Draft Genome Sequence and De Novo Assembly of a Fusarium oxysporum f. sp. lycopersici Isolate Collected from the Andean Region in Colombia.
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ABSTRACT:
SUBMITTER: Yu PL
PROVIDER: S-EPMC8759360 | biostudies-literature |
REPOSITORIES: biostudies-literature
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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:Many studies have shown that several Greek ecosystems inhabit very interesting bacteria with biotechnological properties. Therefore Streptomyces isolates from diverse Greek habitats were selected for their antifungal activity against the common phytopathogenic fungus Fusarium oxysporum. The isolate encoded ACTA1551, member of Streptomyces genus, could strongly suppress the fungal growth when examined in antagonistic bioassays in vitro. The isolate was found phylogenetically relative to Streptomyces rochei after analyzing its 16S rDNA sequence. The influence of different environmental conditions, such as medium composition, temperature, and pH on the expression of the antifungal activity was thoroughly examined. Streptomyces rochei ACTA1551 was able to protect tomato seeds from F. oxysporum infection in vivo while it was shown to promote the growth of tomato plants when the pathogen was absent. In an initial effort towards the elucidation of the biochemical and physiological nature of ACTA1551 antifungal activity, extracts from solid streptomycete cultures under antagonistic or/and not antagonistic conditions were concentrated and fractionated. The metabolites involved in the antagonistic action of the isolate showed to be more than one and produced independently of the presence of the pathogen. The above observations could support the application of Streptomyces rochei ACTA1551 as biocontrol agent against F. oxysporum.
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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:In Colombia, tomato production under protected conditions represents an important economic contribution to the agricultural sector. Fusarium wilt diseases, caused by pathogenic formae speciales of the soil-borne fungus Fusarium oxysporum Schltdl., cause significant yield losses in tomatoes throughout the world. Investigation of the F. oxysporum-tomato pathosystem in Colombia is required to develop appropriate alternative disease management. In this study, 120 fungal isolates were obtained from four different departments in the Central Andean Region in Colombia from tomato crops with symptoms of wilt disease. A molecular characterization of the fungal isolates was performed using the SIX1, SIX3, and SIX4 effector genes of Fusarium oxysporum f. sp. lycopersici W.C. Snyder & H.N. Hansen (Fol). Additionally, we developed a new specific marker to distinguish between Fusarium oxysporum f. sp. radicis-lycopersici Jarvis & Shoemaker (Forl) and Fol isolates. Furthermore, a phylogenetic analysis using the Translation Elongation Factor 1-alpha (EF1a) gene was performed with the collected isolates. Two isolates (named Fol59 and Fol-UDC10) were identified as Fol race 2, four isolates were identified as Forl, six isolates were identified as F. solani, and most of the isolates were grouped within the F. oxysporum species complex. The phylogenetic tree of EF1a showed that most of the isolates could potentially correspond to nonpathogenic strains of F. oxysporum. Additional pathogenicity assays carried out with Fol59 and Fol-UDC10 confirmed that both isolates were highly virulent strains. This study represents a contribution to the understanding of the local interaction between tomatoes and F. oxysporum in Colombia.
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Project description:Fusarium wilt of tomato, caused by the soilborne fungus Fusarium oxysporum f. sp. lycopersici, is an increasingly important disease of tomato. This paper reports the high-quality draft genome assembly of F. oxysporum f. sp. lycopersici isolate D11 (race 3), which consists of 39 scaffolds with 57,281,978 bp (GC content, 47.5%), an N50 of 4,408,267 bp, a mean read coverage of 99.8×, and 17,682 predicted genes.
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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:Fusarium wilt of tomato caused by the ascomycetous fungus Fusarium oxysporum f. sp. lycopersici (Fol) is widespread in most tomato planting areas. Calcineurin is a heterodimeric calcium/calmodulin-dependent protein phosphatase comprised of catalytic (Cna1) and regulatory (Cnb1) subunits. Calcineurin has been studied extensively in human fungal pathogens, but less is known about its roles in plant fungal pathogens. It is known that calcineurin regulates fungal calcium signaling, growth, drug tolerance, and virulence. However, the roles of calcineurin in Fol have not yet been characterized. In this study, we deleted calcineurin CNA1 and CNB1 genes to characterize their roles in conidiation, chlamydospore formation and virulence in Fol. Our results revealed that both cna1 and cnb1 mutants show defects in calcineurin phosphatase activity, vegetative growth and conidiation as compared to the wild type. Furthermore, calcineurin mutants exhibited blunted and swollen hyphae as observed by scanning electron microscopy. Interestingly, we found that Fol calcineurin is critical for chlamydospore formation, a function of calcineurin previously undocumented in the fungal kingdom. According to transcriptome analysis, the expression of 323 and 414 genes was up- and down-regulated, respectively, in both cna1 and cnb1 mutants. Based on the pathogen infection assay, tomato plants inoculated with cna1 or cnb1 mutant have a dramatic reduction in disease severity, indicating that calcineurin has a vital role in Fol virulence. In conclusion, our findings suggest that Fol calcineurin is required, at least in part, for phosphatase activity, vegetative growth, conidiation, chlamydospore formation, and virulence.
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Project description:Temperature shift experiment to assay heat stress response
2018-05-23 | GSE113332 | GEO
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