Transcriptomics

Dataset Information

2

Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis (tga3-2 knockout data)


ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Dafyd J Jenkins   Katherine J Denby  Susanna Atwell  Oliver Stegle  Richard Hickman  Jim Beynon  Steven Kiddle  David L Wild  Youn S Kim  Vicky Buchanan-Wollaston  Jonathan David Moore  Andrew Mead  David Rand  Emily Breeze  Christopher A Penfold  Sascha Ott  Oliver Windram  Laura Baxter  Cunjin Zhang  Roxane Legaie  Priyadharshini Madhou  Karsten Borgwardt  Jonathan Moore  Stuart McHattie  Emma Cooke  Alex Tabrett  Daniel J Kliebenstein  Claire Hill  Bärbel Finkenstadt  Johanna Rhodes 

PROVIDER: E-GEOD-39597 | ArrayExpress | 2012-10-03

SECONDARY ACCESSION(S): GSE39597PRJNA176553

REPOSITORIES: GEO, ArrayExpress

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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 generated a high-resolution time series of gene expression profiles from a single Arabidopsis thaliana leaf during infection by the necrotrophic fungal pathogen Botrytis cinerea. Approximately one-third of the Arabidopsis genom  ...[more]

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