title: Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation.
abstract: BACKGROUND
  The formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants. Although several studies have explored gene expression during flower development in the model plant Arabidopsis thaliana on a genome-wide scale, a continuous series of expression data from the earliest floral stages until maturation has been lacking. Here, we used a floral induction system to close this information gap and to generate a reference dataset for stage-specific gene expression during flower formation.
  
  
  RESULTS
  Using a floral induction system, we collected floral buds at 14 different stages from the time of initiation until maturation. Using whole-genome microarray analysis, we identified 7,405 genes that exhibit rapid expression changes during flower development. These genes comprise many known floral regulators and we found that the expression profiles for these regulators match their known expression patterns, thus validating the dataset. We analyzed groups of co-expressed genes for over-represented cellular and developmental functions through Gene Ontology analysis and found that they could be assigned specific patterns of activities, which are in agreement with the progression of flower development. Furthermore, by mapping binding sites of floral organ identity factors onto our dataset, we were able to identify gene groups that are likely predominantly under control of these transcriptional regulators. We further found that the distribution of paralogs among groups of co-expressed genes varies considerably, with genes expressed predominantly at early and intermediate stages of flower development showing the highest proportion of such genes.
  
  
  CONCLUSIONS
  Our results highlight and describe the dynamic expression changes undergone by a large number of genes during flower development. They further provide a comprehensive reference dataset for temporal gene expression during flower formation and we demonstrate that it can be used to integrate data from other genomics approaches such as genome-wide localization studies of transcription factor binding sites.
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.
authors.forename: Patrick T
authors.initials: PT
authors.lastname: Ryan
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.|Present address: Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany.
authors.forename: Diarmuid S
authors.initials: DS
authors.lastname: Ó'Maoiléidigh
authors.affiliation: Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
authors.forename: Hajk-Georg
authors.initials: HG
authors.lastname: Drost
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.
authors.forename: Kamila
authors.initials: K
authors.lastname: Kwaśniewska
authors.affiliation: Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Gabel
authors.affiliation: Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
authors.forename: Ivo
authors.initials: I
authors.lastname: Grosse
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.|Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Graciet
authors.affiliation: Leibniz Institute of Plant Biochemistry, Department of Molecular Signal Processing, Halle (Saale), Germany. mquint@ipb-halle.de.
authors.forename: Marcel
authors.initials: M
authors.lastname: Quint
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland. wellmerf@tcd.ie.
authors.forename: Frank
authors.initials: F
authors.lastname: Wellmer
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000235:genetics*; D035264:Flowers / Q000235:genetics / Q000254:growth & development*; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods
chemical_list: D029681:Arabidopsis Proteins