title: Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis.
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 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 genome is differentially expressed during the first 48 h after infection, with the majority of changes in gene expression occurring before significant lesion development. We 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 role for TGA3 in defense against necrotrophic pathogens. These data provide an unprecedented level of detail about transcriptional changes during a defense response and are suited to systems biology analyses to generate predictive models of the gene regulatory networks mediating the Arabidopsis response to B. cinerea.
authors.affiliation: School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
authors.forename: Oliver
authors.initials: O
authors.lastname: Windram
authors.forename: Priyadharshini
authors.initials: P
authors.lastname: Madhou
authors.forename: Stuart
authors.initials: S
authors.lastname: McHattie
authors.forename: Claire
authors.initials: C
authors.lastname: Hill
authors.forename: Richard
authors.initials: R
authors.lastname: Hickman
authors.forename: Emma
authors.initials: E
authors.lastname: Cooke
authors.forename: Dafyd J
authors.initials: DJ
authors.lastname: Jenkins
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Penfold
authors.forename: Laura
authors.initials: L
authors.lastname: Baxter
authors.forename: Emily
authors.initials: E
authors.lastname: Breeze
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Kiddle
authors.forename: Johanna
authors.initials: J
authors.lastname: Rhodes
authors.forename: Susanna
authors.initials: S
authors.lastname: Atwell
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Kliebenstein
authors.forename: Youn-Sung
authors.initials: YS
authors.lastname: Kim
authors.forename: Oliver
authors.initials: O
authors.lastname: Stegle
authors.forename: Karsten
authors.initials: K
authors.lastname: Borgwardt
authors.forename: Cunjin
authors.initials: C
authors.lastname: Zhang
authors.forename: Alex
authors.initials: A
authors.lastname: Tabrett
authors.forename: Roxane
authors.initials: R
authors.lastname: Legaie
authors.forename: Jonathan
authors.initials: J
authors.lastname: Moore
authors.forename: Bärbel
authors.initials: B
authors.lastname: Finkenstadt
authors.forename: David L
authors.initials: DL
authors.lastname: Wild
authors.forename: Andrew
authors.initials: A
authors.lastname: Mead
authors.forename: David
authors.initials: D
authors.lastname: Rand
authors.forename: Jim
authors.initials: J
authors.lastname: Beynon
authors.forename: Sascha
authors.initials: S
authors.lastname: Ott
authors.forename: Vicky
authors.initials: V
authors.lastname: Buchanan-Wollaston
authors.forename: Katherine J
authors.initials: KJ
authors.lastname: Denby
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000276:immunology / Q000378:metabolism / Q000382:microbiology; D029681:Arabidopsis Proteins / Q000235:genetics*; D020171:Botrytis / Q000254:growth & development / Q000502:physiology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D053263:Gene Regulatory Networks; D018745:Genome, Plant / Q000235:genetics*; D008957:Models, Genetic; D009154:Mutation; D059372:Nucleotide Motifs; D020411:Oligonucleotide Array Sequence Analysis; D010935:Plant Diseases / Q000276:immunology* / Q000382:microbiology; D057865:Plant Immunity; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism / Q000382:microbiology; D011401:Promoter Regions, Genetic / Q000235:genetics; D015398:Signal Transduction; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome
chemical_list: D029681:Arabidopsis Proteins; D014157:Transcription Factors