Identification of viruses infecting plants and fungi
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB40378 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this work, we have used deep sequencing to study the viral small RNA (vsiRNA) populations from different mycoviruses infecting field isolates of Botrytis spp. The mycoviruses under study belong to different genera and species and have different type of genome (dsRNA, (+)ssRNA, and (-)ssRNA). In general, vsiRNAs derived from mycoviruses are mostly of 21, 20 and 22 nucleotides in length, possess sense or antisense orientation either in a similar ratio or with a predominance of sense polarity depending on the virus species, have predominantly U at their 5' end, and are unevenly distributed along the viral genome showing conspicuous hotspots of vsiRNA accumulation. These characteristics reveal striking concomitances with vsiRNAs produced by plant viruses suggesting similar pathways of viral targeting in plants and fungi
2016-09-15 | GSE83282 | GEO
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 alpha) coding regions and the internal transcribed spacer (ITS) regions of the rRNA gene cassette. For the detection of fungi able to produce mycotoxins, oligonucleotide probes directed towards genes leading to toxin production from different fungal strains were identified in data available in the public domain. The probes selected for fungal identification and the probes specific for toxin producing genes were spotted onto microarray slides. The diagnostic microarray developed can be used to identify single pure strains or cultures of potentially mycotoxigenic fungi as well as genes leading to toxin production in both laboratory samples and maize-derived foods 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
2010-03-01 | GSE19227 | GEO
Project description:ra10-02_viromouv - viromouv - transcriptome analysis of Arabidopsis Companion cells after infection by plants viruses - Transgenic plants expressing GFP under the control of a companion cell specific promoter were infected by two different viruses: LMV and TuYV. Companion cell protoplasts from these plants were sorted by FACS and extracted RNA were compared to healthy companion cell protoplasts.
2012-11-09 | GSE42059 | GEO
Project description:ra10-02_viromouv - viromouv - transcriptome analysis of Arabidopsis Companion cells after infection by plants viruses - Transgenic plants expressing GFP under the control of a companion cell specific promoter were infected by two different viruses: LMV and TuYV. Companion cell protoplasts from these plants were sorted by FACS and extracted RNA were compared to healthy companion cell protoplasts.
2012-11-09 | GSE42059 | GEO
Project description: Not available
| S-EPMC9243621 | biostudies-literature
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.
2010-05-07 | E-GEOD-19227 | biostudies-arrayexpress
Project description:The marine diatom Guinardia delicatula is a cosmopolitan species that dominates seasonal blooms in the English Channel and the North Sea. Several eukaryotic parasites are known to induce the mortality of this key-stone species. Here, we report the isolation and the characterization of the first viruses that infect G. delicatula. Viruses were isolated from the Western English Channel (SOMLIT-ASTAN station) during the late summer bloom decline of G. delicatula. A combination of laboratory approaches revealed that these lytic viruses (GdelRNAV) are small untailed particles of 35-38 nm in diameter that replicated in the host cytoplasm where both unordered particles and crystalline arrays were formed. GdelRNAV displayed a linear single-stranded RNA genome of ~9 kb, including two open reading frames encoding for replication and structural polyproteins. Phylogenetic relationships based on the RNA-dependent-RNA-polymerase gene marker showed that GdelRNAV were new members of the Bacillarnavirus, a monophyletic genus belonging to the order Picornavirales. GdelRNAV were specific to several strains of G. delicatula, they were produced rapidly (< 12h) and in numbers (9.34 x 104 virions per host cell). We recorded a substantial delay (72 h) between virions release and host cell lysis. Our analysis points to variable viral susceptibilities of the host during the early exponential growth phase. Interestingly, we consistently failed to isolate viruses during spring and early summer while G. delicatula developed rapid and massive blooms. While our study suggests that viruses do contribute to the decline of G. delicatula late summer bloom, they may not be the primary mortality agents during the remaining blooms at SOMLIT-ASTAN. Future studies should focus on the relative contribution of the viral and eukaryotic pathogens to the control of Guinardia blooms to understand the fate of these prominent organisms in marine systems.
2019-01-30 | PXD010967 | Pride
Project description:Virophages are small dsDNA viruses dependent on a nucleocytoplasmic large-DNA virus infection of a cellular host for replication. Putative virophages infecting algal hosts are classified together with Polinton-like viruses, transposable elements widely found in algal genomes, yet the lack of isolated strains raises questions about their existence as independent entities. We isolated and characterized a virophage (PgVV-14T) co-infecting Phaeocystis globosa with the Phaeocystis globosa virus-14T (PgV-14T).
2023-02-11 | PXD036892 | Pride
Project description:Arbuscular mycorrhizas (AM) are the most common symbiotic associations between plant’s root compartment and fungi. They can provide both nutritional benefit (mostly inorganic phosphate) leading to improved growth and non-nutritional benefits including defense responses to environmental cues throughout the host plant, which in return delivers carbohydrates to the symbiont. However how transcriptional changes occurring in AM leaves differ from those induced by phosphate fertilization is poorly understood. We investigated systemic changes in the leaves of mycorrhized Medicago truncatula compared to non-mycorrhized control plants, and in phosphate fertilized plants compared to control plants.
2016-04-26 | GSE80610 | GEO
Project description:ra10-02_viromouv - viromouv - transcriptome analysis of Arabidopsis Companion cells after infection by plants viruses - Transgenic plants expressing GFP under the control of a companion cell specific promoter were infected by two different viruses: LMV and TuYV. Companion cell protoplasts from these plants were sorted by FACS and extracted RNA were compared to healthy companion cell protoplasts. 10 dye-swap - normal vs disease comparison
2012-11-09 | E-GEOD-42059 | biostudies-arrayexpress