Glycine max, Fusarium oxysporum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA512928 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8404210.fastq.gz | Fastqsanger.gz | |||
| SRR8404211.fastq.gz | Fastqsanger.gz | |||
| SRR8404212.fastq.gz | Fastqsanger.gz | |||
| SRR8404213.fastq.gz | Fastqsanger.gz | |||
| SRR8404205.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 9 |
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Project description:Fusarium oxysporum is one of the most common fungal pathogens causing soybean root rot and seedling blight in U.S.A. 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.We used RNA-seq analysis to investigate the molecular aspects of the interactions of a partially resistant soybean genotype with non-pathogenic/pathogenic isolates of F. oxysporum at 72 and 96 h post inoculation (hpi). Markedly different gene expression profiles were observed in response to the two isolates. A peak of highly differentially expressed genes (HDEGs) was triggered at 72 hpi in soybean roots and the number of HDEGs was about eight times higher in response to the pathogenic isolate compared to the non-pathogenic one (1,659 vs. 203 HDEGs, respectively). Furthermore, the magnitude of induction was much greater in response to the pathogenic isolate. This response included a stronger activation of defense-related genes, transcription factors, and genes involved in ethylene biosynthesis, secondary and sugar metabolism.The obtained data provide an important insight into the transcriptional responses of soybean-F. oxysporum interactions and illustrate the more drastic changes in the host transcriptome in response to the pathogenic isolate. These results may be useful in the developing new methods of broadening resistance of soybean to F. oxysporum, including the over-expression of key soybean genes.
| S-EPMC4687377 | biostudies-literature
Project description:CdSe quantum dots are often used in industry as fluorescent materials. In this study, CdSe quantum dots were synthesized using Fusarium oxysporum. The cadmium and selenium concentration, pH, and temperature for the culture of F. oxysporum (Fusarium oxysporum) were optimized for the synthesis, and the CdSe quantum dots obtained from the mycelial cells of F. oxysporum were observed by transmission electron microscopy. Ultra-thin sections of F. oxysporum showed that the CdSe quantum dots were precipitated in the intracellular space, indicating that cadmium and selenium ions were incorporated into the cell and that the quantum dots were synthesized with intracellular metabolites. To reveal differences in F. oxysporum metabolism, cell extracts of F. oxysporum, before and after CdSe synthesis, were compared using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The results suggested that the amount of superoxide dismutase (SOD) decreased after CdSe synthesis. Fluorescence microscopy revealed that cytoplasmic superoxide increased significantly after CdSe synthesis. The accumulation of superoxide may increase the expression of various metabolites that play a role in reducing Se4+ to Se2- and inhibit the aggregation of CdSe to make nanoparticles.
| S-EPMC5456586 | biostudies-other
Project description:Cytosine methylation is a base modification that is often used by genomes to store information that is stably inherited through mitotic cell divisions. Most cytosine DNA methylation is stable throughout different cell types or by exposure to different environmental conditions in plant genomes. Here, we profile the epigenomes of ~100 Glycine max lines to explore the extent of natural epigenomic variation. We also use these data to determine the extent to which DNA methylation variants are linked to genetic variations.
2018-05-07 | GSE114074 | GEO
Project description:Molecular characterization of the incompatible and compatible interaction of soybean rust disease in Rpp3-containing PI462312 line
| PRJNA141167 | ENA
Project description:Watermelon (Citrullus lanatus) is one of the most important vegetable crops in the world and accounts for 20% of the world’s total area devoted to vegetable production. Fusarium wilt of watermelon is one of the most destructive diseases in watermelon worldwide. Transcriptome profiling of watermelon during its incompatible interactions with Fusarium oxysporum f.sp. niveum (FON) was generated using an Agilent custom microarray which contains 15,000 probes representing approximately 8,200 watermelon genes. A total of 24, 275, 596, 598, and 592 genes that are differentially expressed genes between FON- and mock-inoculated watermelon roots at 0.5, 1, 3, 5 and 8 days post inoculation (dpi), respectively, were identified. Bioinformatics analysis of these differentially expressed genes revealed that during the incompatible interaction between watermelon and FON, the expression of a number of pathogenesis-related (PR) genes, transcription factors, signaling/regulatory genes, and cell wall modification genes, was significantly induced. A number of genes for transporter proteins such as aquaporins were down-regulated, indicating that transporter proteins might contribute to the development of wilt symptoms after FON infection. In the incompatible interaction, most genes involved in biosynthesis of jasmonic acid (JA) showed expressed stronger and more sustained than those in compatible interaction in FON-infected tissues. Similarly, genes associated with shikimate-phenylpropanoid-lignin biosynthesis were also induced in incompatible interaction, but expression of these genes were not changed or repressed in the compatible interaction. Fusarium oxysporum f.sp. niveum induced gene expression in watermelon root was measured at 0.5,1d, 3d, 5d and 8d after inoculation. Sample inoculated with water were used as the mock controls. Three independent experiments were performed.
2011-06-09 | E-GEOD-29804 | biostudies-arrayexpress
Project description:Watermelon (Citrullus lanatus) is one of the most important vegetable crops in the world and accounts for 20% of the world’s total area devoted to vegetable production. Fusarium wilt of watermelon is one of the most destructive diseases in watermelon worldwide. Transcriptome profiling of watermelon during its incompatible interactions with Fusarium oxysporum f.sp. niveum (FON) was generated using an Agilent custom microarray which contains 15,000 probes representing approximately 8,200 watermelon genes. A total of 24, 275, 596, 598, and 592 genes that are differentially expressed genes between FON- and mock-inoculated watermelon roots at 0.5, 1, 3, 5 and 8 days post inoculation (dpi), respectively, were identified. Bioinformatics analysis of these differentially expressed genes revealed that during the incompatible interaction between watermelon and FON, the expression of a number of pathogenesis-related (PR) genes, transcription factors, signaling/regulatory genes, and cell wall modification genes, was significantly induced. A number of genes for transporter proteins such as aquaporins were down-regulated, indicating that transporter proteins might contribute to the development of wilt symptoms after FON infection. In the incompatible interaction, most genes involved in biosynthesis of jasmonic acid (JA) showed expressed stronger and more sustained than those in compatible interaction in FON-infected tissues. Similarly, genes associated with shikimate-phenylpropanoid-lignin biosynthesis were also induced in incompatible interaction, but expression of these genes were not changed or repressed in the compatible interaction.
2011-06-09 | GSE29804 | GEO
Project description:The biological relevance of the experiment was to mainly understand the F. oxysporum genes that are involved in the colonization of tomato roots during early interaction timepoints of 1, 2, 3 and 7 days post infection as compared to the in vitro grown axenic sample.
2022-11-30 | E-MTAB-10597 | biostudies-arrayexpress
Project description:BACKGROUND: Clustering the ESTs from a large dataset representing a single species is a convenient starting point for a number of investigations into gene discovery, genome evolution, expression patterns, and alternatively spliced transcripts. Several methods have been developed to accomplish this, the most widely available being UniGene, a public domain collection of gene-oriented clusters for over 45 different species created and maintained by NCBI. The goal is for each cluster to represent a unique gene, but currently it is not known how closely the overall results represent that reality. UniGene's build procedure begins with initial mRNA clusters before joining ESTs. UniGene's results for soybean indicate a significant amount of redundancy among some sequences reported to be unique mRNAs. To establish a valid non-redundant known gene set for Glycine max we applied our algorithm to the clustering of only mRNA sequences. The mRNA dataset was run through the algorithm using two different matching stringencies. The resulting cluster compositions were compared to each other and to UniGene. Clusters exhibiting differences among the three methods were analyzed by 1) nucleotide and amino acid alignment and 2) submitting authors conclusions to determine whether members of a single cluster represented the same gene or not. RESULTS: Of the 12 clusters that were examined closely most contained examples of sequences that did not belong in the same cluster. However, neither the two stringencies of PECT nor UniGene had a significantly greater record of accuracy in placing paralogs into separate clusters. CONCLUSION: Our results reveal that, although each method produces some errors, using multiple stringencies for matching or a sequential hierarchical method of increasing stringencies can provide more reliable results and therefore allow greater confidence in the vast majority of clusters that contain only ESTs and no mRNA sequences.
| S-EPMC1637028 | biostudies-literature
Project description:BACKGROUND:Helitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and their ability to capture and copy genes and regulatory elements. They occur widely in plants and animals, and have thus far been relatively little investigated in fungi. RESULTS:Here, we comprehensively survey Helitrons in several completely sequenced genomes representing the F. oxysporum species complex (FOSC). We thoroughly characterize 5 different Helitron subgroups and determine their impact on genome evolution and assembly in this species complex. FOSC Helitrons resemble members of the Helitron2 variant that includes Helentrons and DINEs. The fact that some Helitrons appeared to be still active in FOSC provided the opportunity to determine whether Helitrons occur as a circular intermediate in FOSC. We present experimental evidence suggesting that at least one Helitron subgroup occurs with joined ends, suggesting a circular intermediate. We extend our analyses to other Pezizomycotina and find that most fungal Helitrons we identified group phylogenetically with Helitron2 and probably have similar characteristics. CONCLUSIONS:FOSC genomes harbour non-canonical Helitrons that are characterized by asymmetric terminal inverted repeats, show hallmarks of recent activity and likely transpose via a circular intermediate. Bioinformatic analyses indicate that they are representative of a large reservoir of fungal Helitrons that thus far has not been characterized.
| S-EPMC5148889 | biostudies-literature
Project description:Plants face many different concurrent and consecutive abiotic and biotic stresses during their lifetime. Roots can be infected by numerous pathogens and parasitic organisms. Unlike foliar pathogens, root pathogens have not been explored enough to fully understand root-pathogen interactions and the underlying mechanism of defense and resistance. PR gene expression, structural responses, secondary metabolite and root exudate production, as well as the recruitment of plant defense-assisting "soldier" rhizosphere microbes all assist in root defense against pathogens and herbivores. With new high-throughput molecular tools becoming available and more affordable, now is the opportune time to take a deep look below the ground. In this addendum, we focus on soil-borne Fusarium oxysporum as a pathogen and the options plants have to defend themselves against these hard-to-control pathogens.
| S-EPMC4623376 | biostudies-other