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.

中文翻译：

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全基因组复制和纯化选择有助于谷子 (Setaria italica L.) 中生长素反应因子 (ARF) 基因的功能冗余

生长素反应因子（ARFs）在生长素介导的反应中起关键作用，而在重要作物和C ₄模式植物狗尾草中很少研究ARF基因的分子遗传学。在本研究中，ARFs的全基因组进化分析是在S. italica 中进行的。鉴定出24 个SiARF基因并在S. italica的 9 条染色体中的 8 条染色体上不均匀分布. 复制模式探索表明，13个SiARF蛋白来源于全基因组复制，并进行了纯化选择。通过最大似然和相邻连接树对 SiARFs 的系统发育重建显示 SiARFs 可以分为四个进化枝。聚集在同一进化枝内的 SiARF 具有相似的基因结构和蛋白质结构域组成，这意味着功能冗余。此外，在属于同一进化枝的 SiARF 中，中间区域的氨基酸组成是保守的。SiARFs 根据特定氨基酸的富集程度分为激活剂或阻遏剂。ARF 激活剂的中间区域具有内在障碍。最后，SiARFs 的表达谱在激素和非生物胁迫处理下，不仅揭示了它们在胁迫反应中的潜在功能，而且表明它们的功能冗余。总的来说，我们的结果提供了对SiARF进化方面的见解，并有利于进一步的功能表征。