Abstract
Auxin signaling regulates various auxin-responsive genes via two types of transcriptional regulators, Auxin Response Factors (ARF) and Aux/IAA. ARF transcription factors act as critical components of auxin signaling that play important roles in modulating various biological processes. However, limited information about this gene family in fruit crops is currently available. Herein, 47 ARF genes were identified in banana based on its genome sequence. Phylogenetic analysis of the ARFs from banana, rice, and Arabidopsis suggested that the ARFs could be divided into four subgroups, among which most ARFs from the banana showed a closer relationship with those from rice than those from Arabidopsis. Conserved motif analysis showed that all identified MaARFs had typical DNA-binding and ARF domains, but 12 members lacked the dimerization domain. Gene structure analysis showed that the number of exons in MaARF genes ranged from 5 to 21, suggesting large variation amongst banana ARF genes. The comprehensive expression profiles of MaARF genes yielded useful information about their involvement in diverse tissues, different stages of fruit development and ripening, and responses to abiotic stresses in different varieties. Interaction networks and co-expression assays indicated the strong transcriptional response of banana ARFs and ARF-mediated networks in early fruit development for different varieties. Our systematic analysis of MaARFs revealed robust tissue-specific, development-dependent, and abiotic stress-responsive candidate MaARF genes for further functional assays in planta. These findings could lead to potential applications in the genetic improvement of banana cultivars, and yield new insights into the complexity of the control of MaARF gene expression at the transcriptional level. Finally, they support the hypothesis that ARFs are a crucial component of the auxin signaling pathway, which regulates a wide range of physiological processes.
Highlights
The phytohormone auxin plays crucial roles in various aspects of plant growth and development, such as lateral root initiation, apical dominance, shoot elongation, embryo patterning, and vascular differentiation (Davies, 1995)
A total of 47 non-redundant MaARF genes were identified in the banana genome, and these classifications were supported by conserved domain and multiple sequence alignment analyses
Gene Structure and Conserved Motifs of Banana Auxin Response Factors (ARF) To better understand the structural evolution of the MaARF genes, the exon–intron features of banana ARFs were analyzed based on an evolutionary analysis of the MaARFs
Summary
The phytohormone auxin plays crucial roles in various aspects of plant growth and development, such as lateral root initiation, apical dominance, shoot elongation, embryo patterning, and vascular differentiation (Davies, 1995). Auxin response factors (ARFs), important transcription factors in the auxin signaling pathway, regulate the transcription of auxin-responsive genes by directly binding to the auxin response element (AuxRE, TGTCTC) of their promoters (Hagen and Guilfoyle, 2002). ARF proteins contain three unique domains: a conserved N-terminal DNA-binding domain (DBD), a variable middle transcriptional regulatory region (MR), and a C-terminal dimerization domain (CTD) (Pérez-Rodríguez, et al, 2010; Zhang et al, 2011). The DBD domain can target the AuxRE element in the promoter of auxin-responsive genes (Hagen and Guilfoyle, 2002; Ha et al, 2013). The CTD domain, similar to domains III and IV of Aux/IAA proteins, is involved in protein-protein interactions, mediating the homodimerization of ARFs and the heterodimerization of ARF and Aux/IAA proteins (Tiwari et al, 2003; Guilfoyle and Hagen, 2007)
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