Fusarium
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA289542 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR2098571_1.fastq.gz | Fastqsanger.gz | |||
| SRR2098571_2.fastq.gz | Fastqsanger.gz | |||
| SRR2098563_1.fastq.gz | Fastqsanger.gz | |||
| SRR2098563_2.fastq.gz | Fastqsanger.gz |
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Project description:Sudden death syndrome (SDS) is caused by the ascomycete fungus, Fusarium virguliforme. The pathogen secretes one or more toxins into the infected soybean roots to cause foliar SDS. This study investigated if the xylem sap of F. virguliforme-infected soybean plants contains secreted F. virguliforme-proteins, some of which could be involved in foliar SDS development.
2014-05-23 | PXD000873 | Pride
Project description:Sudden death syndrome (SDS) caused by the fungal pathogen, Fusarium virguliforme, is a major threat to soybean production in North America. There are two major components of this disease: (i) root necrosis and (ii) foliar SDS. Root symptoms consist of root necrosis with vascular discoloration that extends upto several nodes and internodes into the stem. Foliar SDS symptom is characterized by interveinal chlorosis and necrosis in leaves which finally curl and fall off, and in severe cases by flower, pod abscission and immature seed formation. A major toxin involved in initiating foliar SDS has been identified. Nothing is known about how root necrosis develops. In order to unravel the mechanisms used by the pathogen to cause root necrosis, the transcriptome of the pathogen in infected soybean root tissues of a susceptible cultivar (Williams 82) was investigated. The transcriptomes of the germinating conidia and mycelia were also examined. Of the 14,845 predicted F. virguliforme genes, we observed that 12,017 (81%) were expressed in germinating conidial spores and 12,208 (82%) in mycelia and 10,626 (72%) in infected soybean roots. Of the 10,626 genes induced in infected roots, 224 were transcribed only following infection. Expression of several infection-induced genes encoding enzymes with oxidation-reduction properties suggests that degradation of antimicrobial compounds such as the phytoalexin, glyceollin could be important in establishing the biotrophic phase. Enzymes with hydrolytic and catalytic activities could play an important role in the transitioning of the pathogen from biotrophic to necrotrophic phase. Expression of a large number of genes encoding enzymes with catalytic and hydrolytic activities during late infection stage suggests cell wall degradation by some of these enzymes could be involved in root necrosis and establishing the necrotrophic phase in this pathogen.
2016-08-30 | GSE86201 | GEO
Project description:Many of the microorganisms that are normally present in the soil, actually inhabit the rhizosphere and interact with plants. Those plant–microorganisms interactions may be beneficial or harmful. Among the first are the arbuscular mycorrhizal fungi (AMF). These soil fungi have been reported to improve plant resistance/tolerance to pests and diseases. On the other hand, soilborne pathogens represent a threat to agriculture generating important yield losses, depending upon the pathogen and the crop. One example is the “Sudden Death Syndrome” (SDS), a severe disease in soybean (Glycine max (L.) Merr) caused by a complex of at least four species of Fusarium sp., among which Fusarium virguliforme and F. tuccumaniae are the most prevalent in Argentina. This study provides, under strict in vitro culture conditions, a global analysis of transcript modifications in mycorrhizal and non-mycorrhizal soybean root associated with F. virguliforme inoculation. Microarray results showed qualitative and quantitative changes in the expression of defense-related genes in mycorrhizal soybean, suggesting that AMF are good candidates for sustainable plant protection against F. virguliforme.
2018-11-12 | GSE108964 | GEO
Project description:Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and specificity in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and specificity. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by about 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR analysis of a total of 20 randomly selected genes and purine-ureides pathway genes demonstrated an increased specificity after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The results from this study suggested that transcript profiling in common bean can be done using the soybean GeneChip. However, a significant decrease in sensitivity and specificity can be expected. Problems associated with CSH GeneChip data can be mitigated by masking probes targeting ISV regions. In addition to transcript profiling CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies. We hybridized cRNA purified from nodule, leaf, and root of common bean and soybean in, triplicate, to the soybean GeneChip (18 GeneChip hybridizations = 2 species x 3 organs x 3 replicates).
2010-03-07 | E-GEOD-18822 | biostudies-arrayexpress
Project description:Across Canada, infections associated with Fusarium have a devastating impact on the agricultural sector. For example, Fusarium head blight (FHB) costs the Canadian grain industry over $1.5 billion annually in diminished export and domestic sales. For Ontario’s most productive and lucrative crops infection by Fusarium spp., leads to losses of over $200 million annually through yield reduction in corn (i.e., stalk and ear rot), cereals (i.e., FHB), and soybeans (i.e., root rot and sudden death syndrome). Additionally, mycotoxin production by Fusarium spp. (e.g., deoxynivalenol [DON]) has severe consequences for the livestock and poultry industries through consumption of contaminated feed, as well as concerns for human health upon consumption of contaminated processed grains. Current management strategies against FHB rely on fungicide application at heading, which reduces infection but does not limit the accumulation of dangerous mycotoxins within the grains. Moreover, such fungicide applications substantially increase the economic cost to growers, raise public concerns over chemical exposure, and contribute to the development of antimicrobial resistance. The critical role of Fusarium fungal pathogens and their toxins in the health of crops, livestock, and humans underscores the need for innovative strategies to better understand mechanisms of disease and identify novel management strategies to limit the incidence of infection and to critically, reduce the accumulation of mycotoxins within infected grains
2022-09-27 | PXD037035 | Pride
Project description:Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and specificity in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and specificity. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by about 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR analysis of a total of 20 randomly selected genes and purine-ureides pathway genes demonstrated an increased specificity after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The results from this study suggested that transcript profiling in common bean can be done using the soybean GeneChip. However, a significant decrease in sensitivity and specificity can be expected. Problems associated with CSH GeneChip data can be mitigated by masking probes targeting ISV regions. In addition to transcript profiling CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies.
2010-03-01 | GSE18822 | GEO
Project description:Serum samples were collected postmortem from infants dying of Sudden Infant Death Syndrome.
2018-08-02 | MSV000082713 | GNPS
Project description:The fungal pathogen Fusarium moniliforme causes ear rot in maize. Ear rot in maize is a destructive disease globally caused by Fusarium moniliforme , due to decrease of grain yield and increase of risks in raising livestock by mycotoxins production. Plants have developed various defense pathways to cope with pathogens. We used microarrays to detail the global programme of gene expression during the infection process of Fusarium moniliforme in its host plant to get insights into the defense programs and the host processes potentially involved in plant defense against this pathogen.
2009-12-16 | GSE19501 | GEO
Project description:Fusarium oxysporum is one of the most common species causing soybean root rot and seedling blight in the U.S. In a recent study, significant variation in aggressiveness was observed among isolates of F. oxysporum collected from roots in Iowa, ranging from highly pathogenic to weakly or non-pathogenic isolates. In the present work, a RNA-seq-based analysis was used for the first time to investigate the molecular aspect of the interaction of a partially resistant soybean genotype with non-pathogenic/pathogenic isolates of F. oxysporum at 72 and 96 hours post inoculation (hpi). Markedly different gene expression profiles were observed in compatible and incompatible host-pathogen combinations. A peak of differentially expressed genes (DEGs) was observed at 72 hpi in soybean roots in response to both isolates, although the number of DEGs was about eight times higher for the pathogenic isolate compared to the non-pathogenic one (1,659 vs. 203 DEGs, respectively). Furthermore, not only the number of genes, but also the magnitude of induction was much greater in response to the pathogenic isolate. This response included a stronger activation of many well-known defense-related genes, and several genes involved in ethylene biosynthesis and signalling, transcription factors, secondary and sugar metabolism. In addition, 1130 fungal genes were differentially expressed between the F. oxysporum isolates in planta during the infection process. Interestingly, 10% of these genes encode plant cell-wall degrading enzymes, reactive oxygen species-related enzymes and fungal proteins involved in primary metabolic pathways. Such information may be useful in the development of new methods of broadening resistance of soybean to F. oxysporum, including the silencing of important fungal genes, and also to understand the molecular basis of soybean-F. oxysporum interactions. Soybean seedlings mRNA profiles inoculated with a non-pathogenic and pathogenic isolates of F. oxysporum and collected at 72 and 96 hpi, were generated using Illumina HiSeq 2500. Control seedlings were also included for each time of inoculation. Three biological replicates were considered for each condition, 18 samples in total.
2016-03-31 | E-GEOD-66861 | biostudies-arrayexpress