Spatial metabolomics of eggplant (Solanum melongena)
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ABSTRACT: Spatial metabolomics of eggplant (Solanum melongena). This analysis comprehends different regions of the plant, including fruit, leaf, stem, and root.
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).
Project description:Transgenic tomato (Solanum lycopersicum) plants expressing a fragment of the SlSIOGDH gene encoding subunit E1 of the 2-oxoglutarate dehydrogenase protein complex in the antisense orientation and exhibiting considerable reductions in the activity of this enzyme exhibit a considerably reduced rate of respiration. They were, however, characterised by largely unaltered photosynthetic rates and fruit yield but a restricted leaf, stem and root growth rate. The lines displayed markedly altered metabolic profiles including changes in tricarboxylic acid cycle intermediates and in the majority of the amino acids without alterations in pyridine nucleotide content. Moreover, they displayed a generally accelerated development exhibiting early flowering, accelerated fruit ripening and a markedly earlier onset of leaf senescence. In addition, transcript and selective hormone profiling of gibberellins and ABA revealed changes only in the former coupled to changes in transcripts encoding enzymes of gibberellins biosynthesis. The data obtained are discussed in the context of the importance of this enzyme in both photosynthetic and respiratory metabolism as well as in programs of plant development connected to carbon nitrogen interactions.
Project description:Transgenic tomato (Solanum lycopersicum) plants expressing a fragment of the SlSIOGDH gene encoding subunit E1 of the 2-oxoglutarate dehydrogenase protein complex in the antisense orientation and exhibiting considerable reductions in the activity of this enzyme exhibit a considerably reduced rate of respiration. They were, however, characterised by largely unaltered photosynthetic rates and fruit yield but a restricted leaf, stem and root growth rate. The lines displayed markedly altered metabolic profiles including changes in tricarboxylic acid cycle intermediates and in the majority of the amino acids without alterations in pyridine nucleotide content. Moreover, they displayed a generally accelerated development exhibiting early flowering, accelerated fruit ripening and a markedly earlier onset of leaf senescence. In addition, transcript and selective hormone profiling of gibberellins and ABA revealed changes only in the former coupled to changes in transcripts encoding enzymes of gibberellins biosynthesis. The data obtained are discussed in the context of the importance of this enzyme in both photosynthetic and respiratory metabolism as well as in programs of plant development connected to carbon nitrogen interactions. Three biological replicates per genotype were analysed. Genotypes analyzed were tomato var. M82 wild type plants grown under green house conditions with one 2-oxo-glutarate dehydrogenase antisense line grown under the same conditions.
Project description:Gene-to-gene coexpression analysis is a powerful approach to infer function of uncharacterized genes. To perform non-targeted coexpression analysis of tomato genes, we collected a developmental gene expression dataset using various tissues of tomato plant. Expression data are collected from 24 different tissue types including root, hypocotyl, cotyledon, leaf at different stages, and fruit tissues at 4 different ripening stages from 4 different Solanum lycopersicum cultivars. Fruits were separated to the flesh and the peel. These two tissue types indeed showed remarkably different gene expression profiles. We also collected data from 4 different ripening stages (mature green, yellow, orange, and red) to detail the changes during ripening. By using this gene expression dataset, we calculated pair-wise Pearsonâs correlation coefficients, and performed network-based coexpression analysis. The analysis generated a number of coexpression modules, some of which showed an enrichment of genes associated with specific functional categories. This result will be useful in inferring functions of uncharacterized tomato genes, and in prioritizing genes for further experimental analysis. We used Affymetrix GeneChip Tomato genome Arrays to detail the global gene expression change using 24 different tomato tissue types (67 hybridizations). We collected gene expression data from 24 different tomato tissue types using 67 hybridizations. Root, hypocotyl, cotyledon, and leaf were sampled from 3-week-old or 5-weekâold plant of Solanum lycopersicum cultivar Micro-Tom. Fruit tissues were sampled from S. lycopersicum cultivars Micro-Tom, Anthocyanin fruit (Aft, LA1996), Line27859, and Momotaro 8 (Takii, Japan). From Micro-Tom fruit, the peel and the flesh were separately sampled from 4 different ripening stages: mature green (MG, approximately 30 day after anthesis), yellow (Y, approximately 35 days after anthesis), orange (O, approximately 38-40 days after anthesis), and red (R, approximately 45-48 days after anthesis). From fruits of Aft and Line27859, the peel and the flesh were sampled at mature green (MG, approximately 40 days after anthesis) and red (R, approximately 50-55 days after anthesis) stages. From Momotaro 8, the peel and the flesh were sampled at red (R, 50- approximately 50-55 days after anthesis) stages. For each tissue type, 2-4 biological replicates were made in RNA preparation.
Project description:Arabidopsis thaliana (accession- Columbia) is an important model plant. RNA-Seq based study of 36 libraries was carried out to explore transcriptional programs operating in different plant parts (seedling, rosette, root, inflorescence, flower, fruit silique, and seed) and developmental stages (2-leaf stage, 6-leaf stage, 12-leaf stage, senescence stage, dry mature and imbibed seed stage). For each tissue type and developmental stage, three individual plants were used as biological replicates.
Project description:The cell cycle transcription factor E2FB has been overexpressed in tomato plants (Solanum lycopersicum cv. Micro-Tom). This overexpression accelerates plant development and increases fruit yield.
Project description:The crop species Solanum lycopersicum establishes a beneficial root- symbiosis with the widespread group of arbuscular mycorrhizal (AM) fungi. The mycorrhiza establishment leads to a modulation of the plant gene expression which is not restricted to the root compartment but spreads at the organism-wide level. To understand the systemic effect of the fungal presence on the tomato fruit, we performed global transcriptome profiling through RNA-Seq analysis on Moneymaker tomato fruits sampled at the turning ripening stage. Gene expression data were obtained from fruits sampled at 55 days after flowering. Fruits were collected from Funneliformis mosseae colonized plants and from control plants which were fertilized in order to avoid responses related to nutrient deficiency.
Project description:We report a method for analyzing spatial metabolomics at single cell level. In human fibrotic liver samples, we identified a novel hepatocyte subpopulation via SEAM and spatial transcriptomics using modified protocol of Geo-sea. For Geo-seq, we generated cDNA libraries from Hepa69-high (Proximal), Hepa69-low (Distal) and Fibrotic (FB) regions. The differential gene expression analysis between Hepa69-high and Hepa69-low indicates that genes from solute carrier transporter families were elevated in Hepa69-high group.
Project description:As multicellular organisms, plants must integrate responses to environmental cues across different cell types and also over time. Nitrate is the major source of available Nitrogen for plants, and a limiting factor for plant growth and productivity. Plant root s are highly impacted by nitrate availability, modifying their architecture to optimize nitrate uptake from soils. In order to understand how this functional response is dynamically orchestrated across different cell types of the root, space and time must be addressed within the same experimental setup. We performed a transcriptomic analysis in five major root cell types of Arabidopsis plants in response to nitrate treatments considering short and long time exposure to this macronutrient. We found nitrate treatment triggers a dynamic reprogramming of root cell gene expression that follows a spatial pattern over time consistent with an early regulation of nitrate transport and assimilation in external layers of the root and a later regulation of hormonal and developmental processes in more internal layers of the root.