Abstract
Auxin response factors (ARFs) play crucial roles in auxin-mediated response, whereas molecular genetics of ARF genes was seldom investigated in Setaria italica, an important crop and C4 model plant. In the present study, genome-wide evolutionary analysis of ARFs was performed in S. italica. Twenty-four SiARF genes were identified and unevenly distributed on eight of the nine chromosomes in S. italica. Duplication mode exploration implied that 13 SiARF proteins were originated from whole-genome duplication and suffered purifying selection. Phylogeny reconstruction of SiARFs by maximum likelihood and neighbor-joining trees revealed SiARFs could be divided into four clades. SiARFs clustered within the same clade shared similar gene structure and protein domain composition, implying functional redundancy. Moreover, amino acid composition of the middle regions was conserved in SiARFs belonged to the same clade. SiARFs were categorized into either activators or repressors according to the enrichment of specific amino acids. Intrinsic disorder was featured in the middle regions of ARF activators. Finally, expression profiles of SiARFs under hormone and abiotic stress treatment not only revealed their potential function in stress response but also indicate their functional redundancy. Overall, our results provide insights into evolutionary aspects of SiARFs and benefit for further functional characterization.
Highlights
The phytohormone auxin plays remarkable roles in regulating diverse aspects of plant growth and development, through auxin-responsive signaling cascades and gene expressions [1]
Two SiARFs were presented on chromosome 7, but only one SiARF was found on chromosomes 6, 8, and 9, respectively
Evolutionary patterns of Auxin response factors (ARFs) genes in S. italica were genome widely performed. 13 out of the 24 SiARF proteins were originated from whole-genome duplication, suffering purifying selection
Summary
The phytohormone auxin plays remarkable roles in regulating diverse aspects of plant growth and development, through auxin-responsive signaling cascades and gene expressions [1]. Auxin/indole acetic acid (Aux/IAA) and auxin response factor (ARF) proteins are key factors to regulate the expression of auxin-response genes [2]. In the absence of auxin, Aux/IAA interacts with ARFs, inhibiting the transcriptional regulation of auxin-responsive genes. Typical ARF proteins are distinguished by an N-terminal DNA-binding domain (DBD), C-terminal Aux/IAA domains that are committed in homo- and heterointeraction, and a variable middle region (MR) [4]. The DBD generally consists of plant-specific B-type domain, which could bind to AuxREs and the auxin_resp domain with unknown function [5]. Rice plants with OsARF12 silenced showed leaf curl, short stature, and reduced viability compared with wild type [8]
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