Ontology highlight
ABSTRACT:
PROVIDER: PRJNA669287 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12852306.fastq.gz | Fastqsanger.gz | |||
| SRR12852307.fastq.gz | Fastqsanger.gz | |||
| SRR12852308.fastq.gz | Fastqsanger.gz | |||
| SRR12852614.fastq.gz | Fastqsanger.gz | |||
| SRR12852615.fastq.gz | Fastqsanger.gz |
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Project description:Many virus diseases of economic importance to agriculture result from mixtures of different pathogens invading the host at a given time. This contrasts with the relatively scarce studies available on the molecular events associated with virus-host interactions in mixed infections. In comparison to single infections, co-infection of Nicotiana benthamiana with Potato virus X (PVX) and Potato virus Y (PVY) resulted in increased systemic symptoms (synergism) that led to necrosis of the newly emerging leaves, and the plant death. A comparative transcriptional analysis was undertaken to identify quantitative and qualitative differences in gene expression during this synergistic infection, and to correlate these changes with the severe symptoms it caused. Global transcription profiles of doubly-infected leaves were compared with those from singly-infected leaves using gene ontology enrichment analysis and metabolic pathway annotator software. Functional gene categories altered by the double infection comprise suites of genes regulated coordinately, which are associated with chloroplast functions (down-regulated), protein synthesis and degradation (up-regulated), carbohydrate metabolism (up-regulated), and response to biotic stimulus and stress (up-regulated). The expression of reactive oxygen species-generating enzymes as well as several mitogen-activated protein kinases, were also significantly induced. Accordingly, synergistic infection induced a severe oxidative stress in N. benthamiana leaves, as judged by increases in lipid peroxidation, and by the generation of superoxide radicals in chloroplasts, which correlated with the misregulation of antioxidative genes in microarray data. Interestingly, expression of genes encoding oxylipin biosynthesis was uniquely up-regulated by the synergistic infection. Virus-induced gene silencing of alfa-dioxygenase1 delayed cell death during PVX-PVY infection. Using mock inoculated leaf tissue as a reference, we compare the gene expression profiles of Nicotiana benthamiana plants infected with one of two viruses, Potato virus X (PVX) or Potato virus Y (PVY), or the combination PVX plus PVY. 3 biological replicates per treatment were independently grown and haversted.
2010-05-16 | E-GEOD-15538 | biostudies-arrayexpress
Project description:The general aim was to better understand the role of StTGA2.1 in plant immunity by transcriptional profiling of plants overexpressing the salicylic acid pathwas related TGA transcription factor StTGA2.1 after infection with potato virus Y (PVY). Potato non-transgenic cultivar Rywal (NT), Rywal-NahG (NahG), a transgenic line unable to accumulate SA due to salicylate hydroxylase expression, and a transgenic Rywal-NahG line inducibly overexpressing StTGA2.1 (TGA2.1-NahG) using the glucocorticoid-system, in which target gene expression can be controlled by external application of dexamethasone (DEX), were used. The leaves of three plants per genotype were infected with either PVY or mock-inoculum and subsequently treated with DEX. Additionally, three TGA2.1-NahG PVY-infected or mock-inoculated plants were not treated with DEX as control. After four days, PVY infection symtoms appeared as small regions of necrotic tissue called lesions. Tissue sections, containing lesions and their immediate surrounding area, were sampled, allowing us to focus on PVY-affected cells. Total RNA was isolated, DNase treated and sent for library prep and high-throughput sequencing.
2022-12-14 | GSE196078 | GEO
Project description:Potato plants (cv. Russet Burbank) were grown as in vitro plantlets, and transplanted into 12-cm pots in Sunshine Mix #2 (peat/perlite mix) supplemented with slow release fertilizer (Osmocoat) in the greenhouse. The experiment was conducted in the summer of 2004 at Moscow, ID. Plantings were staggered to facilitate collection of volatiles and leaf samples during a short harvest window for all times of all treatments. Infectious Green Peach Aphids were raised on PLRV-infected potato plants; test plants were infected by placing 10 infectious aphids on a leaf in a clip cage for 48 h. The control plants for PLRV were similarly treated with aphids that had been raised on uninfected potato plants. A local isolate of PVYO was inoculated mechanically using purified virus (5 ìg ml-1) in buffer (50 mM Na2HPO4, 20 mM Na2SO3 pH 7.0) lightly rubbed onto a leaf previously dusted with carborundum. Control plants for PVY were treated in the same manner using buffer without PVY. The RNA samples were made from systemically affected leaves, excluding the actual leaves inoculated by aphids or that received the mechanical infection. Leaf volatiles were concurrently collected from equivalent plants; aliquots of frozen leaf samples were sent for metabolite analysis prior to RNA extraction. Leaf harvests were made 1, 3, 7, 14, and 28 d post-inoculation. Keywords: Direct comparison
2007-09-01 | GSE8213 | GEO
Project description:Many virus diseases of economic importance to agriculture result from mixtures of different pathogens invading the host at a given time. This contrasts with the relatively scarce studies available on the molecular events associated with virus-host interactions in mixed infections. In comparison to single infections, co-infection of Nicotiana benthamiana with Potato virus X (PVX) and Potato virus Y (PVY) resulted in increased systemic symptoms (synergism) that led to necrosis of the newly emerging leaves, and the plant death. A comparative transcriptional analysis was undertaken to identify quantitative and qualitative differences in gene expression during this synergistic infection, and to correlate these changes with the severe symptoms it caused. Global transcription profiles of doubly-infected leaves were compared with those from singly-infected leaves using gene ontology enrichment analysis and metabolic pathway annotator software. Functional gene categories altered by the double infection comprise suites of genes regulated coordinately, which are associated with chloroplast functions (down-regulated), protein synthesis and degradation (up-regulated), carbohydrate metabolism (up-regulated), and response to biotic stimulus and stress (up-regulated). The expression of reactive oxygen species-generating enzymes as well as several mitogen-activated protein kinases, were also significantly induced. Accordingly, synergistic infection induced a severe oxidative stress in N. benthamiana leaves, as judged by increases in lipid peroxidation, and by the generation of superoxide radicals in chloroplasts, which correlated with the misregulation of antioxidative genes in microarray data. Interestingly, expression of genes encoding oxylipin biosynthesis was uniquely up-regulated by the synergistic infection. Virus-induced gene silencing of alfa-dioxygenase1 delayed cell death during PVX-PVY infection.
2009-07-07 | GSE15538 | GEO
Project description:The goal of these studies is analysis of gene expression profiles in potato plants infected with potato virus Y (necrotic strain - PVYN). A prototypic plant pathogen interaction system used to study disease resistance is tobacco (Nicotiana tabacum) and tobacco mosaic virus (TMV). In tobacco, the resistance response comprises two phenomena, known as the hypersensitive response (HR) and systemic acquired resistance (SAR). HR is typically characterized by a local necrosis surrounding the site of viral entry leading to restriction of pathogen replication and spread. SAR is the enhanced ability of the plant to resist a secondary challenge by the same or a different pathogen inoculated elsewhere on the plant. The identity of the signal(s) that induces HR and SAR is still poorly understood. Plants of S. tuberosum cv. Rywal, resistant to all known (N, 0, NTN) PVY strains, were grown in growth chambers using 16 h period of light (22°C) and 8 h of darkness (18°C). For all experiments, 6-week-old plants were used. For inoculation with PVY, carborundum-dusted leaves were rubbed with water (mock control) or PVYN solution (1 µg ml-1). Two to four leaves were inoculated on each plant and harvested together at 1, 3, and 6 days post inoculation (dpi). Separately, noninoculated leaves were harvested at the same time points (upper leaves). The first time point (1 dpi) has been chosen to study the early stage of plant response before necrotic lesion formation. At 3 dpi necrotic lesions start to appear, and at 6 dpi necroses are fully developed which correlates with the maximum of salicylic acid increase in virus inoculated leaves. Keywords: Direct comparison
2008-02-13 | GSE10488 | GEO
Project description:Time series response of potato cv. Désirée, which is tolerant to PVY infection, was analysed in both inoculated as well as upper non-inoculated leaves. Additionally, transgenic plants deficient in accumulation of salicylic acid (NahG- Désirée) were studied in the same setting.
2015-08-06 | GSE58593 | GEO
Project description:Pti5 is an ERF transcription factor that was differentially expressed in PVY-infected potato plants. The purpose of generating this dataset was to identify genes with perturbed expression due to silencing the Pti5 gene. Grant ID: P4-0165 Slovenian Research Agency ARRS Biotechnology and Plant Systems Biology Grant ID: J4-7636 Slovenian Research Agency ARRS Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato Grant ID: J4-1777 Slovenian Research Agency ARRS Unraveling mechanisms of effectiveness and specificity in potato immune signaling through innovative data acquisition and modeling
2020-04-11 | GSE136877 | GEO
Project description:Time series response of potato cv. Désirée, which is tolerant to PVY infection, was analysed in both inoculated as well as upper non-inoculated leaves. Additionally, transgenic plants deficient in accumulation of salicylic acid (NahG- Désirée) were studied in the same setting. 2 genotypes, mock and virus inoculated plants, inoculated (1-7dpi) and non-inoculated (1-11 dpi) leaves; one-colour design
2015-08-06 | E-GEOD-58593 | biostudies-arrayexpress
Project description:Time series response of potato cv. Désirée, which is tolerant to PVY infection, was analysed in both inoculated as well as upper non-inoculated leaves. Additionally, transgenic plants deficient in accumulation of salicylic acid (NahG- Désirée) were studied in the same setting.
2019-09-25 | PXD015221 | Pride
Project description:In order to identify cellular proteins interacting with the coat protein (CP) of Potato virus Y (PVY), we used coimmunoprecipitation of GFP-CP in PVY-infected Nicotiana benthamiana plants. To be able to pull down non-abundant interactors and to stabilize transient interactions, we used the crosslinker dithiobis(succinimidyl propionate) (DSP). With this we were able to identify a total of 147 potential CP interactors.
2017-12-18 | PXD007836 | Pride