title: Genome-wide characterization and expression profiling of the AUXIN RESPONSE FACTOR (ARF) gene family in Eucalyptus grandis.
abstract: Auxin is a central hormone involved in a wide range of developmental processes including the specification of vascular stem cells. Auxin Response Factors (ARF) are important actors of the auxin signalling pathway, regulating the transcription of auxin-responsive genes through direct binding to their promoters. The recent availability of the Eucalyptus grandis genome sequence allowed us to examine the characteristics and evolutionary history of this gene family in a woody plant of high economic importance. With 17 members, the E. grandis ARF gene family is slightly contracted, as compared to those of most angiosperms studied hitherto, lacking traces of duplication events. In silico analysis of alternative transcripts and gene truncation suggested that these two mechanisms were preeminent in shaping the functional diversity of the ARF family in Eucalyptus. Comparative phylogenetic analyses with genomes of other taxonomic lineages revealed the presence of a new ARF clade found preferentially in woody and/or perennial plants. High-throughput expression profiling among different organs and tissues and in response to environmental cues highlighted genes expressed in vascular cambium and/or developing xylem, responding dynamically to various environmental stimuli. Finally, this study allowed identification of three ARF candidates potentially involved in the auxin-regulated transcriptional program underlying wood formation.
authors.affiliation: LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France.
authors.forename: Hong
authors.initials: H
authors.lastname: Yu
authors.affiliation: LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France.
authors.forename: Marçal
authors.initials: M
authors.lastname: Soler
authors.affiliation: Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Laboratoire de Génomique et Biotechnologie des Fruits, Castanet-Tolosan, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Mila
authors.affiliation: LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: San Clemente
authors.affiliation: LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Savelli
authors.affiliation: LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Dunand
authors.affiliation: Instituto de Investigação Científica e Tropical (IICT/MCTES), Lisboa, Portugal; Instituto de Biologia Experimental e Tecnológica (IBET), Oeiras, Portugal.
authors.forename: Jorge A P
authors.initials: JA
authors.lastname: Paiva
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Pretoria, South Africa.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Myburg
authors.affiliation: Université de Toulouse, Institut National Polytechnique-Ecole Nationale Supérieure Agronomique de Toulouse, Laboratoire de Génomique et Biotechnologie des Fruits, Castanet-Tolosan, France.
authors.forename: Mondher
authors.initials: M
authors.lastname: Bouzayen
authors.affiliation: LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Grima-Pettenati
authors.affiliation: LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, Castanet Tolosan, France.
authors.forename: Hua
authors.initials: H
authors.lastname: Cassan-Wang
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D002874:Chromosome Mapping; D005052:Eucalyptus / Q000235:genetics*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018745:Genome, Plant; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D011523:Protoplasts / Q000378:metabolism; D014026:Nicotiana / Q000378:metabolism; D014157:Transcription Factors / Q000145:classification / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors