Transcription profiling of roots and leaves of tomato plants colonized by the arbuscular mycorrhizal fungus Glomus mosseae
Ontology highlight
ABSTRACT:
ORGANISM(S): Solanum lycopersicum
SUBMITTER: Laura Miozzi
PROVIDER: E-MTAB-117 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Transcriptional changes triggered by the systemic infection of the tospovirus Tomato Spotted Wilt Virus (TSWV) in roots and shoots of tomato plants (Solanum lycopersicum) mycorrhized by Glomus mosseae
2011-10-31 | E-MTAB-620 | biostudies-arrayexpress
Project description:we deep-sequenced two small RNA libraries made from V. longisporum infected/non-infected roots and employed Brassica rapa and Brassica oleracea genomes as reference for miRNA prediction and characterization as well. We identified 893 B. napus miRNAs representing 360 conserved and 533 novel miRNAs, and mapped 429 and 464 miRNAs to AA and CC genomes, respectively. Among them, 62 miRNAs were responsive to the V. longisporum infection. two small RNA libraries constructed from V. longsiporum infected and non-infected roots after 6 days were sequenced by Illumina’s Solexa sequencing technology (BGI, China)
2014-10-06 | E-GEOD-58322 | biostudies-arrayexpress
Project description:This study was conducted to investigate the changes in gene expression that occurs with the silencing of GmbHLHm1. GmbHLHm1 is a membrane localised DNA binding transcription factor that is important for nodule development. Its activity is linked to ammonium transport. 7 samples
2014-03-14 | E-GEOD-55896 | biostudies-arrayexpress
Project description:The differentiation of specialized feeding sites in Zea mays root cells in response to nematode infestation involves substantial cellular reprogramming of host cells that is not well characterized at the molecular level. Expression data was generated from Zea mays root cells undergoing giant cell formation due to nematode infestation and from non-infested control root cells. Cells were laser captured 14 and 21 days after infestation. Each time point (14 day and 21 day) consisted of three biological replicates per treatment (control root cells or giant cells). Control cells were captured from an area ~13,000,000 um2 in size and giant cells were captured from an area ~5,000,000 um2 in size. RNA samples were isolated using the PicoPure RNA Isolation Kit (Arcturus, Mountain View, USA). RNA amplifications were carried out with the NuGEN WT-Ovation Pico kit.
2012-04-27 | E-GEOD-37556 | biostudies-arrayexpress
Project description:Plants show a remarkable plasticity to adapt their root architecture to biotic and abiotic constraints of the soil environment. Although some of these modifications are fine-tuned by miRNAs, there are still shadow zones in these regulations. In the model legume Medicago truncatula, we analyzed the small RNA (smRNA) transcriptome of roots submitted to symbiotic and pathogenic interactions. Mapping on the genome and prediction of pre-miRNA hairpins allowed the identification of 416 candidates. Out of them, we found known and novel variants of 77 miRNA families, already reported in miRBase. In addition, thanks stringent criteria of miRNA prediction, 53 mtr-miRNAs were discovered, including 27 putative miRtrons. Exploring polymorphism in 26 M. truncatula ecotypes, higher polymorphism was observed in conserved rather than legume-specific miRNA genes. An average of 19 targets, mainly involved in environmental responses and signaling, was predicted per novel miRNA. In addition, taking advantage of our large number of smRNA libraries, we identified sets of miRNAs responsive to root pathogens or to symbiotic interactions and the related Nod and myc-LCO signals. 23 libraries of small RNA (smRNA) of roots submitted to symbiotic and pathogenic interactions.
2014-08-15 | E-GEOD-49226 | biostudies-arrayexpress
Project description:Detailed information: Rice (*Oryza sativa* L. cv. Nipponbare) is a drought-susceptible species which is well suited for studies of abiotic stress response because of the comprehensive bioinformatics resource available. By withholding water from the entire root system of young rice plants, or half the root system only, it was possible to infer the relative impact of signals arriving from roots growing in wet and dry soil on the shoot proteome. The global proteome of shoots had 685 proteins in common to all three drought treatments but there were major shifts in abundance of individual proteins within 16 functional categories. The dominant changes were analyzed more deeply. First, we investigated transport and cell component organization, where some proteins were up-regulated by drought but many more down-regulated. Proteins involved in protein metabolism were up-regulated in general by drought when they were responsible for protein degradation but those involved in protein synthesis were down-regulated when water was withheld. Stress-related proteins behaved very consistently by increasing in droughted plants but notably some proteins were most abundant when roots of the same plant were growing in both wet and dry soil. This suggests that drought signals are complex interactions and not simply the additive effect of water supply to the roots. Changes in carbohydrate-processing proteins were consistent with the passive accumulation of soluble sugars in shoots under drought, with hydrolysis of sucrose and starch synthesis both enhanced. Data analysis information: The result raw files were converted to mzXML format and processed through the global proteome machine (GPM) software (version 2.1.1) of the X!Tandem algorithm (freely available at http://www.thegpm.org). The 16 gel fractions were processed serially for each experiment and the output files were generated as non-redundant, merged files with protein identifications with log (e) values less than -1, for each individual gel fraction. A protein database compiled from NCBI *O*. *sativa* with 26938 protein sequences (August 2011) was used in GPM to search the tandem mass spectra; the database also included common trypsin and human peptide contaminants. False discovery rates (FDR) were evaluated by searching against a reversed sequence database. Search parameters included MS and MS/MS tolerances of +2 Da and +0.2 Da, carbamidomethylation of cysteine as fixed modifications, oxidation of methionine as variable modifications and tolerance of two missed tryptic cleavages and K/R-P cleavages.
2020-01-22 | PXD000319 | Pride
Project description:Transcription profiling of roots and shoots of tomato plants as a result of systemic infection with the tospovirus Tomato Spotted Wilt Virus (TSWV).
2009-08-04 | E-MTAB-133 | biostudies-arrayexpress
Project description:Abscisic acid (ABA) determines mycorrhiza functionality and arbuscule development. Transcriptome analysis in response to different mycorrhization status according to the ABA concentration in the root was performed to identify genes that may play a role in arbuscule functionality. Tomato Affymetrix GeneChip (around 10,000 probes) allowed us to detect and compare the transcriptional root profiling of tomato (Solanum lycopersicum) wild-type and ABA-deficient sitiens plants colonized by the arbuscular mycorrhizal fungus Glomus intraradices. <br><br>
2010-07-01 | E-MEXP-2356 | biostudies-arrayexpress
Project description:Bacillus thuringiensis, a well-known and effective bio-insecticide, has attracted considerable attention as a potential biological control agent for the suppression of plant diseases. Treatment of tomato roots with a filter-sterilized cell-free filtrate (CF) of B. thuringiensis systemically suppresses bacterial wilt caused by Ralstonia solanacearum through systemic activation of the plant defense system. Comparative analysis of the expression of the Pathogenesis-Related 1(P6) [PR-1(P6)] gene, a marker for induced resistance to pathogens, in various tissues of tomato plants treated with CF on their roots suggested that the B. thuringiensis-induced defense system was activated in the leaf, stem, and main root tissues, but not in the lateral root tissue. At the same time, the growth of R. solanacearum was significantly suppressed in the CF-treated main root tissue but not in the CF-treated lateral root tissue. This distinct activation of the defense reaction and suppression of R. solanacearum were reflected by the differences in the transcriptional profiles of the main and lateral tissues in response to the CF. In the CF-treated main root tissue, but not CF-treated lateral root tissue, the expression of several salicylic acid (SA)-responsive defense-related genes was specifically induced, whereas jasmonic acid (JA)-related gene expression was either down-regulated or not induced in response to the CF. On the other hand, genes encoding ethylene (ET)-related proteins were induced equally in both the main and lateral root tissues. Taken together, the co-activation of SA-dependent signaling pathway with ET-dependent signaling pathway and suppression of JA-dependent signaling pathway may play key roles in B. thuringiensis-induced resistance to R. solanacearum in tomato plants. Gene expression was measured in main and lateral root tissues of tomato treated with Bacillus thuringiensis or distilled water-treated control at 48 hours after treatment. Two independent experiments were performed at each tissue (main root or lateral root tissue) for each treatment (Bacillus thuringiensis or distilled water control).
2013-08-29 | E-GEOD-50402 | biostudies-arrayexpress
Project description:Trees establish a symbiotic relationship with specialized soil fungi, called ectomycorrhizae, which is essential for nutrition, growth and health of temperate forest ecosystems. Understanding the mechanisms governing the establishment and functioning of ectomycorrhiza is important because of the role of forests in sequestering CO2 and also to develop ways to optimize tree productivity and sustainability. Here, we investigated the response of an oak species to ectomycorrhiza formation using a two dimensional differential in gel electrophoresis (2D-DIGE) and MALDI-TOF/TOF mass spectrometry proteomics approach. At the root level, changes in the abundance of 34 unique oak proteins were detected and revealed proteins involved in carbon and energy metabolism, protein processing and degradation, response to oxidative stress, lipid metabolism/transport, nitrogen and phosphorous assimilation and cell wall modification. Proteins supporting the importance of the secretory pathway functioning, in particular of the endoplasmic reticulum, during ectomycorrhiza functioning were identified. These proteins were identified as components of the endoplasmic reticulum folding/chaperoning machinery and proteins involved in the ER quality control system. This study constitutes an important contribution for the understanding of the mechanisms underlying the response of plants to ectomycorrhizal symbiosis establishment.
2017-07-14 | PXD003009 | Pride