CIRCLES-TOMATO
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB80388 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13701700_1.fastq.gz | Fastqsanger.gz | |||
| ERR13701700_2.fastq.gz | Fastqsanger.gz | |||
| ERR13701800_1.fastq.gz | Fastqsanger.gz | |||
| ERR13701800_2.fastq.gz | Fastqsanger.gz | |||
| ERR13701900_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 502 |
Similar Datasets
Project description:Iron (Fe) deficiency is a yield-limiting factor for a variety of field crops across the world and generally results from the interaction of limited soil Fe bioavailability and susceptible genotype cultivation. Tomato, a Strategy I, model plant for Fe deficiency, is an important economical crop. Tomato responses in order to improve Fe uptake are based on acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells. Transcriptional profile obtained by roots (27-d) of 21-d-old tomato plants starved of iron for an additional week was compared with the transcriptional profile obtained for roots (27-d) of 21-d-old tomato plants grown for an additional week at 100 M-NM-<M Fe. Tomato plants were hydroponically grown in both cases. Three different biological replicates were used for each sample repeating the experiment three times. All samples were obtained pooling roots of six plants (27-d-old).
2012-03-22 | E-GEOD-31112 | biostudies-arrayexpress
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:An intriguing new paradigm in plant biology is that systemically-mobile mRNAs play a role in coordinating development. In this process, specific mRNAs are loaded into the phloem transport stream for translocation to distant tissues, where they may impact developmental processes. However, despite its potential significance for plant growth regulation, mRNA trafficking remains poorly understood and challenging to study. Here we show that phloem-mobile mRNAs can also traffic between widely divergent species from a host to the plant parasite, lespedeza dodder (Cuscuta pentagona Engelm.). Reverse transcriptase PCR (RT-PCR) and microarray analysis were used to detect specific tomato transcripts in dodder grown on tomato (Lycopersicon esculentum Mill.) that were not present in control dodder grown on other host species. The foreign transcripts included LeGAI, which has been previously shown to be translocated in the phloem, as well as nine other transcripts not reported to be mobile. Dodders are parasitic plants that obtain resources by drawing from the phloem of a host plant, and have joint plasmodesmata with host cortical cells. Although viruses are known to move between dodder and its hosts, translocation of endogenous plant mRNA has not been reported. These results point to a potentially new level of interspecies communication, and raise questions about the ability of parasites to recognize, use, and respond to transcripts acquired from their hosts. Experiment Overall Design: In order to identify potential tomato transcripts in dodder, microarray analysis was performed on RNA from dodder and hosts. Total RNA was extracted from the tomato host and from dodder grown on tomato, Arabidopsis, tobacco, or pumpkin. The host tomato RNA was included to verify that any transcripts detected in the parasite were in fact expressed in the host. The dodder samples grown on tobacco, Arabidopsis, and pumpkin served as controls for dodder genes that may cross-hybridize with tomato array probes, with three different host species used to minimize any host-specific effects on dodder gene expression. Samples were analyzed using the Affymetrix GeneChip Tomato Array and transcripts scored for presence or absence in each sample. Considering that host transcripts present in dodder would be at low levels and diluted with dodder transcripts, a P-value of 0.06 in at least two of three biological replicates was used as the threshold for scoring a transcript as being present.
2008-06-15 | E-GEOD-6736 | biostudies-arrayexpress
Project description:Generalist arthropod herbivores rapidly adapt to a broad range of host plants. However, the extent of transcriptional reprogramming in the herbivore and its hosts associated with adaptation remains poorly understood. Using the spider mite Tetranychus urticae and tomato as models with available genomic resources, we investigated the reciprocal genome-wide transcriptional changes in both spider mite and tomato as a consequence of mite’s adaptation to tomato We used microarray to assess global gene expression in Solanum lycopersicum cv. Moneymaker upon Tetranychus urticae attack by tomato-adapted and non-adapted spider mite lines.
2015-07-20 | GSE70375 | GEO
Project description:Climate change and industrial pollution are responsible for major losses in crop yield worldwide. Tomato plants are subjected to multiple stress conditions in combination when growing in the natural field. In this work, we analyzed the transcriptomic response of tomato plants to the combination of salinity and heat stress, when plants were or were not inoculated with the beneficial bacteria Pseudomonas Putida. The results suggest that specific transcripts are regulated only under stress combination in plants inoculated with the bacteria. These transcripts could be related with the enhanced tolerance of inoculated plants under conditions of stress combination.
2024-12-31 | GSE245759 | GEO
Project description:Transcriptional changes in greenhouse-grown plants of tomato varieties Monaymaker and Mogeor infected with Pyrenochaeta lycopersici compared to uninfected control plants. The objective of the the study was to give an insight into the establishment of compatible and incompatible interactions between tomato and the pathogen using susceptible (Moneymaker) and resistant (Mogeor) varieties of tomato. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Justyna Anna Milc. The equivalent experiment is LE4 at PLEXdb]
2016-02-11 | GSE44230 | GEO
Project description:In this study, we obtain FoAPY1 transgenic tomato plants (2417-GFP) and control plants (GFP). All target tomato plants were identified by WB using anti-GFP antibody and all transgenic tomato plants has no differences in morphological and growth rate compared with wild type tomato plants. In order to detect the potential functional mechanism of FoAPY1 protein in the host plant, the proteomic analysis was performed to analyze differentially abundant proteins in two type tomato plants
2022-08-09 | PXD035875 | Pride
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:Lycopersicon esculentum cv. Moneymaker tomato plants were grown for 4 weeks in greenhouse conditions (16h/8h light/darkness, 27 °C). L. esculentum was randomly sorted into two groups of 16 plants each and a third reference group of 6 plants. All plants were contained individually in mesh bags. One group of 16 plants was infested with 25 female adult tomato psyllids that were 2-3 days old per plant. The other two groups of 16 and 6 plants were not infested (healthy control, and reference pool). After 3 days, the adults were removed from the infested plants to allow for egg eclosion and eventually nymphal development. In this study, leaves infested and healthy plants were harvested for RNA extraction at 0, 3, 11, and 17 days after infestation with tomato psyllids. The reference pool was harvested on day 0. Tissue (all-leaflets) from at least three plants per group was collected, flash frozen in liquid nitrogen and pooled for each time point (0, 3, 11 and 17 days after infestation) to represent treatments for before feeding (0 d), adult feeding and egg deposition (3 d), 1st and 2nd instar feeding (11 d) and 3rd to 5th instar feeding (17 d ), respectively. The whole experiment was repeated three times (three biological replicates). Plant tissues were ground using a cold mortar and pestle. Total tomato leaf RNA was extracted using the hot-phenol protocol. The RNA was precipitated, pooled, cleaned with a kit and stored at –80C. Two populations of single-stranded cDNAs will be generated from the aliquots and labeled with the cyanine Cy3 and Cy5 fluorophores. RNA isolated from the reference pool (0 d) will be pooled from each replicate and will be labeled with Cy5; this is the reference sample for each hybridization. RNA isolated from leaves infested with tomato psyllids and healthy uninfested plants from each time point will be query samples labeled with Cy3. The two samples of labeled cDNA will be simultaneously hybridized to the same microarray. Keywords: Reference design
2008-02-21 | GSE10550 | GEO
Project description:An intriguing new paradigm in plant biology is that systemically-mobile mRNAs play a role in coordinating development. In this process, specific mRNAs are loaded into the phloem transport stream for translocation to distant tissues, where they may impact developmental processes. However, despite its potential significance for plant growth regulation, mRNA trafficking remains poorly understood and challenging to study. Here we show that phloem-mobile mRNAs can also traffic between widely divergent species from a host to the plant parasite, lespedeza dodder (Cuscuta pentagona Engelm.). Reverse transcriptase PCR (RT-PCR) and microarray analysis were used to detect specific tomato transcripts in dodder grown on tomato (Lycopersicon esculentum Mill.) that were not present in control dodder grown on other host species. The foreign transcripts included LeGAI, which has been previously shown to be translocated in the phloem, as well as nine other transcripts not reported to be mobile. Dodders are parasitic plants that obtain resources by drawing from the phloem of a host plant, and have joint plasmodesmata with host cortical cells. Although viruses are known to move between dodder and its hosts, translocation of endogenous plant mRNA has not been reported. These results point to a potentially new level of interspecies communication, and raise questions about the ability of parasites to recognize, use, and respond to transcripts acquired from their hosts. Keywords: mRNA trafficking, parasitism, parasitic plant
2007-02-01 | GSE6736 | GEO