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

PLoS One. 2014 Sep 30;9(9):e108906. doi: 10.1371/journal.pone.0108906. eCollection 2014.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics
  • Chromosome Mapping
  • Eucalyptus / genetics*
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental
  • Genome, Plant*
  • Multigene Family
  • Nicotiana / metabolism
  • Phylogeny
  • Plant Proteins / classification
  • Plant Proteins / genetics
  • Plant Proteins / metabolism*
  • Protoplasts / metabolism
  • Transcription Factors / classification
  • Transcription Factors / metabolism*
  • Transcriptome

Substances

  • Plant Proteins
  • Transcription Factors

Grants and funding

This work was supported by the Centre National pour la Recherche Scientifique (CNRS), the University Paul Sabatier Toulouse III (UPS), the French Laboratory of Excellence project “TULIP” (ANR-10-LABX-41; ANR-11-IDEX-0002-02) and the Plant KBBE TreeForJoules project (ANR-2010-KBBE-007-01 (FR) and P-KBBE/AGR_GPL/0001/2010 (FCT, PT)). HY was supported by PhD grants from the China Scholarship council. MS was supported by a Postdoc fellowship “Beatriu de Pinós” thanks to the Departament d'Universitats, Recerca i Societat de la Informació de la Generalitat de Catalunya. JAPP acknowledges Fundação para a Ciência e a Tecnologia (FCT, Portugal) and his research contract funded by Programa Ciência 2008 and POPH (QREN). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.