title: Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa.
abstract: BACKGROUND
  Auxin/Indole-3-Acetic Acid (Aux/IAA) and Auxin Response Factor (ARF) transcription factors are key regulators of auxin responses in plants. We identified the suites of genes in the two gene families in Populus and performed comparative genomic analysis with Arabidopsis and rice.
  
  
  RESULTS
  A total of 35 Aux/IAA and 39 ARF genes were identified in the Populus genome. Comparative phylogenetic analysis revealed that several Aux/IAA and ARF subgroups have differentially expanded or contracted between the two dicotyledonous plants. Activator ARF genes were found to be two fold-overrepresented in the Populus genome. PoptrIAA and PoptrARF gene families appear to have expanded due to high segmental and low tandem duplication events. Furthermore, expression studies showed that genes in the expanded PoptrIAA3 subgroup display differential expression.
  
  
  CONCLUSIONS
  The present study examines the extent of conservation and divergence in the structure and evolution of Populus Aux/IAA and ARF gene families with respect to Arabidopsis and rice. The gene-family analysis reported here will be useful in conducting future functional genomics studies to understand how the molecular roles of these large gene families translate into a diversity of biologically meaningful auxin effects.
authors.affiliation: Environmental Sciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA. kalluriudayc@ornl.gov
authors.forename: Udaya C
authors.initials: UC
authors.lastname: Kalluri
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Difazio
authors.forename: Amy M
authors.initials: AM
authors.lastname: Brunner
authors.forename: Gerald A
authors.initials: GA
authors.lastname: Tuskan
mesh_terms: D020727:ADP-Ribosylation Factors / Q000235:genetics*; D017360:Arabidopsis / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics*; D020869:Gene Expression Profiling; D017343:Genes, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D005810:Multigene Family / Q000235:genetics*; D009687:Nuclear Proteins / Q000235:genetics*; D010802:Phylogeny; D032107:Populus / Q000235:genetics*; D040081:Protein Array Analysis; D014157:Transcription Factors / Q000235:genetics
chemical_list: D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D014157:Transcription Factors; D020727:ADP-Ribosylation Factors