Arbuscular mycorrhizal fungi in the Himalayas
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ABSTRACT:
PROVIDER: PRJEB64855 | ENA |
REPOSITORIES: ENA
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Project description:The virtual transcriptome of G. intraradices (based on >430,000 reads) served as the basis for the design of an EST expresson array and for a number of analyses of gene expression in germinating spores, extraradical mycelium (ERM) and symbiotic root tissues.
2011-11-01 | GSE29866 | GEO
Project description:The virtual transcriptome of G. intraradices (based on >430,000 reads) served as the basis for the design of an EST expresson array and for a number of analyses of gene expression in germinating spores, extraradical mycelium (ERM) and symbiotic root tissues. The G. intraradices EST expression array (4 x 72K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products/exp/index.html) contained three independent, non identical, 60-mer probes per sequence. Included in the oligoarray were 22,402 G. intraradices sequences, 5785 random 60-mer control probes and labeling controls. We performed 12 hybridisations with samples from germinating spores (three biological replicates), extraradical mycelium (three biological replicates), symbiotic root tissues from Medicago (three biological replicates) and rice (1 replicate) as well as from microdissected arbuscule-colonized cortical cells of Medicago and rice (1 replicate each).
2011-11-01 | E-GEOD-29866 | biostudies-arrayexpress
Project description:<p>Arbuscular mycorrhiza (AM) is known to be a mutually beneficial plant-fungal symbiosis; however, the effect of mycorrhization is heavily dependent on multiple biotic and abiotic factors. Therefore, for the proper employment of such plant-fungal symbiotic systems in agriculture, a detailed understanding of the molecular basis of the plant developmental response to mycorrhization is needed. The aim of this work was to uncover the physiological and metabolic alterations in pea (<em>Pisum sativum L.</em>) leaves associated with mycorrhization at key plant developmental stages. Plants of pea cv. Finale were grown in constant environmental conditions under phosphate deficiency. The plants were analyzed at six distinct time points, which corresponded to certain developmental stages of the pea: I: 7 days post inoculation (DPI) when the second leaf is fully unfolded with one pair of leaflets and a simple tendril; II: 21 DPI at first leaf with two pairs of leaflets and a complex tendril; III: 32 DPI when the floral bud is enclosed; IV: 42 DPI at the first open flower; V: 56 DPI when the pod is filled with green seeds; and VI: 90-110 DPI at the dry harvest stage. Inoculation with <em>Rhizophagus irregularis</em> had no effect on the fresh or dry shoot weight, the leaf photochemical activity, accumulation of chlorophyll a, b or carotenoids. However, at stage III (corresponding to the most active phase of mycorrhiza development), the number of internodes between cotyledons and the youngest completely developed leaf was lower in the inoculated plants than in those without inoculation. Moreover, inoculation extended the vegetation period of the host plants, and resulted in increase of the average dry weight per seed at stage VI. The leaf metabolome, as analyzed with GC-MS, included about three hundred distinct metabolites and showed a strong correlation with plant age, and, to a lesser extent, was influenced by mycorrhization. Metabolic shifts influenced the levels of sugars, amino acids and other intermediates of nitrogen and phosphorus metabolism. The use of unsupervised dimension reduction methods showed that (i) at stage II, the metabolite spectra of inoculated plants were similar to those of the control, and (ii) at stages IV and V, the leaf metabolic profiles of inoculated plants shifted towards the profiles of the control plants at earlier developmental stages. At stage IV the inoculated plants exhibited a higher level of metabolism of nitrogen, organic acids, and lipophilic compounds in comparison to control plants. Thus, mycorrhization led to the retardation of plant development, which was also associated with higher seed biomass accumulation in plants with an extended vegetation period. The symbiotic crosstalk between host plant and AM fungi leads to alterations in several biochemical pathways the details of which need to be elucidated in further studies.</p>
2020-02-09 | MTBLS893 | MetaboLights
Project description:Arbuscular mycorrhizal fungi arguably form the most successful and wide-spread endosymbiosis with plants. In general terms there is very little host-specificity in this interaction, indicating an extremely broad compatibility. However, host preferences as well as varying symbiotic efficiencies have been observed, the molecular basis of which is still largely unknown. Secreted proteins (SPs) may act as fungal effectors to control symbiotic efficiency in a host-dependent manner. Therefore, we studied whether AM fungi adjust their secretome in a host- and stage-dependent manner to contribute to their extremely wide host-range. We investigated the expression of SP encoding genes of R. irregularis DAOM197198 in three evolutionary distantly related plant species, Medicago truncatula (Medicago), Nicotiana benthamiana (Nicotiana) and Allium schoenoprasum (Chives). In addition we used laser microdissection in combination with RNAseq to study SP expression at different stages of the symbiotic interaction in Medicago. Our data indicate that the vast majority of 288 expressed SPs show equal expression levels in the interaction with all three host plants. In addition, a subset (~15%) of the SPs show significant differential expression depending on the host plant and/or environmental condition. This host-dependent expression appears to be controlled locally in the hyphal network in response to host metabolic cues. Overall, this study offers a comprehensive analysis of the R. irregularis secretome, which now offers a solid basis to direct functional studies on the role of fungal SPs in AM symbiosis.
2018-03-27 | GSE99655 | GEO
Project description:The symbiotic interaction of plants with arbuscular mycorrhizal fungi (AM fungi) is ancient and widespread. Plants provide AM fungi with carbon in exchange for nutrients and water, making this interaction a prime target for crop improvement. However, plant-fungal interactions are restricted to a small subset of root cells, precluding the application of most conventional functional genomic techniques to study the molecular bases of these interactions. Here we used single-nucleus and spatial RNA sequencing to explore both M. truncatula and R. irregularis transcriptomes in AM symbiosis at cellular and spatial resolution. Integrated spatially-registered single-cell maps of interacting cells revealed major infected and uninfected plant root cell types. We observed that cortical cells exhibit distinct transcriptome profiles during different stages of colonization by AM fungi, indicating dynamic interplay between both organisms during establishment of the cellular interface enabling successful symbiosis. Our study provides insight into a symbiotic relationship of major agricultural and environmental importance and demonstrates a paradigm combining single-cell and spatial transcriptomics for the analysis of complex organismal interactions.
2023-08-11 | GSE240102 | GEO
Project description:The symbiotic interaction of plants with arbuscular mycorrhizal fungi (AM fungi) is ancient and widespread. Plants provide AM fungi with carbon in exchange for nutrients and water, making this interaction a prime target for crop improvement. However, plant-fungal interactions are restricted to a small subset of root cells, precluding the application of most conventional functional genomic techniques to study the molecular bases of these interactions. Here we used single-nucleus and spatial RNA sequencing to explore both M. truncatula and R. irregularis transcriptomes in AM symbiosis at cellular and spatial resolution. Integrated spatially-registered single-cell maps of interacting cells revealed major infected and uninfected plant root cell types. We observed that cortical cells exhibit distinct transcriptome profiles during different stages of colonization by AM fungi, indicating dynamic interplay between both organisms during establishment of the cellular interface enabling successful symbiosis. Our study provides insight into a symbiotic relationship of major agricultural and environmental importance and demonstrates a paradigm combining single-cell and spatial transcriptomics for the analysis of complex organismal interactions.
2023-08-11 | GSE240098 | GEO
Project description:In this work we aimed to get a first overview on S-stress responses in leaf and root tissues of mycorrhized and non mycorrhized plants. Several hundred genes showed a significant different transcript accumulation. Their annotation and GO ID association allowed us to investigate the our data in order to identify biological processes and molecular functions preferentially affected, and to better understand in which terms the symbiotic relation avoid the plant to face deleterious S-deficiency effects.
2015-01-01 | GSE61357 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2007-03-08 | GSE5477 | GEO
Project description:Casuarina glauca belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia. They can also develop arbuscular mycorrhizae (AM) while associated with Glomeromycota fungi. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program in AM and to identify new key plant genes involved in endosymbioses.
2012-10-22 | GSE36676 | GEO
Project description:The mutualistic arbuscular mycorrhizal (AM) symbiosis arose in land plants more than 450 million years ago. This symbiosis is still widely found across major land plant lineages, including bryophytes. Despite its broad taxonomic distribution, little is known about the molecular components underpinning symbiosis outside of flowering plants. Here, we demonstrate that a broad AM genetic programme is conserved amongst land plants. In this study, we characterised the dynamic response of the liverwort Marchantia paleacea to Rhizophagus irregularis colonization by time-resolved transcriptomics across three stages of symbiosis. Comparative analysis of transcriptional responses to symbiosis in the liverwort M. paleacea and the legume Medicago truncatula further revealed evolutionarily conserved expression patterns for genes underpinning pre-symbiotic signalling, intracellular colonization and nutrient exchange. This study demonstrates that the genetic machinery regulating key aspects of symbiosis in plant hosts is largely conserved and coregulated across land plants.
2024-08-08 | GSE245702 | GEO