Evidence of small interfering RNA in the fungus Fusarium fujikuroi (RNA-Seq)
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ABSTRACT:
PROVIDER: PRJNA1064136 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27533872.fastq.gz | Fastqsanger.gz | |||
| SRR27533873.fastq.gz | Fastqsanger.gz | |||
| SRR27533874.fastq.gz | Fastqsanger.gz | |||
| SRR27533875.fastq.gz | Fastqsanger.gz | |||
| SRR27533876.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Evidence of small interfering RNA in the fungus Fusarium fujikuroi
| PRJNA1064131 | ENA
Project description:Evidence of small interfering RNA in the fungus Fusarium fujikuroi (miRNA-Seq)
| PRJNA1064138 | ENA
Project description:RNA interference (RNAi) mechanisms play key regulatory roles in many biological systems, and components of the RNAi pathway are conserved in a wide range of eukaryotic genomes, including those of filamentous fungi. The biotechnological fungus Fusarium fujikuroi, widely used in secondary metabolism studies, contains the complete set of genes expected for RNAi pathways, including dcl1 and dcl2 dicer genes. We have analyzed by means of a high-throughput sequencing technology the content of sRNAs in F. fujikuroi grown in the dark or after one hour of illumination. For comparative purposes, the study was extended to the phytopathogenesis model Fusarium oxysporum, grown under the same conditions. Total RNA samples from each species and growth condition were used to construct RNA libraries, which were subjected to massive sequencing. sRNA preparations included a size cut-off below 150 nt, which covered sRNAs and their precursors. The size distributions and 5' nucleotide preferences of the sRNA reads showed a higher proportion of 5' uracil in the RNA samples of the expected sizes in both species, more noticeable in F. fujikuroi, indicating the occurrence of genuine sRNAs. Consistently, the number of sRNAs mapped at CDS loci was significantly higher in F. fujikuroi compared to F. oxysporum. F. fujikuroi carries at least one transcriptionally expressed copy of a Ty1/copia-like retrotransposable element, in which sRNAs were found in both sense and antisense DNA strands, whereas in F. oxysporum Skippy-like elements are expressed and show siRNA formation. The finding of sRNA in these mobile elements is an indication of an active siRNA-based RNAi pathway. The dcl2 deletion mutants did not show phenotypic alterations or changes in their global transcriptome, while no dcl1 deletion mutants could be obtained.
2024-01-21 | GSE253159 | GEO
Project description:RNA interference (RNAi) mechanisms play key regulatory roles in many biological systems, and components of the RNAi pathway are conserved in a wide range of eukaryotic genomes, including those of filamentous fungi. The biotechnological fungus Fusarium fujikuroi, widely used in secondary metabolism studies, contains the complete set of genes expected for RNAi pathways, including dcl1 and dcl2 dicer genes. We have analyzed by means of a high-throughput sequencing technology the content of sRNAs in F. fujikuroi grown in the dark or after one hour of illumination. For comparative purposes, the study was extended to the phytopathogenesis model Fusarium oxysporum, grown under the same conditions. Total RNA samples from each species and growth condition were used to construct RNA libraries, which were subjected to massive sequencing. sRNA preparations included a size cut-off below 150 nt, which covered sRNAs and their precursors. The size distributions and 5' nucleotide preferences of the sRNA reads showed a higher proportion of 5' uracil in the RNA samples of the expected sizes in both species, more noticeable in F. fujikuroi, indicating the occurrence of genuine sRNAs. Consistently, the number of sRNAs mapped at CDS loci was significantly higher in F. fujikuroi compared to F. oxysporum. F. fujikuroi carries at least one transcriptionally expressed copy of a Ty1/copia-like retrotransposable element, in which sRNAs were found in both sense and antisense DNA strands, whereas in F. oxysporum Skippy-like elements are expressed and show siRNA formation. The finding of sRNA in these mobile elements is an indication of an active siRNA-based RNAi pathway. The dcl2 deletion mutants did not show phenotypic alterations or changes in their global transcriptome, while no dcl1 deletion mutants could be obtained.
2024-01-21 | GSE253160 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2024-01-21 | GSE253166 | GEO
Project description:Genome-wide search for AreA-dependent and -independent nitrogen-regulated genes in Fusarium fujikuroi by cross-species hybridization with F. verticillioides microarrays. Keywords: glutamine treatmet Compare expression of genes of Fusarium fujikuroi wild-type and areA mutant strains responding to nitrogen limitation or sufficiency.
2010-05-15 | E-GEOD-10692 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression of the Fusarium fujikuroi wild type IMI58289 under gibberellin-inducing and -repressing conditions. Fusarium fujikuroi is a biotechnologically important fungus due to its almost unique ability to produce gibberellic acids (GAs), a family of phytohormones. The fungus was already described about 100 years ago as the causative agent of Bakanae (foolish seedling) disease of rice. Beside GAs, the fungus is known to produce some pigments and mycotoxins, but for only eight products the biosynthetic genes are known. Here we present a high-quality genome sequence of the first member of the Gibberella fujikuroi species complex (GFC), that allowed de novo genome assembly with 12 scaffolds corresponding to the 12 chromosomes. In this work, we focused on identification of all potential secondary metabolism-related gene clusters and their regulation in response to nitrogen availability by transcriptome, proteome, HPLC-FLPC and ChIP-seq analyses. We show that most of the cluster genes are regulated in a nitrogen-dependent manner, and that expression profiles fit to proteome and ChIP-seq data for some but not all clusters. Comparison with genomes of all available Fusarium species, including the recently sequenced F. mangiferae and F. circinatum, showed only a small number of common gene clusters and provides new insights into the divergence of secondary metabolism in the genus Fusarium. Phylogenetic analyses suggest that some gene clusters were acquired by horizontal gene transfer, while others were present in ancient Fusarim species and have evolved differently by gene duplications and losses. One PKS and one NRPS gene cluster are unique for F. fujikuroi. Their products were identified by combining overexpression of cluster genes with HPLC-FLPC -based product analyses. In planta, expression studies suggest a specific role of the PKS19 product in rice infection. Our results indicate that comparative genomics together with the used genome-wide experimental approaches is a powerful tool to uncover new secondary metabolites and to understand their regulation on the transcript, protein and epigenetic levels. In this study, we hybridized in total 15 microarrays using total RNA recovered from wild-type cultures of F. fujikuroi IMI58289. Two cultures were grown on a 6 mM Gln medium. Additionally, two technical replicates were created. Four cultures were grown on a 60 mM Gln medium. Again, two technical replicates were created. On a 6 mM NO3 medium, three cultures were grown, and two cultures on a 120 mM NO3 medium, with no technical replicates. Each chip measures the expression level of 14,397 genes from F. fujikuroi IMI58289 with eight 60-mer probes.
2013-07-01 | E-GEOD-43745 | biostudies-arrayexpress
Project description:Sequencing of the ascomycetous phytopathogenic fungus Fusarium fujikuroi.
| PRJEB185 | ENA
Project description:Histone modifications have been shown to be crucial for secondary metabolism in various filamentous fungi. Here we studied the influence of histone acetylation on secondary metabolite production in the phytopathogenic fungus Fusarium fujikuroi, a known producer of several secondary metabolites including pigments and mycotoxins. Deletion of the classical HDACs FfHdF1, FfHdF2 and FfHdF3 indicated that FfHdF1 and FfHdF2 are major regulators of secondary metabolism, whereas FfHdF3 is involved in developmental processes but dispensable for secondary metabolite production in F. fujikuroi. Microarray analysis with the major HDAC FfHdF2 revealed differential regulation of several secondary metabolite gene clusters, subsequently verified by a combination of chemical and biological approaches. These results indicate that HDACs are responsible for gene silencing but also gene activation. Chromatin immunoprecipitation assays with M-NM-^TffhdF2 revealed significant alterations regarding the acetylation state in the landscape of secondary metabolite gene clusters thereby providing insights into the regulatory mechanism. In addition, the class I HDAC FfHdF1 also has major impact on secondary metabolism in F. fujikuroi. Furthermore, deletion of both ffhdF1 and ffhdF2 resulted in de-repression of secondary metabolites under normally repressing conditions. Thus, manipulation of HDAC encoding genes might provide a powerful tool for the activation of cryptic secondary metabolites. Investigation of whole genome gene expression of the Fusarium fujikuroi wild type IMI58289, M-NM-^TffhdF2 mutant under nitrogen starvation and nitrogen sufficient conditions. In this study we hybridized in total 12 microarrays using total RNA recovered from a wild-type culture of F. fujikuroi IMI58289 and M-NM-^TffhdF2 mutant culture. All cultures were grown on a 6 mM Gln (10%) and a 60 mM Gln medium (100%). For each combination of culture and medium a biological replicate was created. Each chip measures the expression level of 14,397 genes from F. fujikuroi IMI58289 with eight 60-mer probes.
2013-10-05 | E-GEOD-43768 | biostudies-arrayexpress
Project description:Genome-wide search for AreA-dependent and -independent nitrogen-regulated genes in Fusarium fujikuroi by cross-species hybridization with F. verticillioides microarrays. Keywords: glutamine treatmet
2008-11-21 | GSE10692 | GEO