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

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...

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Bibliographic Details
Published in:PloS one 2014-09, Vol.9 (9), p.e108906-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: Article
Language:English
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
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0108906