Solanum lycopersicum strain:cv. Renaissance
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB16205 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR492876.fastq.gz | Fastqsanger.gz | |||
| DRR492877.fastq.gz | Fastqsanger.gz | |||
| DRR492878.fastq.gz | Fastqsanger.gz | |||
| DRR492879.fastq.gz | Fastqsanger.gz | |||
| DRR492880.fastq.gz | Fastqsanger.gz |
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Project description:Induction of Plant Disease Resistance by Oligosaccharide Elicitors
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Project description:The plant response may be triggered by various factors, including pathogens, non-pathogenic microbes, and natural or synthetic molecules, such as salicylic acid (SA), benzo(1,2,3)-Thiadiazole-7-Carbothioic Acid S-Methyl Ester (BTH) that are considered as plant resistance inducers. Resistance inducers mobilize the plant for the synthesis of defense compounds, but they are not directly toxic for the plant. The BTH is an analogue of SA, a molecule naturally synthesized in the plant during systemic acquired resistance (SAR). In this study, we hypothesized that challenging the plant with resistance inducer causes an increase in the level of proteins associated with defence response to external stimuli with primary metabolism and that the action of the choline derivative of the BTH (in the form of the ionic liquid) during induction of resistance in tomato plants is mediated by to some extent similar signaling pathways as it is in the case of unmodified BTH compound. Therefore, this study aimed to identify global proteome changes occurring in tomato plants exposed to resistance inducers as well as to identify common pathways associated with the plant's defense response to (+)ssRNA viruses induced upon both, viral infection and prior resistance inducer treatment. The effect of ionic liquids on changes in plant proteome is not described in the literature. The ionic character of compounds offers a great advantage of using them as the plant resistance inducer. The high chemical and thermal stability, as well as low volatility, guarantees safe application in fields. For that reason, comparing the action of the resistance inducer in the form of an ionic liquid with the core compound (BTH) will help to elucidate the mode of action of ionic liquid derivatives in plant resistance induction. To this end, two RNA-type viruses from different families were tested: tomato mosaic virus (ToMV, Virgaviridae) and potato virus Y (PVY, Potyviridae). The most affected processes presented in the results were: photosynthesis, regulation of oxidative stress, metabolism of glutathione and chitin, cell wall reorganization. The increased impact on the regulation of primary metabolism in inducer-treated plants (both for BTH and cholinium ionic liquid derivative). The response to ToMV and PVY was more intense when infected plants were pre-treated with inducers. The increased abundances of defense priming proteins with changes in cell wall organization may block virus transport from infected spots to other tissue of the host plant so that the losses caused by the disease will be lower.
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Project description:3 sRNA-seq bioreps of WT and sulfurea samples. The aim of this experiment was to compare sRNA abundance at between the two genotypes with particular interest on SlTAB2 (Solyc02g005200) which has been previously associated with paramutation in the sulfurea background.
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Project description:Plant pathogens with a broad host range are able to infect plant lineages that diverged over 100 million years ago. They exert similar and recurring constraints on the evolution of unrelated plant populations. Plants generally respond with quantitative disease resistance (QDR), a form of immunity relying on complex genetic determinants. In most cases, the molecular determinants of QDR and how they evolve is unknown. Here we identify in Arabidopsis thaliana a gene mediating QDR against Sclerotinia sclerotiorum, agent of the white mold disease, and provide evidence of its convergent evolution in multiple plant species. Using genome wide association mapping in A. thaliana, we associated the gene encoding the POQR prolyl-oligopeptidase with QDR against S. sclerotiorum. Loss of this gene compromised QDR against S. sclerotiorum but not against a bacterial pathogen. Natural diversity analysis associated POQR sequence with QDR. Remarkably, the same amino acid changes occurred after independent duplications of POQR in ancestors of multiple plant species, including A. thaliana and tomato. Genome-scale expression analyses revealed that parallel divergence in gene expression upon S. sclerotiorum infection is a frequent pattern in genes, such as POQR, that duplicated both in A. thaliana and tomato. Our study identifies a previously uncharacterized gene mediating QDR against S. sclerotiorum. It shows that some QDR determinants are conserved in distantly related plants and have emerged through the repeated use of similar genetic polymorphisms at different evolutionary time scales.
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Project description:Genetic dissection of late blight disease resistance in tomato
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Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Solanum licopersicum tissues (including leaves, flowers and fruit). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.
2011-09-30 | GSE32470 | GEO
Project description:At present, the development of plants with improved traits like superior quality, high yield, or stress resistance, are highly desirable in agriculture. Accelerated crop improvement, however, must capitalize on revolutionary new plant breeding technologies, like genetically modified and gene-edited crops, to heighten food crop traits. Genome editing still faces ineffective methods for the transformation and regeneration of different plant species and must surpass the genotype dependency of the transformation process. Tomato is considered an alternative plant model system to rice and Arabidopsis, and a model organism for fleshy-fruited plants. Furthermore, tomato cultivars like Micro-Tom are excellent models for tomato research due to its short life cycle, small size, and capacity to grow at high density. Therefore, we developed an indirect somatic embryo protocol from cotyledonary tomato explants and used this to generate epigenetically edited tomato plants for the SlWRKY29 gene via CRISPR-activation (CRISPRa). We found that epigenetic reprogramming for SlWRKY29 establishes a transcriptionally permissive chromatin state, as determined by an enrichment of the H3K4me3 mark. A whole transcriptome analysis of CRISPRa-edited pro-embryogenic masses and mature somatic embryos allowed us to characterize the mechanism driving somatic embryo induction in the edited tomato cv. Micro-Tom. Furthermore, we show that enhanced embryo induction and maturation are influenced by the transcriptional effector employed during CRISPRa, as well as by the medium composition and in vitro environmental conditions such as osmotic components, plant growth regulators, and light intensity.
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Project description:PAMP (Pathogen-Associated Molecular Pattern) recognition plays an important role in innate immune responses both in plants and animals. Lipopolysaccharides (LPS) of gram-negative bacteria are a typical PAMP molecule and have been reported to induce defense-related responses such as suppression of hypersensitive responses, defense gene espression and systemic resistance in plant. However the detailed analysis of these cellular responses and the molecular machinery involved in the perception and transduction of LPS molecule largely remains to be studied. Furthermore, the biological activities of LPS on plants have so far been reported only for dicots and no information is available on the action of LPS on monocots. We report here that bacterial LPSs, both from plant pathogens and non-pathogens, could induce various defense responses in rice cells, including reactive oxygen generation and defense gene expression. Global analysis of gene expression induced by two PAMP elicitors, LPS and chitin oligosaccharide elicitor, showed a close correlation between the gene responses induced by these elicitors, indicating the convergence of signaling cascades downstream of corresponding receptors. Further, we show that the defense responses induced by LPS are associated with programmed cell death, a finding so far not reported for LPS action on plant cells. Experiment Overall Design: 1. LPS treatment (WT), 2. LPS treatment (WT) color-swap, 3. N-acetylchitooctaose treatment (WT), 4. N-acetylchitooctaose treatment (WT) color-swap
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Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Solanum licopersicum tissues (including leaves, flowers and fruit). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study. Small RNA libraries were derived from leaves, flowers and fruit of Solanum licopersicum. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Harry Klee for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.
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