Fungi
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA593731 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR12873401.fastq.gz | Fastqsanger.gz | |||
| SRR12873402.fastq.gz | Fastqsanger.gz | |||
| SRR12873403.fastq.gz | Fastqsanger.gz | |||
| SRR12873404.fastq.gz | Fastqsanger.gz |
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Project description:Genomic and transcriptomic analyses of sebacinoid fungi
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Project description:The recent release of a large number of genomes from ectomycorrhizal, orchid mycorrhizal and root endophytic fungi have provided deep insight into fungal lifestyle-associated genomic adaptation. Comparative analyses of symbiotic fungal taxa showed that similar outcomes of interactions in distant related root symbioses are examples of convergent evolution. The order Sebacinales represents a sister group to the Agaricomycetes (Basidiomycota) that is comprised of ectomycorrhizal, ericoid-, orchid- mycorrhizal, root endophytic fungi and saprotrophs (Oberwinkler et al., 2013). Sebacinoid taxa are widely distributed from arctic to temperate to tropical ecosystems and are among the most common and species-rich groups of ECM, OM and endophytic fungi (Tedersoo et al., 2012, Tedersoo et al., 2010, Oberwinkler et al., 2013). The root endophyte Piriformospora indica and the orchid mycorrhizal fungus S. vermifera (MAFF 305830) are non-obligate root symbionts which were shown to be able to interact with many different experimental hosts, including the non-mycorrhizal plant Arabidopsis thaliana. These two fungi display similar colonization strategies in barley and in Arabidopsis and the ability to establish beneficial interactions with different hosts (Deshmukh et al., 2006). Colonization of the roots by P. indica and S. vermifera results in enhanced seed germination and biomass production as well as increased resistance against biotic and abiotic stresses in its experimental hosts, including various members of the Brassicaceae family, barley, Nicotiana attenuata and switchgrass (Ghimire, 2011, Ghimire et al., 2009, Ghimire et al., 2011, Waller et al., 2008, Barazani et al., 2007, Deshmukh et al., 2006). Microarray experiments were performed to identify and characterize conserved sebacinoid genes as key determinants in the Sebacinales symbioses.
2015-06-01 | GSE60736 | GEO
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Project description:Genomic analysis of trichothecene-producing fungi
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Project description:Decomposition of soil organic matter in forest soils is thought to be controlled by the activity of saprotrophic fungi, while biotrophic fungi including ectomycorrhizal fungi act as vectors for input of plant carbon. The limited decomposing ability of ectomycorrhizal fungi is supported by recent findings showing that they have lost many of the genes that encode hydrolytic plant cell-wall degrading enzymes in their saprophytic ancestors. Nevertheless, here we demonstrate that ectomycorrhizal fungi representing at least four origins of symbiosis have retained significant capacity to degrade humus-rich litter amended with glucose. Spectroscopy showed that this decomposition involves an oxidative mechanism and that the extent of oxidation varies with the phylogeny and ecology of the species. RNA-Seq analyses revealed that the genome-wide set of expressed transcripts during litter decomposition has diverged over evolutionary time. Each species expressed a unique set of enzymes that are involved in oxidative lignocellulose degradation by saprotrophic fungi. A comparison of closely related species within the Boletales showed that ectomycorrhizal fungi oxidized litter material as efficiently as brown-rot saprotrophs. The ectomycorrhizal species within this clade exhibited more similar decomposing mechanisms than expected from the species phylogeny in concordance with adaptive evolution occurring as a result of similar selection pressures. Our data shows that ectomycorrhizal fungi are potential organic matter decomposers, yet not saprotrophs. We suggest that the primary function of this decomposing activity is to mobilize nutrients embedded in organic matter complexes and that the activity is driven by host carbon supply. Comparative transcriptomics of ectomycorrhizal (ECM) versus brown-rot (BR) fungi while degrading soil-organic matter
2015-09-24 | E-GEOD-64897 | biostudies-arrayexpress
Project description:Mycotoxins are secondary metabolites which are produced by numerous fungi and pose a continuous challenge to the safety and quality of food commodities in South Africa. These toxins have toxicologically relevant effects on humans and animals that eat contaminated foods. In this study, a diagnostic DNA microarray was developed for the identification of the most common food-borne fungi, as well as the genes leading to toxin production. A total of 40 potentially mycotoxigenic fungi isolated from different food commodities, as well as the genes that are involved in the mycotoxin synthetic pathways, were analyzed. For fungal identification, oligonucleotide probes were designed by exploiting the sequence variations of the elongation factor 1-alpha (EF-1 α) coding regions and the internal transcribed spacer (ITS) regions of the rRNA gene cassette. For the detection of fungi able to produce mycotoxins, oligonucleotides directed towards genes leading to toxin production from different fungal strains were identified in data available in the public domain. The oligonucleotides selected for fungal identification and the oligonucleotides specific for toxin producing genes were spotted onto microarray slides. The diagnostic microarray developed can be used to identify potentially mycotoxigenic fungi as well as genes leading to toxin production in both laboratory and food samples offering an interesting potential for microbiological laboratories. Keywords: Development of a diagnostic microarray for the identification of potentially mycotoxigenic fungi as well as genes leading to toxin production, 40 food-borne fungi, mycotoxins Development of a diagnostic array for the identification of food-borne fungi and their potential mycotoxin-producing genes. Oligonucleotide probes to be printed onto the array were designed by exploiting the sequence variations of the elongation factor 1-alpha (EF-1 α) coding regions and the internal transcribed spacer (ITS) regions of the rRNA gene cassette. For the detection of fungi able to produce mycotoxins, oligonucleotides directed towards genes leading to toxin production from different fungal strains were identified in data available in the public domain. Analysis was performed with 40 fungal cultures were obtained from the Agricultural Research Council culture collection (ARC), Pretoria, South Africa.an in-house spotted oligonucleotide microarray. The identity of each fungus was confirmed by standard laboratory procedures. For DNA isolation, the fungal strains were grown on 1.5% malt extract agar at 25°C for 1-2 weeks and total genomic fungal DNA was extracted following the DNA extraction protocol described by Raeder and Broda (1985). The internal transcribed spacer oligonucleotides ITS1, ITS3 and ITS4 were used as a reference for normalization of all spot intensity data.Samples were fluorescently labelled with Cy5 dye by using a Cyâ¢Dye Post-labelling Reactive Dye Pack and wre hybridized to the oligonucleotide microarray overnight. Two biological and one technical replicate (using independent labelling reactions) was performed, each replication consisting of a reverse labelling experiment.
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Project description:Decomposition of soil organic matter in forest soils is thought to be controlled by the activity of saprotrophic fungi, while biotrophic fungi including ectomycorrhizal fungi act as vectors for input of plant carbon. The limited decomposing ability of ectomycorrhizal fungi is supported by recent findings showing that they have lost many of the genes that encode hydrolytic plant cell-wall degrading enzymes in their saprophytic ancestors. Nevertheless, here we demonstrate that ectomycorrhizal fungi representing at least four origins of symbiosis have retained significant capacity to degrade humus-rich litter amended with glucose. Spectroscopy showed that this decomposition involves an oxidative mechanism and that the extent of oxidation varies with the phylogeny and ecology of the species. RNA-Seq analyses revealed that the genome-wide set of expressed transcripts during litter decomposition has diverged over evolutionary time. Each species expressed a unique set of enzymes that are involved in oxidative lignocellulose degradation by saprotrophic fungi. A comparison of closely related species within the Boletales showed that ectomycorrhizal fungi oxidized litter material as efficiently as brown-rot saprotrophs. The ectomycorrhizal species within this clade exhibited more similar decomposing mechanisms than expected from the species phylogeny in concordance with adaptive evolution occurring as a result of similar selection pressures. Our data shows that ectomycorrhizal fungi are potential organic matter decomposers, yet not saprotrophs. We suggest that the primary function of this decomposing activity is to mobilize nutrients embedded in organic matter complexes and that the activity is driven by host carbon supply.
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