Tomato system bacteriome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB27033 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2640150.fastq.gz | Fastqsanger.gz | |||
| ERR2640160.fastq.gz | Fastqsanger.gz | |||
| ERR2640170.fastq.gz | Fastqsanger.gz | |||
| ERR2640180.fastq.gz | Fastqsanger.gz | |||
| ERR2640190.fastq.gz | Fastqsanger.gz |
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Project description:The gram- positive bacterial pathogen Clavibacter michiganensis subsp. michiganensis (Cmm) causes huge economic losses by infecting tomato plants worldwide. Cmm can be spread by contaminated seeds and transplants, penetrating the plant through natural openings or wounds and is transferred through the plant xylem. While in recent years significant progress has been made to elucidate plant responses to pathogenic gram-negative bacteria by gene expression studies, the molecular mechanisms that lead to disease symptoms caused by gram-positive bacteria like Cmm remain elusive. An indigenous virulent Cmm strain isolated from a farm crop of Pomodoro tomatoes in southern Greece was used for the infection of EKSTASIS F1 hybrid tomato seedlings. Here, we present the results of a deep RNA- sequencing (RNA-seq) analysis performed to characterize the dynamic expression profile of tomato genes upon Cmm infection.
2021-08-10 | GSE160971 | GEO
Project description:Southern tomato virus (STV) often infects healthy tomato plants (Solanum lycopersicum). In this study, we compared STV-free and STV-infected cultivar M82 plants to determine the effect of STV infection on the host plant. STV-free plants exhibited a short and bushy phenotype, whereas STV-infected plants exhibited increased height. STV-infected plants produced more fruit than STV-free plants, and the germination rate of seeds from STV-infected plants was higher than that of seeds from STV-free plants. This phenotypic difference was also observed in progeny plants (siblings) derived from a single STV-infected plant in which the transmission rate of STV to progeny plants via the seeds was approximately 86%. These results suggest that the interaction between STV and host plants is mutualistic. Transcriptome analyses revealed that STV infection affected gene expressions in host plants, notably evidenced by down-regulation of genes involved in ethylene biosynthesis and signaling. STV-infected tomato plants thus might be artificially selected due to their superior traits as a crop.
2019-09-13 | GSE137303 | GEO
Project description:To evaluate the role of seeds in fruit quality, we induced parthenocarpy in tomato by regulating ovule-specific auxin synthesis or responsiveness using the INO promoter from A. thaliana, which is expressed in the outer layer of the integuments during early stages of ovule development. We compared these to fruit where the same coding regions were expressed from the DeFH9 promoter which is expressed in carpel tissues during early stages of ovule development. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic tomato fruit. We compared fruit samples using the Affymetrix tomato GeneChip (GPL4741) to determine how gene regulation and expression differed between wild-type and transgenic fruit. Experiment Overall Design: Wild-type fruit with seeds was compared with transgenic lines INO-IaaM, DefH9-IaaM, INO-RolB, and DefH9-RolB. To find genes with seed-specific expression, we also compared the control with wild-type fruit from which seeds had been manually removed. We had three biological replicates for each treatment and control except DefH9-RolB, for which only two replicates were available. Each CEL file from the microarray represents one plant from each line.
2009-09-15 | E-GEOD-14358 | biostudies-arrayexpress
Project description:Fruits and leaves of the tomato (Solanum lycopersicum L.) cultivar MicroTom were investigated. MicroTom wild type and lecer6 mutant with a deficiency in a fatty acid beta-ketoacyl-CoA synthase (LeCER6) were used. The samples were composed of mature green, whole fruits with seeds being removed (fruit developmental category II). The locular tissue (gel) that surrounded the seeds and fills the locular cavity were detached. Otherwise, the samples contained fully developed leaves. After sampling point the plant material was immediately frozen in liquid nitrogen and stored at -80 C until use.
2009-06-09 | E-MEXP-2162 | biostudies-arrayexpress
Project description:DNA methylation confers epigenetic regulation on gene expression and thereby on various biological processes. Tomato has emerged as an excellent system to study the function of DNA methylation in plant development. In contrast to recent discoveries that DNA demethylation is critical for tomato fruit ripening, regulation and function of DNA methylation maintenance remains unclear in tomato plants. Here we report the critical function of tomato (Solanum lycopersicum) Methyltransferase 1 (SlMET1) in plant development and DNA methylome and transcriptome regulation. Using CRISPR-Cas9 gene editing, we generated slmet1 mutants and discovered that SlMET1 is required for normal development of flowers and seeds in tomato. Mutations in SlMET1 caused CG hypomethylation and CHH hypermethylation on a whole-genome scale, leading to a disturbed transcriptome including defects in the expression of key genes involved in meristem formation, seed development and fruit ripening. Consistently, the slmet1 mutants showed impaired flower production, elevated lycopene levels in fruits, and pathenocarpic fruits. In the slmet1 mutants, hypomethylated CG and hypermethylated CHH cytosines are preferentially located in genes and transposable elements (TEs), respectively. Neither the CG hypomethylation nor CHH hypermethylation in the slmet1 mutants is related to tissue culture-induced non-CG hypomethylation, which prefers genes over TEs and is more stable in the former regions than the latter during subsequent inbreeding. Our results depict SlMET1- and tissue culture-dependent tomato DNA methylomes, and that SlMET1 is required for normal development of flowers and seeds, thereby highlighting a role of DNA methylation in determining the yield of normal tomato fruits.
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Project description:Sl2183 is an updated version of the previous tomato metabolic model (iHY3410), with additional reactions and metabolites, IDs converted into the BiGG nomenclature and biomass reactions for leaf, stem and root, allowing to generate a multi-organ model (see Gerlin et al., Plant Physiol. for additional information).
2022-04-07 | MODEL2111120001 | BioModels
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: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:Excess levels of Al3+ become highly harmful to plant roots. The epidermal and outer cortical layers of root-tips experience more severe damages than the inner tissues from Al toxicity. This project used laser capture microdissection (LCM) technology to isolate the outer and inner cell layers of cells in root-tips. Tomato "MicroTom" plants were grown in hydroponic solution supplemented with Al. Seeds derived from plants previously exposed to four generations of Al-treated solutions were considered stress-acclimated, these seeds were named G4Al+. Seeds harvested from soil-grown plants were also used, these seeds were named G0 seeds. Tandem mass tag (TMT) proteomics was used to identify differential proteomics responses among cells localized at different spaces in root-tips and those between the stress-acclimated and non-acclimated plants.
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Project description:Biotic and abiotic stress factors induce microbiome shifts and enrichment of distinct beneficial bacteria in tomato roots
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