Fusarium oxysporum f. sp. lycopersici 4287
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA18813 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| AAXH01.dat.gz | Other | |||
| AAXH01.fasta.gz | Fasta.gz | |||
| AAXH01.master.dat | Other | |||
| AAXH01.dat.gz | Other |
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Project description:To further understand the abnormal phenotype of the calcineurin mutant strains and identify calcineurin-mediated genes in F. oxysporum f. sp. lycopersici, we performed RNA sequencing to compare the transcriptome profiles of the wild-type (WT), Δcna1(HFW1) and Δcnb1 (HFW3) mutants. By pairwise analysis, a total of 2139 genes were differentially expressed between WT and Δcna1 mutant based on the selection criteria of four-fold change in expression (Log2 fold change > 2 or < -2, P < 0.05). Among these, 1079 genes were upregulated and 1060 genes were downregulated. Moreover, from the comparison of WT against Δcnb1 mutant, 1412 gene were being regulated, and 840 genes were upregulated while 572 genes were downregulated. To elucidate genes that were regulated by calcineurin in F. oxysporum f. sp. lycopersici, the gene sets obtained from the pairwise analyses were compared, giving an overlap of 737 genes. Among these, 414 genes were found to be downregulated and 323 were upregulated, indicating that these genes possibly involved in the calcineurin pathway. GO functional analysis showed these transcripts were mainly involved in the oxidation-reduction process, single-organism metabolic process, transporter activity, cofactor binding, and other metabolic and biological processes.
2020-11-16 | GSE137468 | GEO
Project description:Fusarium oxysporum f. sp. lycopersici 4287 Genome sequencing and assembly
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Project description:Fusarium oxysporum f. sp. lycopersici 4287 Genome sequencing and assembly
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Project description:The genomes of many filamentous fungi consist of a 'core' part containing conserved genes essential for normal development as well as conditionally dispensable (CD) or lineage-specific (LS) chromosomes. In the plant-pathogenic fungus Fusarium oxysporum f. sp. lycopersici, one LS chromosome harbours effector genes that contribute to pathogenicity. We employed flow cytometry to select for events of spontaneous (partial) loss of either the two smallest LS chromosomes or two different core chromosomes. We determined the rate of spontaneous loss of the 'effector' LS chromosome in vitro at around 1 in 35 000 spores. In addition, a viable strain was obtained lacking chromosome 12, which is considered to be a part of the core genome. We also isolated strains carrying approximately 1-Mb deletions in the LS chromosomes and in the dispensable core chromosome. The large core chromosome 1 was never observed to sustain deletions over 200 kb. Whole-genome sequencing revealed that some of the sites at which the deletions occurred were the same in several independent strains obtained for the two chromosomes tested, indicating the existence of deletion hotspots. For the core chromosome, this deletion hotspot was the site of insertion of the marker used to select for loss events. Loss of the core chromosome did not affect pathogenicity, whereas loss of the effector chromosome led to a complete loss of pathogenicity.
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Project description:Fusarium oxysporum f. sp. lycopersici 4287 Genome sequencing
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Project description:Temperature shift experiment to assay heat stress response
2018-05-23 | GSE113332 | GEO
Project description:Fusarium oxysporum f. sp. lycopersici 4287 Raw sequence reads
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Project description:The present study aimed at the molecular characterization of pathogenic and non pathogenic F. oxysporum f. sp. lycopersici strains isolated from tomato. The causal agent isolated from symptomatic plants and soil samples was identified based on morphological and molecular analyses. Pathogenicity testing of 69 strains on five susceptible tomato varieties showed 45% of the strains were highly virulent and 30% were moderately virulent. Molecular analysis based on the fingerprints obtained through ISSR indicated the presence of wide genetic diversity among the strains. Phylogenetic analysis based on ITS sequences showed the presence of at least four evolutionary lineages of the pathogen. The clustering of F. oxysporum with non pathogenic isolates and with the members of other formae speciales indicated polyphyletic origin of F. oxysporum f. sp. lycopersici. Further analysis revealed intraspecies variability and nucleotide insertions or deletions in the ITS region among the strains in the study and the observed variations were found to be clade specific. The high genetic diversity in the pathogen population demands for development of effective resistance breeding programs in tomato. Among the pathogenic strains tested, toxigenic strains harbored the Fum1 gene clearly indicating that the strains infecting tomato crops have the potential to produce Fumonisin.
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Project description:Fusarium oxysporum is a pathogenic fungus that infects hundreds of plant species. This paper reports the improved genome assembly of a reference strain, F. oxysporum f. sp. lycopersici Fol4287, a tomato pathogen.
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Project description:Endophytic fungal-based biopesticides are sustainable and ecologically-friendly biocontrol agents of several pests and diseases. However, their potential in managing tomato fusarium wilt disease (FWD) remains unexploited. This study therefore evaluated effectiveness of nine fungal isolates against tomato fusarium wilt pathogen, Fusarium oxysporum f. sp. lycopersici (FOL) in vitro using dual culture and co-culture assays. The efficacy of three potent endophytes that inhibited the pathogen in vitro was assessed against FWD incidence, severity, and ability to enhance growth and yield of tomatoes in planta. The ability of endophytically-colonized tomato (Solanum lycopersicum L.) plants to systemically defend themselves upon exposure to FOL were also assessed through defence genes expression using qPCR. In vitro assays showed that endophytes inhibited and suppressed FOL mycelial growth better than entomopathogenic fungi (EPF). Endophytes Trichoderma asperellum M2RT4, Hypocrea lixii F3ST1, Trichoderma harzianum KF2R41, and Trichoderma atroviride ICIPE 710 had the highest (68.84-99.61%) suppression and FOL radial growth inhibition rates compared to EPF which exhibited lowest (27.05-40.63%) inhibition rates. Endophytes T. asperellum M2RT4, H. lixii F3ST1 and T. harzianum KF2R41 colonized all tomato plant parts. During the in planta experiment, endophytically-colonized and FOL-infected tomato plants showed significant reduction of FWD incidence and severity compared to non-inoculated plants. In addition, these endophytes contributed to improved growth promotion parameters and yield. Moreover, there was significantly higher expression of tomato defence genes in T. asperellum M2RT4 colonized than in un-inoculated tomato plants. These findings demonstrated that H. lixii F3ST1 and T. asperellum M2RT4 are effective biocontrol agents against FWD and could sustainably mitigate tomato yield losses associated with fusarium wilt.
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