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:To understand the AtJUB1 mediated regulation of tomato fruit development. To test how the NAC transcription factor JUNGBRUNNEN1 from Arabidopsis thaliana (AtJUB1, identical to ANAC042; At2g43000) affects the development of tomato fruits, AtJUB1-GFP was expressed in transgenic tomato plants under the control of the CaMV 35S promoter. AtJUB1-GFP fusion protein was previously shown to encode a functionally active transcription factor in Arabidopsis (Wu et al., 2012). We then performed gene expression profiling of fruits from AtJUB1-GFP lines (AtJUB1-OX plants) and non-modified wild-type (WT) plants. Fruits at two developmental stages, namely mature green (MG) and Breaker+7 days (B+7), were analysed. To this end, the pericarp was separated from the rest of the fruits and quickly frozen in liquid nitrogen for subsequent RNA extraction. Gene expression analysis was performed using GeneChip Tomato Genome Arrays (Affymetrix). Probe preparation and microarray hybridizations were performed by ATLAS Biolabs (Berlin, Germany).
Project description:By using parallel analysis of RNA ends (PARE) for global identification of miRNA targets and comparing four different stages of tomato fruit development we identified a large number of target genes of miRNAs. PARE libraries were produced, one each, for tomato fruits at 5 days after pollination, mature green fruit, Breaker fruit, and 7 days after Breaker stge fruits
Project description:The proteins accumulated in tomato young fruits were investigated by mass spectrometry-based label-free proteomics. Protein accumulation pattern was investigated during the time course of young fruits and the effect of pollination was compared with emasculated fruits.
Project description:Deep transcriptome sequencing of various tomato tissues. We describe the coupling of pyrosequencing technology with laser capture microdissection to characterize the transcriptomes of the five principal tissues of the pericarp from tomato fruits (outer and inner epidermal layers, collenchyma, parenchyma, and vascular tissues) at their maximal growth phase. NOTE: Not all samples from SRP004923 were imported in this accession.
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.
Project description:To investigate the function of SlNOR-like1 in the regulation of cuticle formation in tomato fruits, we established nor-like1 mutants by CRISPR/Cas9. We then performed gene expression profiling analysis using data obtained from RNA-seq of tomato exocarp of wild type (WT) and nor-like1 mutant at mature green (MG) stage.
