Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1277813 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR34006216_1.fastq.gz | Fastqsanger.gz | |||
| SRR34006216_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Frequently observed in tropical and sub-tropical regions, crops contamination by aflatoxin B1 (AFB1) produced by Aspergillus flavus, is emerging in Europe, due to climate change. Many alternative methods are currently developed to reduce the use of chemical inputs to prevent mycotoxin contamination, such as biocontrol agents (BCAs). Actinobacteria are known to produce many bioactive compounds and some of them are able to reduce in vitro AFB1 concentration. In this context, the present study aims to analyze the effect of a cell free supernatant (CFS) from Streptomyces roseolus liquid culture on A. flavus development, as well as on its transcriptome profile using microarray assay and its impact on AFB1 concentration. To study the impact of Streptomyces roseolus cell free supernatant on global transcriptome of Aspergillus flavus we have employed whole genome microarray expression profiling.
2023-09-06 | GSE232607 | GEO
Project description:Aspergillus flavus first gained scientific attention for its production of aflatoxin, the most potent naturally occurring toxin and hepatocarcinogenic secondary metabolite. For several decades, The DNA methylation status of A. flavus remains to be controversial. We first applied bisulfite sequencing, the gold standard at present, in conjunction with a biological replicate strategy to investigate the DNA methylation profiling of A. flavus genome. Our results reveal that the DNA methylation level of this fungus turns out to be negligible, comparable to the unmethylated lambda DNA we set as the false positive control of our bisulfite experiments. When comparing the DNA methyltransferase homolog of A. flauvs with that from several selected hypermethylated speices, we find that the DNA methyltransferase homolog of A.flavus as well as the other Aspergillus members groups closely with the RID from Neurospora crassa and Masc1 from Ascobolus immerses, which has been reported as DMT-incapable, but it diverges distantly from the other capable DNA methyltransferases. We observe significant depletion of repeat components within the A. flavus, which may possibly explain the lack of DNA methylation in this fungus. What's more, the RIP-index of the repeat of A. flavus turns out to be higher than the fungi without RID-like enzyme, suggesting this asexual fungus may possibly possess RIP process during the obscure sexual-stage which is very evanescent and may potentially related to DNA methylation. This work contributes to our understanding on the DNA methylation status of A. flavus. Also, it reinforces our views on the DNA methylation in fungal species. What's more, our strategy of applying bisulfite sequencing to DNA methylation detection on species with low DNA methylation may serve as a reference for later scientific investigations on other hypomethylated species. Two replicates were subjected to bisulfite conversion independently, unmethylated lambda DNA as a false positive control is added to both replicates.
2012-03-01 | E-GEOD-32177 | biostudies-arrayexpress
Project description:In this study, we used RNA-seq to obtain and compare transcriptomic profiles of a resistant genotype J11 in pre-harvest seeds, with A. flavus inoculation at the whole-genome level. The TMT method was also implemented to help further understand the molecular mechanism of peanut resistance to A. flavus invasion at proteome level. Meanwhile, we conducted a thorough research on a chitinase and a NBS-LRR gene, which were found in our data. This study is our first step towards a comprehensive genome-scale platform for developing Aspergillus resistant peanut cultivars through genetic engineering.
2020-08-17 | GSE102782 | GEO
Project description:Aspergillus flavus and A. parasiticus are two of the most important aflatoxin-producing species that contaminate agricultural commodities worldwide. Both species are heterothallic and undergo sexual reproduction in laboratory crosses. Here, we examine the possibility of interspecific matings between A. flavus and A. parasiticus. These species can be distinguished morphologically and genetically, as well as by their mycotoxin profiles. Aspergillus flavus produces both B aflatoxins and cyclopiazonic acid (CPA), B aflatoxins or CPA alone, or neither mycotoxin; Aspergillus parasiticus produces B and G aflatoxins or the aflatoxin precursor O-methylsterigmatocystin, but not CPA. Only four out of forty-five attempted interspecific crosses between compatible mating types of A. flavus and A. parasiticus were fertile and produced viable ascospores. Single ascospore strains from each cross were isolated and were shown to be recombinant hybrids using multilocus genotyping and array comparative genome hybridization. Conidia of parents and their hybrid progeny were haploid and predominantly monokaryons and dikaryons based on flow cytometry. Multilocus phylogenetic inference showed that experimental hybrid progeny were grouped with naturally occurring A. flavus L strain and A. parasiticus. Higher total aflatoxin concentrations in some F1 progeny strains compared to midpoint parent aflatoxin levels indicate synergism in aflatoxin production; moreover, three progeny strains synthesized G aflatoxins that were not produced by the parents, and there was evidence of putative allopolyploidization in one strain. These results suggest that hybridization is an important diversifying force resulting in the genesis of novel toxin profiles in these agriculturally important species.
2015-10-01 | GSE61981 | GEO
Project description:RNA-seq was used to compare differential gene expressions for Aspergillus flavus wild type strain and ASPES transcription factor deletion strains.The goals of this study are to explore the aflatoxin regulation pathway in A. flavus.
2018-12-25 | GSE107025 | GEO
Project description:Purpose: Aflatoxin B1 is the most toxic and carcinogenic compound in nature produced by Aspergillus fungi. In our study, we applied RNA-seq to compare the transcriptomic profiles of Aspergillus flavus strains in the presence and absence of medicinal plant Zanthoxylum bungeanum. Methods: mRNA profiles of Aspergillus flavus supplemented with 250 µg/ml of methanolic extract fraction (treated samples) or DMSO (control samples) were generated in triplicate, by an Illumina platform using paired-end 150 bp sequencing strategy. Clean paired-end reads were mapped to the reference genome of A. flavus NRRL3357. Gene expression quantification was calculated by FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced). The differentially expressed genes (DGEs) between the control and test samples were analyzed using the DESeq2 R package. Results: RNA-seq produced 24.5–32.1 million clean paired-end reads (150 bp read length) per sample and most of them (83–91%) were uniquely mapped to the reference genome of A. flavus NRRL3357. Eighty-two percent of genes displayed FPKM value ≥1 and were thus classified as expressed genes. Ninety-six percent of the expressed genes were expressed both in the control and test groups whereas 2.3% and 1.8% of the genes were expressed only in the control or test group, respectively. With the combination of FPKM fold change ≥2 and adjusted p-value <0.05, we found in total 950 DEG’s. Among them, 515 genes were downregulated and 435 genes were upregulated. We used FungiFun software to analyze the functions of the DEGs based on FunCat pathways and categories. About half of the DEG’s had a relevant annotation in the FunCat database, and 60–70% of the annotated DEG’s were found to be enriched in specific functional pathways. Conclusions: we showed that simple organic extracts from Z. bungeanum inhibit both the growth and aflatoxin production by Aspergillus flavus. The repression of AF pathway is mediated by global regulators instead of pathway specific regulators AflR or AflS. Consistently, the expression of Velvet complex, a prominent regulator of fungal secondary metabolism and development, was substantially reduced. Natural compound extracts from Z. bungeanum have potential to facilitate the development of safe and economical control strategies that shutdown aflatoxin production in aflatoxigenic Aspergillus species.
2022-04-10 | GSE179477 | GEO
Project description:Aflatoxins are toxic and carcinogenic secondary metabolites produced by the fungi Aspergillus flavus and A. parasiticus. In order to better understand the molecular mechanisms that regulate aflatoxin production, the biosynthesis of the toxin in A. flavus and A. parasticus grown in yeast extract sucrose media supplemented with 50 mM tryptophan (Trp) were examined. A. flavus grown in the presence of 50 mM tryptophan was found to have significantly reduced aflatoxin B1 and B2 biosynthesis, while A. parasiticus cultures had significantly increased B1 and G1 biosynthesis. Microarray analysis of RNA extracted from fungi grown under these conditions revealed seventy seven genes that are expressed significantly different between A. flavus and A. parasiticus, including the aflatoxin biosynthetic genes aflD (nor-1), aflE (norA), and aflO (omtB). It is clear that the regulatory mechanisms of aflatoxin biosynthesis in response to Trp in A. flavus and A. parasiticus are different. These candidate genes may serve as regulatory factors of aflatoxin biosynthesis. Keywords: Aflatoxin, Aspergillus, flavus, Amnio Acids, Tryptophan
2007-06-07 | GSE6182 | GEO
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:Aspergillus flavus is the major producer of carcinogenic aflatoxins in crops worldwide. Natural populations of A. flavus show tremendous variation in aflatoxin production some of which can be attributed to extreme environmental conditions (e.g., drought), differential regulation of the aflatoxin biosynthetic pathway, missing cluster genes or loss-of-function mutations. Understanding the evolutionary processes that generate genetic diversity in A. flavus may also explain quantitative and qualitative differences in aflatoxigenicity. Several population studies provide indirect evidence of recombination in the aflatoxin gene cluster and genome-wide, using multilocus genealogical approaches. More recently A. flavus has been shown to be functionally heterothallic and capable of sexual reproduction in laboratory crosses. In the present study, we characterize the progeny from nine A. flavus crosses and show that crossovers in the aflatoxin cluster coincide with inferred recombination blocks and hotspots in natural populations, which suggests that recombination in the cluster is primarily driven by sex. Moreover, we show that a single crossover event in the cluster can restore aflatoxigenicity, which is significant as mycotoxin production in A. flavus is highly heritable. aCGH was used to corroborate inferences from cluster-based MLSTs and to possibly identify additional crosovers within the cluster.
2012-03-07 | GSE27484 | GEO
Project description:DNA methylation is an important epigenetic modification widespread in eukaryotes and bacteria. However, genomic methylation levels show a dramatic diversity throughout the evolution of life, varying even between closely-related species and strains. In Aspergillus, a genus of filamentous fungi, the existence of DNA methylation has been controversial with previous studies reporting different conclusions using different species and detection methods. Here, we report DNA methylation analysis of Aspergillus oryzae, an important species in the Japanese fermentation industry, and a close relative of the pathogen Aspergillus flavus whose DNA methylation has been denied by the recent previous study using bisulfite sequencing. In this study, we conduct bisulfite-seq and RNA-seq of A. oryzae using three biological replicates from each of liquid and solid culture conditions. The statistical analysis of these data reveals thousands of highly-confident methylated cytosines (mCs), while the re-analysis of data from A. flavus detects few mCs being consistent with the previous study. Based on the comparative genome analysis of A. oryzae and A. flavus, we find that a substantial fraction of mCs are observed in syntenic segments including the aflatoxin biosynthesis gene cluster. Together, our results are the first evidence of DNA methylation in A. oryzae, providing a new example of the evolutionary diversity of DNA methylation as well as a new insight into its industrial applications.
2025-04-01 | GSE130260 | GEO