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Omics score: 9

High-throughput sequencing of small RNAs from different developmental stages of tomato fruits

ABSTRACT: Comparison of endogenous small RNA profiles from different developmental stages of tomato fruits Size fractionated small RNA from total RNA extracts was ligated to adaptors, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.

OTHER RELATED OMICS DATASETS IN: PRJNA119405

ORGANISM(S): Solanum Lycopersicum

TISSUE(S): Flower, Fruit, Closed Bud

SUBMITTER: Frank Schwach Tamas Dalmay Irina Mohorianu Vincent Moulton Simon Moxon Runchun Jing

PROVIDER: E-GEOD-18110 | ArrayExpress | 2011-06-02

SECONDARY ACCESSION(S): SRP002313GSE18110PRJNA119405

REPOSITORIES: GEO, ArrayExpress, ENA

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			Action	DRS
	E-GEOD-18110.idf.txt	Idf
	E-GEOD-18110.processed.1.zip	Processed
	E-GEOD-18110.sdrf.txt	Txt

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Publications

Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns.

Mohorianu Irina I Schwach Frank F Jing Runchun R Lopez-Gomollon Sara S Moxon Simon S Szittya Gyorgy G Sorefan Karim K Moulton Vincent V Dalmay Tamas T

The Plant journal : for cell and molecular biology 20110509 2

Plants feature a particularly diverse population of short (s)RNAs, the central component of all RNA silencing pathways. Next generation sequencing techniques enable deeper insights into this complex and highly conserved mechanism and allow identification and quantification of sRNAs. We employed deep sequencing to monitor the sRNAome of developing tomato fruits covering the period between closed flowers and ripened fruits by profiling sRNAs at 10 time-points. It is known that microRNAs (miRNAs) p ...[more]

PMID: 21443685

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Microarray analysis of gene expression from different developmental stages of the tomato fruit

Project description:The goal of this research was to measure the gene expression levels thoughout 10 stages of tomato fruit development. Whole buds, flowers or fruits were collected at various developmental timepoints. Total RNA was extracted from 10 stages of flower and fruit development. A single technical and biological repeat was performed. cDNA was amplified and labelled using standard Affymetrix protocols.

2012-08-29 | E-GEOD-22300 | ArrayExpress

High-throughput sequencing of small RNAs from different developmental stages of tomato fruits

Project description:Comparison of endogenous small RNA profiles from different developmental stages of tomato fruits Size fractionated small RNA from total RNA extracts was ligated to adaptors, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.

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44K Agilent microarray analysis of SlBIM1a overexpressing tomato fruits

Project description:The steroid hormone brassinosteroids (BRs) play considerable roles in plant development and defence. Harnessing the extensive knowledge on Arabidopsis BR signalling network for improving productivity in crop species requires first to identify the conserved network components and their function in the target species. To investigate the function of SlBIM1a, the tomato closest homolog of AtBIM1, which is highly expressed in the developing fruit, we generated transgenic tomatoes, which overexpress or down-regulate SlBIM1a gene. Main alterations were observed in SlBIM1a overexpressing lines, which displayed a severe plant and fruit dwarfism. To unravel the molecular basis of phenotypical modifications in SlBIM1a overexpressing fruits, a microarray (Agilent) analysis was performed on Pro35S:SlBIM1aOX and WT fruits harvested at 15 DPA.

2020-10-26 | E-MTAB-9502 | ArrayExpress

High-throughput sequencing of small RNAs from different developmental stages of tomato fruits

Project description:Comparison of endogenous small RNA profiles from different developmental stages of tomato fruits Overall design: Size fractionated small RNA from total RNA extracts was ligated to adaptors, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.

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The composition and function of chaperone networks in Solanum lycopersicum explored by transcriptome sequencing and microarray meta-analysis

Project description:Heat shock proteins (Hsps) are molecular chaperones primarily involved in maintenance of protein homeostasis. Their function has been best characterized in heat stress (HS) response during which Hsps are transcriptionally controlled by heat stress transcription factors (Hsfs). The role of Hsfs and Hsps in HS-response in tomato was initially examined by transcriptome analysis using the Massive Analysis of cDNA Ends (MACE) method. Approximately 9.6% of all genes expressed in leaves are enhanced in response to HS, including a subset of Hsfs and Hsps. The underlying Hsp-Hsf networks with potential functions in stress responses or developmental processes were further explored by meta-analysis of existing microarray datasets. We identified clusters with differential transcript profiles with respect to abiotic stresses, plant organs and developmental stages. The composition of two clusters points toward two major chaperone networks. One cluster consisted of constitutively expressed plastidial chaperones and other genes involved in chloroplast protein homeostasis. The second cluster represents genes strongly induced by heat, drought and salinity stress, including HsfA2 and many stress-inducible chaperones, but also potential targets of HsfA2 not related to protein homeostasis. This observation attributes a central regulatory role to HsfA2 in controlling different aspects of abiotic stress response and tolerance in tomato. 2 samples

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Effect of overexpressing E2FB in tomato plants

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2010-09-03 | E-GEOD-23971 | ArrayExpress

HsfA2 controls the activity of developmentally and stress-regulated heat stress protection mechanisms in tomato male reproductive tissues

Project description:Male reproductive tissues are more sensitive to heat stress compared to vegetative tissues, however the basis of this phenomenon is poorly understood. Heat stress transcription factors (Hsfs) regulate the transcriptional changes required for protection and recovery from heat stress. HsfA2 has been characterized as co-activator of HsfA1a in tomato and is considered as one of the major Hsfs accumulating in response to elevated temperatures. The role of HsfA2 in heat stress response of different tissues was examined by exploring the composition and structure of the tissue-specific regulatory networks in transgenic tomato plants with suppressed HsfA2 expression (A2AS). Transcriptome analysis revealed that HsfA2 acts in condition- and tissue-specific manner and that only a subset of heat stress induced genes require HsfA2 for higher expression. Remarkably, although HsfA2 is not essential for thermotolerance in seedlings and flowering plants, it is required for maintenance pollen viability under stress conditions. We show that the activation of Hsf networks is important for the developmentally regulated priming of heat stress response occurring at early stages of anther and pollen development. Thereby, HsfA2 is involved in pollen thermotolerance by directly regulating heat stress responsive genes but also by stimulating the synthesis of molecular chaperones under non-stress conditions. 8 samples

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Microarray analysis of developing fruits from transgenic lines with increased or reduced SlARF9 mRNA levels in tomato.

Project description:The transformation of the ovary into a fruit after successful completion of pollination and fertilization has been associated with many changes at transcriptomic level. These changes are part of a dynamic and complex regulatory network that is controlled by phytohormones, with a major role for auxin. One of the auxin-related genes differentially expressed upon fruit set and early tomato fruit development is Solanum lycopersicum ARF9 (SlARF9). To explore the physiological role of SlARF9 in tomato fruit set and development, we generated transgenic tomato lines in which the gene was overexpressed or silenced, and used microarray analysis to identify possible transcriptomic changes associated with the fruit developmental phenotypes observed in the transgenic lines. The transcript profiling analysis was done using pericarp tissue from fruits, 3-4mm in diameter, with each sample containing the pericarp of two fruits. For each seperate transgenic line, tissues were pooled from 2-3 plants (T2), resulting in a total of 6 samples for SlARF9-OE, 7 samples for SlARF9-RNAi, and 2 samples for wild type. The transcript profiling analysis was carried out using affymetrix EUTOM3 tomato exon array.

2014-11-26 | E-GEOD-63637 | ArrayExpress

Transcription profiling by array of M82 GAME1-RNAi tomato plants vs wild-type tomato plants

Project description:We introduced the GAME1i construct into the indeterminate M82 cultivar by crossing, obtaining plants that displayed a phenotype of severe growth retardation, deformed leaves and abortion of flower buds . In addition, leaves of these plants exhibited dark necrotic spots resembling symptoms typically seen after infection of tomato by pathogenic bacteria like Xanthamonas campestris pv. vesicatoria (Xcv) or Pseudomonas syringae pv. tomato (Pst) . As no other tomato lines grown in the same greenhouse at the same time showed similar disease-like symptoms, we hypothesized that silencing GAME1 might mimic induction of disease symptoms in the absence of a pathogen. Indeed, we were able to isolate neither Xcv nor Pst (or other putative pathogens) from GAME1i leaves that displayed necrotic spots. Microarray analysis was performed to examine if the transgene, and possibly, the corresponding changes in the metabolic profile, induced the plant response system at the transcriptional level.

2011-11-28 | E-MEXP-3455 | ArrayExpress

Plastoglobules are a biosynthetic platform contributing to carotenoid accumulation during tomato fruit maturation

Project description:Chloroplasts and chromoplasts of tomato fruits contain lipid droplets known as plastoglobules (PG). Recent studies have shown that PG act as a metabolic sink to store triacylglycerol (TAG), carotenoids, vitamin E, and K as well as other lipophile compounds. In addition, it has been shown that proteins associated with PG contribute to prenyl lipid metabolic pathways and homeostasis. Proteome studies in Arabidopsis and bell pepper, have demonstrated that PG contains a specific proteome containing around 30 proteins. So far, the tomato PG proteome particularly that of red fruit (chromoplast) has not yet been established. We have investigated the chromoplast PG proteome and metabolome and identified 17 new candidate proteins of chromoplast PG with known PG proteins. Interestingly, most of the carotenoid biosynthetic pathway enzymes such as PSY‐1, PDS, ZDS, CRTISO, and β‐LYC are enriched in chromoplast PG compared with chloroplast PG. In this study, we propose a model of chromoplast PG acting as a carotenoid biosynthesis platform.

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