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Abstract
Auxin response factors (ARFs) are an important family of proteins in auxin-mediated response, with key roles in various physiological and biochemical processes. To date, a genome-wide overview of the ARF gene family in citrus was not available. A systematic analysis of this gene family in citrus was begun by carrying out a genome-wide search for the homologs of ARFs. A total of 19 nonredundant ARF genes (CiARF) were found and validated from the sweet orange. A comprehensive overview of the CiARFs was undertaken, including the gene structures, phylogenetic analysis, chromosome locations, conserved motifs of proteins, and cis-elements in promoters of CiARF. Furthermore, expression profiling using real-time PCR revealed many CiARF genes, albeit with different patterns depending on types of tissues and/or developmental stages. Comprehensive expression analysis of these genes was also performed under two hormone treatments using real-time PCR. Indole-3-acetic acid (IAA) and N-1-napthylphthalamic acid (NPA) treatment experiments revealed differential up-regulation and down-regulation, respectively, of the 19 citrus ARF genes in the callus of sweet orange. Our comprehensive analysis of ARF genes further elucidates the roles of CiARF family members during citrus growth and development process.
Highlights
Auxin plays a central role in controlling plant developmental and physiological processes, including embryogenesis, apical dominance, vascular elongation, flowering, fruit development, and lateral root initiation (Woodward and Bartel, 2005; Fleming, 2006)
Because the sweet orange genome was sequenced with a whole-genome shotgun strategy, some of these Auxin response factors (ARFs) genes may be redundant even though they were located on distinct scaffolds
The nomenclature system for CiARF in the present study provisionally uses the names CiARF1 to CiARF9 and CiARF16 to CiARF19 to distinguish each of the ARF genes based on the homology between AtARF and CiARF genes
Summary
Auxin plays a central role in controlling plant developmental and physiological processes, including embryogenesis, apical dominance, vascular elongation, flowering, fruit development, and lateral root initiation (Woodward and Bartel, 2005; Fleming, 2006). Previous studies indicated that two types of transcription factor families are necessary to modulate / regulate the expression of auxin response genes during growth and development process: auxin response factors (ARFs) and Aux/IAA (Guilfoyle and Hagen, 2007). Most ARF proteins consist of an N-terminal B3-type DNA binding domain, a variable middle region that may function as an activation or repression domain, and two C-terminal Aux/IAA domains, which are involved in protein– protein interaction by dimerizing with Aux/IAA family genes (Ulmasov et al, 1999b; Hagen and Guilfoyle, 2002). ARF proteins can either activate or repress auxin responsive gene transcription. Irrespective of auxin status, ARF proteins are competent to bind to auxin responsive cis-elements present upstream of the coding sequence of auxin responsive genes. Activation domains of ARFs are rich in leucine, serine, and glutamine residues, while the repression domains are rich in serine, proline, glycine, threonine, and serine residues (Ulmasov et al, 1997, 1999a)
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