Genome-wide characterization and expression profiling of the AUXIN RESPONSE FACTOR (ARF) gene family in Eucalyptus grandis

• Published in: PloS one Vol. 9; no. 9; p. e108906
• Main Authors: Yu, Hong, Soler, Marçal, Mila, Isabelle, San Clemente, Hélène, Savelli, Bruno, Dunand, Christophe, Paiva, Jorge A P, Myburg, Alexander A, Bouzayen, Mondher, Grima-Pettenati, Jacqueline, Cassan-Wang, Hua
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 30.09.2014; Public Library of Science (PLoS)
• Subjects: Agricultural biotechnology; Angiosperms; Arabidopsis; Arabidopsis - genetics; ARF protein; Biology and Life Sciences; Cell division; Chromosome Mapping; Comparative analysis; Cues; Economic importance; Environmental effects; Eucalyptus; Eucalyptus - genetics; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Developmental; Genes; Genetic aspects; Genetics; Genome, Plant; Genomes; Genomics; Life Sciences; Liriodendron tulipifera; MicroRNAs; Multigene Family; Nicotiana - metabolism; Nitrogen; Nucleotide sequence; Organs; Phylogeny; Plant Proteins - classification; Plant Proteins - genetics; Plant Proteins - metabolism; Plants genetics; Proteins; Protoplasts - metabolism; Signal transduction; Signaling; Stem cells; Tissues; Transcription; Transcription Factors - classification; Transcription Factors - metabolism; Transcriptome; Wood; Xylem; Plant hormone auxin; Woody plant; Cambial region; Organogenesis
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0108906

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.