Project description:This SuperSeries is composed of the following subset Series: GSE29642: Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis (time series) GSE39597: Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis (tga3-2 knockout data) Refer to individual Series
Project description:To investigate NUP62 in the regulation of plant defense against Botrytis cinerea , we performed gene expression profiling analysis using data obtained from RNA-seq of nup62 mutant and WT arabidopsis with or without Botrytis cinerea infection.
Project description:Transcriptional reprogramming forms a major part of a plant's response to pathogen infection. Many individual components and pathways operating during plant defense have been identified but our knowledge of how these different components interact is still rudimentary. We have generated a high-resolution time series of gene expression profiles from a single Arabidopsis leaf during infection by the necrotrophic fungal pathogen, Botrytis cinerea. Approximately one-third of the Arabidopsis genome is differentially expressed during the first 48 hours after infection, with the majority of gene expression changes occurring before significant lesion development. We have used computational tools to obtain a detailed chronology of the defense response against B. cinerea, highlighting the times at which signaling and metabolic processes change, and identify transcription factor families operating at different times after infection. Motif enrichment and network inference predicted regulatory interactions and testing of one such prediction identified a novel role for TGA3 in defense against necrotrophic pathogens. These data provide an unprecedented level of detail about transcriptional change during a defense response and are suited to systems biology analyses to generate predictive models of the gene regulatory networks underlying the Arabidopsis response to B. cinerea.
Project description:Transcriptional reprogramming forms a major part of a plant's response to pathogen infection. Many individual components and pathways operating during plant defense have been identified but our knowledge of how these different components interact is still rudimentary. We have generated a high-resolution time series of gene expression profiles from a single Arabidopsis leaf during infection by the necrotrophic fungal pathogen, Botrytis cinerea. Approximately one-third of the Arabidopsis genome is differentially expressed during the first 48 hours after infection, with the majority of gene expression changes occurring before significant lesion development. We have used computational tools to obtain a detailed chronology of the defense response against B. cinerea, highlighting the times at which signaling and metabolic processes change, and identify transcription factor families operating at different times after infection. Motif enrichment and network inference predicted regulatory interactions and testing of one such prediction identified a novel role for TGA3 in defense against necrotrophic pathogens. These data provide an unprecedented level of detail about transcriptional change during a defense response and are suited to systems biology analyses to generate predictive models of the gene regulatory networks underlying the Arabidopsis response to B. cinerea. Samples were compared at three time points: 16, 24 and 32 hours post infection. Time points were chosen based on the expression profile of TGA3 in the high-resolution time series also presented in this paper. Samples were collected for three different conditions: tga3-2 mock inoculated, tga3-2 infected and Col-0 infected. Four individual leaves (biological replicates) from separate plants were collected for each treatment-time point totalling 36 samples. The four biological replicates for each treatment-time point were pooled. At each time point, the expression of the 4 pooled replicates was compared between tga3-2 mock inoculated vs. tga3-2 infected and tga3-2 infected vs. Col-0 infected using four technical replicates for each comparison which included balanced dye swaps.
Project description:Next generation sequencing was performed to identify genes changed in Arabidopsis thaliana upon Botrytis cinerea infection. The goal of the work is to find interesting genes involved in plant defense. The object is to reveal the molecular mechanism of plant defense.
Project description:The Arabidopsis rosette core can display full resistance against Botrytis cinerea. To reveal potential players in this resistance, the transcriptome of the Arabidopsis rosette core was determined.
Project description:Next generation sequencing (NGS) was performed to identify genes changed in ginseng upon Botrytis cinerea △BcSpd1 treatment. The goal of the work is to find interesting genes involved in ginseng in response to fungi induction. The object is to reveal the molecular mechanism of ginseng defense induced by Botrytis cinerea △BcSpd1 .
Project description:Plant food production is severely affected by fungi; to cope with this problem, farmers use synthetic fungicides. However, the need to reduce fungicide application has led to a search for alternatives, such as biostimulants. Rare-earth elements (REEs) are widely used as biostimulants, but their mode of action and their potential as an alternative to synthetic fungicides have not been fully studied. Here, the biostimulant effect of gadolinium (Gd) is explored using the plant-pathosystem Arabidopsis thaliana–Botrytis cinerea . We determine that Gd induces local, systemic, and long-lasting plant defense responses to B. cinerea, without affecting fungal development. The physiological changes induced by Gd have been related to its structural resemblance to calcium. However, our results show that the calcium-induced defense response is not sufficient to protect plants against B. cinerea, compared to Gd. Furthermore, a genome-wide transcriptomic analysis shows that Gd induces plant defenses and modifies early and late defense responses. However, the resistance to B. cinerea is dependent on JA/ET-induced responses. These data support the conclusion that Gd can be used as a biocontrol agent for B. cinerea. These results are a valuable tool to uncover the molecular mechanisms induced by REEs.
