Host-based markers for the early stage of infection by the grapevine trunk pathogen Neofusicoccum parvum

Project description:In the vineyard, symptoms of the grapevine trunk disease Botryosphaeria dieback do not appear until 1 or 2 years after the causal fungus Neofusicoccum parvum establishes a necrotic canker in the permanent woody structure of the vine. There are preventative management practices, but growers tend to wait until symptoms are widespread, at which point prevention has limited efficacy. Toward development of an early detection tool, we examined the leaves of inoculated vs. non-inoculated plants for differential gene expression via RNASeq. Stems were examined to monitor spread of the infection, and its spatial and temporal relationship to anatomical changes via light microscopy and high resolution computed tomography (HRCT). The early stage of infection occurred prior to 2 months post-inoculation (MPI), at which point spread of the pathogen beyond the inoculation site was greatest. This incubation period was also characterized by the largest stem lesions, the highest levels of fungal colonization and xylem vessels fully-occluded by gels, and the lowest starch content of xylem fibers and rays. Prior to 2 MPI, RNASeq and validative qPCR analysis identified eight candidate markers, which are transcriptionally activated by infection, but not by wounding alone. Our best marker genes, a dehydrin, a BURP domain containing protein and an abscissic acid-induced wheat plasma membrane polypeptide 19 (AWPM-19), identified the pathogenâ??s presence with high specificity. Screening of genome-wide expression data revealed that this signature is not affected by many abiotic and biotic stresses. Asymptomatic leaf mRNA profiles of Neofusicoccum parvum infected wounded plants (IW) and non-infected wounded plants (NIW) at two different time points post inoculation (0 MPI, 0.5-1.5 MPI) were generated by deep sequencing in biological triplicates using Illumina HiSeq2500 technology.

2015-03-24 | E-GEOD-58653 | biostudies-arrayexpress

Aggressive Potato virus YNTN (PVYNTN) and mild PVYN isolates trigger different specific responses in susceptible potato

Project description:Potato virus YNTN (PVYNTN) is one of the most devastating potato virus causing great losses in the potato production industry. PVYNTN induces severe symptoms on inoculated leaves and a disease known as potato tuber necrosis ringspot disease (PTNRD) develops on tubers. Closely related PVYN isolate induces only mild symptoms on inoculated potato leaves and no symptoms on tubers. The early response of sensitive potato cvs. Igor and Nadine to inoculation with PVYNTN and PVYN was analysed allowing identification of genes involved in severe symptoms induction. Microarray and quantitative-PCR analysis was carried out to identify differentially expressed genes after inoculation with both virus isolates. Two distinct groups of genes were shown to have a role in severe symptoms development – one group of genes related to energy production and a second group of genes connected with virus spread. Earlier accumulation of sugars and decrease in photosynthesis was observed in leaves inoculated with aggressive PVYNTN isolate than in leaves inoculated with milder PVYN isolate. PVYNTN isolate was shown not to activate differential expression of antioxidant metabolism and pectinmethylesterase inhibitor (PMEI) leading to a delay in plant response and on the other hand it limited callose deposition enabling faster virus spread through the plant.

2009-10-01 | GSE18196 | GEO

Aggressive Potato virus YNTN (PVYNTN) and mild PVYN isolates trigger different specific responses in susceptible potato

Project description:Potato virus YNTN (PVYNTN) is one of the most devastating potato virus causing great losses in the potato production industry. PVYNTN induces severe symptoms on inoculated leaves and a disease known as potato tuber necrosis ringspot disease (PTNRD) develops on tubers. Closely related PVYN isolate induces only mild symptoms on inoculated potato leaves and no symptoms on tubers. The early response of sensitive potato cvs. Igor and Nadine to inoculation with PVYNTN and PVYN was analysed allowing identification of genes involved in severe symptoms induction. Microarray and quantitative-PCR analysis was carried out to identify differentially expressed genes after inoculation with both virus isolates. Two distinct groups of genes were shown to have a role in severe symptoms development â one group of genes related to energy production and a second group of genes connected with virus spread. Earlier accumulation of sugars and decrease in photosynthesis was observed in leaves inoculated with aggressive PVYNTN isolate than in leaves inoculated with milder PVYN isolate. PVYNTN isolate was shown not to activate differential expression of antioxidant metabolism and pectinmethylesterase inhibitor (PMEI) leading to a delay in plant response and on the other hand it limited callose deposition enabling faster virus spread through the plant. Each microarray was hybridized with PVYNTN inoculated sample and PVYN inoculated sample from the same biological replicate. Three biological replicates were analyzed.

2010-05-22 | E-GEOD-18196 | biostudies-arrayexpress

Host gene expression signatures of influenza A H1N1 and H3N2 virus infection in adults

Project description:Diagnosis of influenza A infection is currently based on clinical symptoms and pathogen detection. Use of host peripheral blood gene expression data to classify individuals with influenza A virus infection represents a novel approach to infection diagnosis We used microarrays to assay peripheral blood gene expression at baseline and every 8 hours for 7 days following intranasal influenza A H1N1 or H3N2 inoculation in healthy volunteers. We determined groups of coexpressed genes that classified symptomatic influenza infection. We then tested this gene expression classifier in patients with naturally acquired respiratory illness. We experimentally inoculated healthy volunteers with intranasal influenza A H1N1 and H3N2. Symptoms were documented and peripheral blood samples drawn into PAXgene RNA tubes for RNA isolation. We further enrolled patients presenting to the Emergency Department with naturally acquired respiratory illness, and documented symptoms and collected PAXgene RNA samples for RNA isolation.

2013-11-16 | E-GEOD-52428 | biostudies-arrayexpress

Early response of potato plants to virus (PVY-NTN) inoculation

Project description:Potato virus YNTN (PVYNTN), causing potato tuber ring necrosis disease, dramatically lowers the quantity and the quality of the potato yield all over the world. The cultivar Igor is one of the most susceptible cultivars, developing severe disease symptoms on plants as well as on tubers. Finding genes differentially expressed in the early response to infection, when the host response is more defense- than infection- related, could improve our understanding of the potato - PVYNTN interaction. Differential gene expression in early response of potato cv. Igor plants to PVYNTN infection was studied using potato TIGR cDNA-microarrays. Expression was compared between mock inoculated and virus infected plants 12 hours after inoculation, in four biological replicates. Keywords: direct comparison Each microarray was hybridized with a virus inoculated sample and mock inoculated sample from the same biological replicate. Four biological replicates were analyzed.

2010-05-25 | E-GEOD-10903 | biostudies-arrayexpress

Early response of potato plants to virus (PVY-NTN) inoculation

2008-03-21 | GSE10903 | GEO

1918 pandemic influenza virus and pneumococcus co-infection results in activation of coagulation and widespread pulmonary microvascular thrombosis in mice and humans

Project description:To study the effects of secondary bacterial infection during 1918 pandemic H1N1 influenza virus infection, BALB/c mice were inoculated with the fully reconstructed 1918 influenza virus followed by inoculation with pneumococcus 72h later.

2015-09-20 | GSE70445 | GEO

Arabidopsis protoplasts : TMV*rep vs. TMV*CP.MP transfected

Project description:Transcriptional profiling of Arabidopsis in response to infection with TMV in the initial infection stage (0.5, 4 and 6 hours post inoculation). Analyze the relative transcriptome change of TMV*CP.MP- and TMV*rep-inoculated samples.

2013-04-15 | GSE45283 | GEO

Differential gene expression and physiological changes during acute or persistent plant virus interactions may contribute to viral symptom differences (microarray)

Project description:Viruses have different strategy to infect their hosts. Acute type infection is fast resulting in severe symptoms or in the death of the plant, while in persistent type of interaction the virus can survive within its host for a long period of time with mild symptoms. During our studies we investigated gene expression changes of virus infected Nicotiana benthamiana and Solanum lycopersicum after systemic spread of the virus by two different methods: microarray hybridization and RNA sequencing. Using these high throughput techniques we could easily differentiate between acute and persistent type of infection and validate key expression changes by Northern blot hybridization. We also demonstrated that in persistent infection not only drastic downregulation of important housekeeping genes, but induction of stress genes are missing, making possible for the virus to survive in its host for a long period of time. Symptoms of acute and persistent type virus infection differ markedly and according to our results the type of infection can be distinguished even at an early point by characterizing the photosynthetic activity of virus infected plants. RNA-Seq was made from PVX, TMV infected and mock inoculated leafs in 3 biological replicates and 1 technical repeat

2019-05-06 | GSE113772 | GEO

Transcriptome analysis of Clavibacter michiganensis subsp. michiganensis infected tomato seedlings

Project description:The gram- positive bacterial pathogen Clavibacter michiganensis subsp. michiganensis (Cmm) causes huge economic losses by infecting tomato plants worldwide. Cmm can be spread by contaminated seeds and transplants, penetrating the plant through natural openings or wounds and is transferred through the plant xylem. While in recent years significant progress has been made to elucidate plant responses to pathogenic gram-negative bacteria by gene expression studies, the molecular mechanisms that lead to disease symptoms caused by gram-positive bacteria like Cmm remain elusive. An indigenous virulent Cmm strain isolated from a farm crop of Pomodoro tomatoes in southern Greece was used for the infection of EKSTASIS F1 hybrid tomato seedlings. Here, we present the results of a deep RNA- sequencing (RNA-seq) analysis performed to characterize the dynamic expression profile of tomato genes upon Cmm infection.

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