Tomato microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB48124 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR7057070.fastq.gz | Fastqsanger.gz | |||
| ERR7057080.fastq.gz | Fastqsanger.gz | |||
| ERR7057090.fastq.gz | Fastqsanger.gz | |||
| ERR7057100.fastq.gz | Fastqsanger.gz | |||
| ERR7057110.fastq.gz | Fastqsanger.gz |
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Project description:Characterization of the transcriptomic responses of grafted tomato seedlings leaves after the root inoculations with the two beneficial microorganisms Paraburkholderia graminis and Azospirillum brasiliensis. Paraburkholderia graminis treatment led to a higher number of differentially expressed genes than Azospirillum brasiliensis, with a higher amount of up-regulated than down-regulated genes for both treatments. These DEGs were manly involved in response to oxidative stress, response to biotic and abiotic stress, water transport, regulation of transcription and hormones. Only few DEGs were shared among the two treatments, including genes involved in flowering time and in tolerance against abiotic stresses.
2022-10-16 | E-MTAB-11398 | biostudies-arrayexpress
Project description:To elucidate the molecular and metabolic changes in tomato plants that occur by the interaction of tomato roots and MBI600 elicitors, fifteen-day-old tomato seedlings were transferred to liquid MS (2 seedlings/2mL of medium in wells of 24-well-plates) and after 3 hours the medium was supplied with MBI600 CFCF to 1/5 v/v volume or with flg22 peptide (Eurogentec) to a final concentration of 1μΜ. Seedlings were collected in different time points after treatment (6 and 24h). Three independent experiments were performed. Each experiment included 2 biological replicates per treatment and each replicate was a pool of two seedlings. Sixteen genes were selected and their transcript levels were tested by Real-Time qPCR. A pathway analysis was performed and the complex signaling network that is implicated in MBI600-host interactions was mapped. The coordinated expression of genes that participate in biosynthetic pathways or are responsive to auxin, JA/ET, SA and redox signalling of biotic and abiotic stress responses, suggests that PGPR elicitors and metabolites activate (non-specifically) plant defense.
2018-12-11 | GSE123589 | GEO
Project description:To test the hypothesis that gene expression by the fungal partner in this beneficial interaction is modulated by the plant host, Trichoderma virens was co-cultured with maize or tomato in a hydroponic system allowing interaction with the roots. The transcriptomes for T. virens alone were compared with fungus-inoculated tomato or maize roots by hybridization on oligonucleotide microarrays Based on the relevant role of Trichoderma virens as a biological control agent this study provides a better knowledge of its crosstalk with plants in a host-specific manner. Trichoderma virens was co-cultured for three days with maize or tomato in a hydroponic system allowing interaction with the roots. 3 experiments were performed for each treatment, and compared to 5 experiments with T. virens grown under the same conditions without plants.
2014-12-19 | E-GEOD-64344 | biostudies-arrayexpress
Project description:To test the hypothesis that gene expression by the fungal partner in this beneficial interaction is modulated by the plant host, Trichoderma virens was co-cultured with maize or tomato in a hydroponic system allowing interaction with the roots. The transcriptomes for T. virens alone were compared with fungus-inoculated tomato or maize roots by hybridization on oligonucleotide microarrays Based on the relevant role of Trichoderma virens as a biological control agent this study provides a better knowledge of its crosstalk with plants in a host-specific manner.
2014-12-19 | GSE64344 | GEO
Project description:Anthocyanins are high value plant antioxidants which are not present in the fruits of cultivated tomato. However, both the dominant gene Anthocyanin fruit (Aft) and the recessive gene atroviolacea (atv), introgressed into domesticated tomato from two different wild Solanum species, stimulate a limited anthocyanin pigmentation. Surprisingly, double mutant Aft/Aft atv/atv tomatoes are characterised by the presence of anthocyanins in the fruit peel, resulting in intensely purple pigmented fruit. We carried out a transcript profiling analysis using GeneChip® Tomato Genome Arrays, in order to identify differentially expressed genes when comparing wild type, Aft/Aft, atv/atv, and Aft/Aft atv/atv fruits. The expression pattern of several genes involved in the anthocyanin pathway was analyzed in detail. Among the fruit peel-associated differentially expressed transcripts, genes involved in phenylpropanoid pathway, cell wall composition, biotic and abiotic stress responses, sugar and hormone metabolism were overrepresented in Aft/Aft atv/atv. Transcriptomic analysis thus revealed that the activation of anthocyanin synthesis in tomato fruit was accompanied by a complex remodulation of gene expression, likely affecting important agronomic and merceological traits.
2010-07-31 | GSE19792 | GEO
Project description:Purpose: The tomato psyllid, Bactericera cockerelli Šulc (Hemiptera: Triozidae), is a pest of tomato (Solanum lycopersicum) and potato (S. tuberosum) in the U.S. and vectors the disease-causing pathogen ‘Candidatus Liberibacter solanacearum’. Plants undergo physiological, transcriptomic, or epigenetic changes in order to mount a stronger, faster response against secondary challenges by previously perceived threats. This is called defense ‘priming’ and it likely has an impact on vectored disease transmission. Currently, it is still unknown whether or not psyllid infestation has any lasting consequences for tomato gene expression or defense. To characterize the genes potentially involved in tomato priming against psyllids, RNA was extracted from psyllid-primed and uninfested tomato (Moneymaker) leaves three weeks after infestation. Methods: RNA was extracted and sequenced from plants three weeks after psyllid infestation. Plants were either left alone (Control or C) or infested with psyllids (Primed or J1). Libraries were developed using the TruSeq RNA Library Prep Kit v2. Sequencing was performed on the Illumina PE HiSeq 2500 v4 platform. Processed sequences were uploaded to the CyVerse Discovery Environment computational infrastructure where bioinformatic analysis was performed using the Tuxedo Suite 2 workflow. Results: Illumina HiSeq sequencing of tomato cDNA libraries produced 132,428,443 total reads that met FastQC quality control criteria. 94.6% of all reads mapped to vSL3.0 of the S. lycopersicum genome. CuffDiff2 analysis identified 310 differentially expressed genes (DEGs) between control and psyllid-primed plants (q-value <0.01). Conclusions: A week-long infestation by a small number of B. cockerelli had lasting consequences for gene expression in tomato plants. Homologs of the DEGs were associated with 1) defense against abiotic and biotic stress, 2) growth and development, and 3) components of plant biology indirectly involved in plant growth and development such as homeostasis, transcription/translation, and molecular transport.
2019-04-11 | GSE129610 | GEO
Project description:The tomato psyllid, Bactericera cockerelli Šulc (Hemiptera: Triozidae), is a pest of solanaceous crops such as tomato (Solanum lycopersicum L.) in the U.S. and vectors the disease-causing pathogen ‘Candidatus Liberibacter solanacearum’ (or Lso). Lso disease symptom severity is dependent on Lso haplotype: tomato plants infected with Lso haplotype B experience more severe symptoms and higher mortality compared to plants infected with Lso haplotype A. By characterizing the molecular differences in the tomato plant’s responses to Lso haplotypes, the key components of LsoB virulence can be identified and, thus, targeted for disease mitigation strategies. To characterize the tomato plant genes putatively involved in the differential immune responses to Lso haplotypes A and B, RNA was extracted from tomato ‘Moneymaker’ leaves three weeks after psyllid infestation. Gene expression levels were compared between uninfected tomato plants (i.e., controls and plants infested with Lso-free psyllids) and infected plants (i.e., plants infested with psyllids infected with either Lso haplotype A or Lso haplotype B). Furthermore, expression levels were compared between plants infected with Lso haplotype A and plants infected with Lso haplotype B. A whole transcriptome analysis identified 578 differentially expressed genes (DEGs) between uninfected and infected plants as well as 451 DEGs between LsoA- and LsoB-infected plants. These DEGs were primarily associated with plant defense against abiotic and biotic stressors, growth/development, plant primary metabolism, transport and signaling, and transcription/translation. These gene expression changes suggested that tomato plants traded off plant growth and homeostasis for improved defense against pathogens, especially when infected with LsoB. Consistent with these results, tomato plant growth experiments determined that LsoB-infected plants were significantly stunted and had impaired negative geotropism. However, it appeared that the defense responses mounted by tomatoes were insufficient for overcoming the disease symptoms and mortality caused by LsoB infection, while these defenses could compensate for LsoA infection. The transcriptomic analysis and growth experiments demonstrated that Lso-infected tomato plants underwent gene expression changes related to abiotic and biotic stressors, impaired growth/development, impaired plant primary metabolism, impaired transport and signaling transduction, and impaired transcription/translation. Furthermore, the transcriptomic analysis also showed that LsoB-infected plants, relative to LsoA-infected, experienced more severe stunting, had improved responses to some stressors and impaired responses to others, had poorer transport and signaling transduction, and had impaired carbohydrate synthesis and photosynthesis.
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Project description:Phloem is the primary conduit through which photosynthates, hormones, and other biologically important molecules are distributed from aerial plant organs downward and throughout the plant. Increasing evidence suggests that phloem contents are diverse and play a critical role in biotic and abiotic stress adaptation. Drought causes the greatest decreases in agricultural crop productivity among all biotic and abiotic stresses, and the link between water deficiency and phloem protein contents is relatively unexplored. Here we employed the EDTA-facilitated phloem exudate collection method from Solanum lycopersicum leaves during a period of drought stress and recovery. Our analysis resulted in the confident identification and quantification of 2,558 proteins. Comparing our data with previous findings confirms that our exudate collection strategy enriched for known phloem proteins. Independent of drought, enrichment analysis of the total phloem exudate protein profiles from all samples suggest that the exchange of proteins into the phloem is more complex than previously thought, including additional protein chaperone systems, branched-chain amino acid synthesis proteins, trehalose metabolism, and RNA silencing proteins. During the experiment we observed 169 proteins whose abundance changed significantly within the phloem sap, the majority of which were impacted specifically in response to drought. Among these were proteins involved in lipid metabolism, chaperone-mediated protein folding, carboxylic acid metabolism, abscisic acid signaling, cytokinin biosynthesis, and amino acid metabolism are significantly upregulated during drought. Conversely, proteins involved in lipid signaling, sphingolipid metabolism, cell wall organization, carbohydrate metabolism, and a mitogen-activated protein kinase are downregulated in response to drought. Many of these observations are consistent with previous literature findings at the whole plant level but have not been localized to the vasculature in tomato, suggesting phloem plays a critical role in adaptation to drought stress in tomato .
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Project description:DEX inducible expression system for Rosea1 and Delila transcription factors was introduced in tomato. Seedlings and callus tissues were induced by DEX. RNA of induced and uniniduced roots and calli was isolated after 3 and 24h.
2018-01-30 | GSE109772 | GEO