Project description:The aim of this study was to compare the tomato global transcriptional profiles in response to host attack by ToMV and Fol in order to identify genomic differences and similarities in incompatible interactions between a foliar and a vascular pathogen. In order to identify a set of genes of interest in tomato plants infected with F. oxysporum f. sp. lycopersici (Fol) and Tomato Mosaic Virus (ToMV) a transcriptional analysis was performed. Tomato genes differentially expressed upon inoculation with Fol and ToMV were identified at 2 days post-inoculation, using an un-inoculated sample as reference.
Project description:This submission comprises all raw sequencing reads generated and/or utilised in the analyses presented in the associated manuscript. The dataset comprises two independent experimental datasets, each designed to address distinct biological questions regarding the transcriptional behaviour of Fusarium oxysporum f. sp. lycopersici (Fol) under varying physiological and conditions of host-interaction. Experiment 1: Raw reads from Fusarium oxysporum f. sp. lycopersici (Fol) grown under four distinct nutrient and substrate conditions: minimal-media broth (Fol-Min-Media), granular microjammed (Gamborg's B5 Microjammed Granular hydrogel), monolithic agarose (Gamborg's B5 in conventional homogeneous agarose), and broth (Gamborg's B5 in liquid). This design enables dissection of transcriptional responses attributable to nutritional composition and substrate mechanical architecture. Experiment 2 Raw reads from a Microjammed Granular hydrogel-based tomato root–Fol infection system. Samples were collected at 12, 24, and 36 hours post-inoculation (hpi). At 12 hpi, tomato root, tip and fungal samples ex-planta surrounding the root surface were profiled. At 24 hpi, tomato root samples and spatially stratified fungal samples collected from ex-planta at the root-proximal and root-distal zones were profiled to characterise host-induced transcriptional rewiring in Fol in proximity to the root surface when the fungus is approaching a host plant before the physical contact. At 36 hpi, only tomato root/tip samples were collected to capture the plant transcriptional responses to infection after establishment of the fungal compatibility within the root.
Project description:Transcriptome analysis reveals the response mechanism of Frl-mediated resistance to Fusarium oxysporum f. sp. radicis-lycopersici (FORL) infection in tomato
Project description:To compare the genome-wide transcriptional effect of ABA and iSB09 in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 20 uM iSB09-treated plants. Differential gene expression analysis between mock- and ABA-treated or iSB09-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. iSB09 upregulated and downregulated genes represent a subset of the ABA-responsive genes, which reflects the activation of PYL1-like and PYL4-like ABA receptors in tomato seedlings. Additionally, to compare the genome-wide transcriptional effect of ABA and iCB in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 10 uM iCB-treated plants. Differential gene expression analysis between mock- and ABA-treated or iCB-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. iCB mimics ABA transcriptional response through activation of the three subfamilies of ABA receptors.
Project description:RNA interference (RNAi) is a widely-used approach to generate virus-resistant transgenic crops. However, durability of RNAi-mediated resistance under extreme field conditions and side-effects of stable RNAi expression have not been thoroughly investigated. Here we performed field trials and molecular characterization of two RNAi-transgenic Solanum lycopersicum lines resistant to Tomato yellow leaf curl virus (TYLCV) disease, the major constraint for tomato cultivation in Cuba and worldwide. In order to determine potential impact of the hairpin RNA transgene expression on tomato genome expression and development, differences in the phenotypes and the transcriptome profiles between the transgenic and non-transgenic plants were examined. Transcriptome profiling revealed a common set of up- and down-regulated tomato genes, which correlated with slight developmental abnormalities in both transgenic lines.