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ABSTRACT:
PROVIDER: PRJNA471795 | ENA |
REPOSITORIES: ENA
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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 mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel cell-type specific gene expression during late stages of Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on laser-microdissected cells. We used Medicago GeneChips to detail the cell-type specific programme of gene expression in late stages of colonization by arbuscular mycorrhizal fungi and identified genes differentially expressed during these stages. Medicago truncatula Gaertn M-bM-^@M-^XJemalongM-bM-^@M-^Y genotype A17 plantlets were grown in the climate chamber. Plants grown for the collection of root cortical cells containing arbuscules (ARB), root cortical cells from mycorrhizal roots (CMR), and root epidermal cells from mycorrhizal roots (EPI) were mycorrhized after 2 weeks with Glomus intraradices and mycorrhizal roots were harvested at around 21 days post inoculation (dpi).
2013-04-28 | E-GEOD-42747 | biostudies-arrayexpress
Project description:The autoregulation of mycorrhization (AOM) describes a plant regulatory mechanism that limits the number of infection events by arbuscular mycorrhizal fungi. The key signal mediator is a receptor kinase (GmNARK) that acts in the shoots. Early signals of the mycorrhizal symbiosis induce a root-derived signal that activates GmNARK in the shoot finally leading to a systemic repression of subsequent infections in the root. So far, less is known about the signals down-stream of GmNARK. To find genes regulated by GmNARK in a mycorrhiza-dependent as well as in a mycorrhiza-independent manner, we used the Affymetrix GeneChip for soybean. In general, mycorrhizal root systems consist of both colonized and non-colonized, but autoregulated roots. To physically separate those two root types for transcript analysis of specifically regulated genes, we used the split-root system. Transcript profiling during AOM was done with material of Bragg wild-type and of the nark mutant nts1007, either non-inoculated or partially inoculated with the mycorrhizal fungus Rhizophagus irregularis (formerly Glomus intraradices). Wild-type and nark mutants were inoculated with R. irregularis on one half of the root-systems (root-parts "A") only. The remaining half of the root-systems stayed non-infected (root-parts "B"). Corresponding controls stayed completely non-infected. Gene expression was analyzed in inoculated root-parts, non-inoculated root-parts and shoots of three individual plants per treatment. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Sara Schaarschmidt. The equivalent experiment is GM53 at PLEXdb.]
2013-05-09 | GSE44685 | GEO
Project description:Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel gene expression during early stages of Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on mycorrhizal root fragments enriched for early fungal infection stages. We used Medicago GeneChips to detail the global programme of gene expression in response to early stages of colonization by arbuscular mycorrhizal fungi and identified genes differentially expressed during these early stages. Medicago truncatula GFP-HDEL hairy roots (genotypes A17 and DMI3) were grown in vertically-oriented petri dishes, incubated at 26M-BM-0C and inoculated with 8 Gigaspora margarita spores, which were positioned between the lateral roots. G.margarita spores germinated in 2 to 4 days. Hyphopodia were observed after 5-6 days. Root fragments which reacted to the fungal contact were collected and frozen. Non-inoculated control root fragments were harvested at a comparable age.
2012-03-27 | E-GEOD-34617 | biostudies-arrayexpress
Project description:Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel gene expression in Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on whole mycorrhizal roots. We used GeneChips to detail the global programme of gene expression in response to colonization by arbuscular mycorrhizal fungi and in response to a treatment with phosphate and identified genes differentially expressed during this process.
2011-10-29 | GSE32208 | GEO
Project description:Roots of Arabidopsis thaliana do not engage in symbiotic association with mycorrhizal fungi but host taxonomically diverse fungal communities that influence health and disease states. We sequenced the genomes of 41 isolates representative of the A. thaliana root mycobiota for comparative analysis with 79 other plant-associated fungi. We report that root mycobiota members evolved from ancestors having diverse lifestyles and retained diverse repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identified a set of 84 gene families predicting best endophytism, including families encoding PCWDEs acting on xylan (GH10) and cellulose (AA9). These genes also belong to a core transcriptional response induced by phylogenetically-distant mycobiota members in A. thaliana roots. Recolonization experiments with individual fungi indicated that strains with detrimental effects in mono-association with the host not only colonize roots more aggressively than those with beneficial activities but also dominate in natural root samples. We identified and validated the pectin degrading enzyme family PL1_7 as a key component linking aggressiveness of endophytic colonization to plant health.
2021-11-03 | GSE169629 | GEO
Project description:Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel gene expression in Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on whole mycorrhizal roots. We used GeneChips to detail the global programme of gene expression in response to colonization by arbuscular mycorrhizal fungi and in response to a treatment with phosphate and identified genes differentially expressed during this process. Medicago truncatula roots were harvested at 28 days post inoculation with the two different arbuscular mycorrhizal fungi Glomus intraradices (Gi-Myc) and Glomus mosseae (Gm-Myc) under low phosphate conditions (20 µM phosphate) or after a 28 days treatment with 2 mM phosphate in the absence of arbuscular mycorrhizal fungi (2mM-P). As a control, uninfected roots grown under low phosphate conditions (20 µM phosphate) were used (20miM-P). Three biological replicates consisting of pools of five roots were used for RNA extraction and hybridization on Affymetrix GeneChips.
2011-10-28 | E-GEOD-32208 | biostudies-arrayexpress
Project description:Arbuscular mycorrhizal (AM) symbiosis that associates roots of most land plants with soilborne fungi (Glomeromycota), is characterized by reciprocal nutritional benefits. Fungal colonization of plant roots induces massive changes in cortical cells where the fungus differentiates an arbuscule, which drives proliferation of the plasma membrane, and the de novo synthesis of the periarbuscular membrane. Despite the recognized importance of membrane proteins in sustaining AM symbiosis, the root microsomal proteome elicited upon mycorrhiza still remains to be explored. In this study, we first examined the qualitative composition of the root membrane proteome of Medicago truncatula after microsome enrichment and subsequent in depth analysis by GeLC-MS/MS. The results obtained highlighted the identification of 1226 root membrane protein candidates whose cellular and functional classifications predispose plastids and protein synthesis as prevalent organelle and function, respectively. Changes at the protein abundance level between the membrane proteomes of mycorrhizal and nonmycorrhizal roots were further monitored by spectral counting, which retrieved a total of 97 proteins that displayed a differential accumulation upon AM symbiosis. Besides the canonical markers of the periarbuscular membrane, new candidates supporting the importance of membrane trafficking events during mycorrhiza establishment/functioning were identified, including flotillin-like proteins.
2014-06-30 | PXD000875 | Pride
Project description:Orchids form an endomycorrhizal association with fungal symbionts mainly belonging to Basidiomycetes. The molecular events taking place in orchid mycorrhiza are poorly understood, although the cellular changes necessary to accommodate the fungus and to control nutrient exchange between the symbionts imply a modulation of gene expression. In this study, we used proteomic and transcriptomic approaches to identify changes in the steady-state levels of proteins and transcripts in roots of the green terrestrial orchid Oeceoclades maculata. When mycorrhizal and non-mycorrhizal roots from the same individuals of O. maculata were compared, 94 proteins showed differential accumulation using the label-free protein quantitation approach, 86 using isobaric tagging (iTRAQ) and 60 using 2D-differential electrophoresis. After de novo assembly of transcriptomic data, 11,179 plant transcripts were found to be differentially expressed and 2175 were successfully annotated. The annotated plant transcripts allowed the identification of up- and down-regulated metabolic pathways in mycorrhizal roots, as compared to non-mycorrhizal roots. Overall, proteomics and transcriptomics revealed in mycorrhizal roots increased levels of transcription factors and nutrient transporters, as well as ethylene-related proteins. The expression pattern of proteins and transcripts involved in plant defense responses suggest that plant defense is reduced in mycorrhizal roots. These results expand our current knowledge towards a better understanding of the orchid mycorrhizal symbiosis in adult plants under natural conditions.
2020-08-07 | GSE155822 | GEO
Project description:Analysis of cell specific gene expression in mycorrhizal rice roots. Described in Roth, Chiapello et al. 2019 We used LCM to harvest arbusculated and adjacent systemic cells from mycorrhizal rice roots, along with cortical cells from mock inoculated plants
2018-09-20 | GSE120215 | GEO