Ontology highlight
ABSTRACT:
PROVIDER: PRJNA718015 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14089924.fastq.gz | Fastqsanger.gz | |||
| SRR14089924_1.fastq.gz | Fastqsanger.gz | |||
| SRR14089924_2.fastq.gz | Fastqsanger.gz | |||
| SRR14089925_1.fastq.gz | Fastqsanger.gz | |||
| SRR14089925_2.fastq.gz | Fastqsanger.gz |
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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
Project description:Arbuscular mycorrhizal symbiosis improves water and nutrient uptake by plants and provides them other ecosystem services. Grapevine is one of the major crops in the world. V. vinifera scions are generally grafted onto a variety of rootstocks that confer different levels of resistance against different pests, tolerance to environmental stress, and influence the physiology of the scions. Arbuscular mycorrhizal fungi are involved in the root architecture and in the immune response to soil-borne pathogens. However, the fine-tuned regulation and the transcriptomic plasticity of rootstocks in response to mycorrhization are still unknown. We compared the responses of 10 different grapevine rootstocks to arbuscular mycorrhizal symbiosis (AMS) formed with Rhizophagus irregularis DAOM197198 using RNA sequencing-based transcriptome profiling. We have highlighted a few shared regulation mechanisms, but also specific rootstock responses to R. irregularis colonization. A set of 353 genes was regulated by AMS in all ten rootstocks. We also compared the expression level of this set of genes to more than 2,000 transcriptome profiles from various grapevine varieties and tissues to identify a class of transcripts related to mycorrhizal associations in these 10 rootstocks. Then, we compared the response of the 351 genes upregulated by mycorrhiza in grapevine to their Medicago truncatula homologs in response to mycorrhizal colonization based on available transcriptomic studies. More than 97% of these homologs were expressed in at least one transcriptome profile, and 64% in all profiles. At the intra-specific level, we described for the first time shared and specific grapevine rootstock genes in response to R. irregularis symbiosis. At the inter-specific level, we defined a shared subset of mycorrhiza-responsive genes
2023-06-10 | GSE234583 | GEO
Project description:The study of orchid mycorrhizal interactions is particularly complex because of the peculiar life cycle of these plants and their diverse trophic strategies. Here, large-scale transcriptomics has been applied to investigate gene expression in the mycorrhizal roots of the terrestrial mixotrophic orchid Limodorum abortivum under natural conditions. Our results provide new insights into the mechanisms underlying plant-fungus interactions in orchids and in particular on the plant responses to the mycorrhizal symbiont(s) in adult roots. Comparison with gene expression in mycorrhizal roots of another orchid species, Oeceoclades maculata, suggests that amino acids may represent the main nitrogen source in both protocorms and adult orchids, at least for mixotrophic species. The upregulation, in mycorrhizal L. abortivum roots, of some symbiotic molecular marker genes identified in mycorrhizal roots from other orchids as well as in arbuscular mycorrhiza, suggests a common plant core of genes in endomycorrhizal symbioses. Further efforts will be required to understand whether the specificities of orchid mycorrhiza depend on fine-tuned regulation of these common components, or whether specific additional genes are involved.
2021-01-31 | GSE159700 | GEO
Project description:<p>Plant monocultures growing for extended periods face severe losses of productivity. This phenomenon, known as 'yield decline', is often caused by the accumulation of above- and below-ground plant antagonists. The effectiveness of plant defences against antagonists might help explain differences in yield decline among species. Using a trait-based approach, we studied the role of 20 physical and chemical defence traits of leaves and fine roots on yield decline of 4- and 18-year-old monocultures of 27 grassland species. We hypothesized that yield decline is lower for species with high defences, that root defences are better predictors of yield decline than leaf defences, and that in roots, physical defences better predict yield decline than chemical defences, while the reverse is true for leaves. We additionally hypothesized that the relationship between defences and yield decline increase with time and that species increasing the expression of defence traits after long-term monoculture growth would suffer less yield decline. We summarized leaf and fine root defence traits using principal component analysis and analysed the relationship between the most informative components as well as their temporal changes and monoculture yield decline. The significant predictors of yield decline were traits related to the so-called collaboration gradient of the root economics space (specific root length and root diameter) as well as their temporal changes and traits related to the leaf physical vs chemical defence trade-off (leaf dry matter, silicon and cellulose content, toughness and phytochemical diversity). We were unable to unequivocally identify the mechanisms relating the effect of those traits to yield decline as they could mediate plant responses to several stressor such as antagonist nutrient depletion and drought. Further studies are needed to differentiate between these alternative mechanisms and gain a comprehensive understanding of the drivers behind the impact of root and leaf defence traits on yield decline.</p>
2023-11-03 | MTBLS4286 | MetaboLights
Project description:We have recently identified an ethylene response factor, StPti5, as a susceptibility factor that negatively regulates immune response to diverse pathogens. Here, we investigated the processes involved in colonisation of potato with beneficial organisms. RNA-seq showed that at the time of Bacillus subtilis biofilm establishment, immune responses in interacting roots were attenuated, and complex transcriptional network was triggered, with ethylene signalling being a central module and StPti5 strongly induced. Interestingly, the response is intensified if plants are inoculated by two antagonistic B. subtilis strains. While StPti5 is not involved in the establishment of biofilm on roots, we show that bacterial abundance increases in shoots of StPti5-silenced plants. Remarkably, root colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis was also higher in the StPti5-silenced plants. StPti5 is involved both in suppressing defence against harmful and limiting colonisation with beneficial microbes. Such mechanistic understanding of plant–microbe interaction paves the way for sustainable crop management.
2026-01-06 | GSE313812 | GEO
Project description:Trichoderma species promote growth and strengthen immunity of Arabidopsis and crop species through multiple mechanisms. However, how fungal proteins mediate growth-defense tradeoffs is unknown. We analyzed the growth, root architecture, defense and global gene expression profiles in Arabidopsis seedlings co-cultivated with T. atroviride WT, and Δnox1, Δnox2, and ΔnoxR mutants, defective on the catalytic and regulatory subunits of NADPH oxidase, respectively. The gene expression profile in the fungus was also characterized in standard growth conditions and in the presence of plants. The results revealed the critical role of Trichoderma NoxR in mediating growth-defense tradeoffs in Arabidopsis. The effects of T. atroviride WT in improving root branching and biomass production decreased in all three related NADPH defective mutants, particularly in ΔnoxR. In contrast, induction of jasmonic acid-related defense responses in roots and shoots were exacerbated in ΔnoxR compared to the WT strain. Transcriptome analyses showed a tight plant-fungus communication based on reactive oxygen species and availability of carbon resources. The ΔnoxR is unable to perceive changes in nutrient sources and activate signaling cascades, which suppresses the metabolic change from saprophyte to commensal. Thus we conclude that Trichoderma NoxR orchestrates fungal-induced development and defense tradeoffs in Arabidopsis and plays an important role in cross-kingdom plant-fungus communication.
2019-10-01 | GSE138203 | GEO
Project description:Most vascular flowering plants have the ability to form mutualistic associations with soil fungi from the Glomeromycota. The resulting symbiosis is called an arbuscular mycorrhiza and they are widespread in terrestrial ecosystems throughout the world. Significant alteration occurs at physiological and molecular levels in both symbionts. To gain a better understanding of the AM symbiosis, we use a 16000 feature oligonucleotide based array to examine gene expression in an arbuscular mycorrhizal symbioses, M. truncatula/Gigaspora gigantea. Keywords: Medicago truncatula, Mycorrhizal, Gigaspora gigantea, microarray profiling
2007-03-08 | GSE5471 | GEO
Project description:Most vascular flowering plants have the ability to form mutualistic associations with soil fungi from the Glomeromycota. The resulting symbiosis is called an arbuscular mycorrhiza and they are widespread in terrestrial ecosystems throughout the world. Significant alteration occurs at physiological and molecular levels in both symbionts. To gain a better understanding of the AM symbiosis, we use a 16000 feature oligonucleotide based array to examine gene expression in an arbuscular mycorrhizal symbioses, M. truncatula/G. intraradices. Keywords: Medicago truncatula, Mycorrhizal, Glomus intraradices, microarray profiling
2007-03-08 | GSE5467 | GEO
Project description:<p>The increased positive impact of plant diversity on ecosystem functioning over time is often attributed to the gradual accumulation of mutualists and dilution of antagonists in diverse plant communities. While increased plant diversity alters traits related to resource acquisition, it remains unclear whether it reduces defence allocation, whether this reduction differs between roots and leaves, or varies among species.</p><p>To answer these questions, we assessed the effect of plant species richness, plant species identity and their interaction on the expression of twenty-three physical and chemical leaf and fine root defence traits of sixteen plant species in a nineteen-year-old biodiversity experiment.</p><p>Only leaf mass per area, leaf and root dry matter content, and root nitrogen, traits related to both, resource acquisition and physical defence, responded consistently to species richness. However, species richness promoted a decoupling of these physical defences in leaves and fine roots, possibly in response to resource limitations in diverse communities. Changes in traits related to chemical defence and mutualist collaboration, however, varied among species, possibly in response to species-specific antagonists’ dilution.</p><p>Overall, our study suggests that resource limitation in diverse communities mediates the relationship between plant defence traits and antagonist dilution.</p>
2025-02-13 | MTBLS8464 | MetaboLights