Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Tomato fruit wound inoculation by C. coccodes and ammonium treated

ABSTRACT: Colletotrichum coccodes secretes ammonium during germination and colonization of host tissue as a mechanism for dual activation of fungal pathogenicity factors and plant cell death via activation of host NADPH oxidase. Ammonium accumulation during colonization of tomato fruits by C. coccodes induced host nucleus integrity changes and program cell death (PCD). Transcriptome analysis at the leading edge of colonized tissue and ammonium treated tomato fruits revealed 82 and 237 common up-regulated and common down-regulated genes, respectively. The common-up-regulated genes showed over representation of pathogen related (PR) proteins, salicylic acid (SA) dependent and systemic acquired resistance (SAR) related genes and genes related to biotic stress. The down regulated genes showed over representation of Jasmonic acid (JA) dependent genes. Consistent with this observation the direct application of SA enhanced C. coccodes colonization, whereas the application of JA delayed colonization. Candidate genes were selected for QRT-PCR analysis of transcripts in normal and transgenic RBOH antisense plants and showed dependence on RBOH regulation. In all, the results suggest that ammonia accumulation during C. coccodes colonization activates SA and suppress JA pathways through activation of RBOH. The effects of ammonium on the expression of the selected up-and down regulated genes were examined in fruit of different maturation stages. Red, susceptible and green resistant, tomato fruit displayed similar behavior, suggesting that resistance of green fruits to C. coccodes colonization is not modulated by the JA and SA pathways but depends on other factors Ten micrograms of total RNA was processed for the microarray hybridizations using the Affymetrix GeneChip one-cycle target-labeling kit (Affymetrix). The four treatments were: C. coccodes "mat inoculation" compared to a wound control (24 hours after the tomato fruit peel was removed). 5 mM Ammonium treatment in PBS compared to PBS treatments as a control for ammonium treatment, the treatments applied every four hours. Each treatment had a duplicate. The biotinylated complementary RNA was fragmented and hybridized to the GeneChip Tomato Genome Array (10,038 tomato probe sets for more than 9,200 tomato genes). The arrays were washed, stained, and scanned at the biological services (Weizmann institute of science, Rehovot, Israel). CEL files for the Affymetrix microarray data arising from the microarray experiments were analyzed utilizing the Partek genomics software (Downey, 2006).

ORGANISM(S): Solanum lycopersicum

SUBMITTER: Robert Fluhr

PROVIDER: E-GEOD-21999 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

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Tomato fruit wound inoculation by C. coccodes and ammonium treated

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