Zhou Xiaojian, Wu Xiaozhu, Li Tongjian, Jia Mingliang, Liu Xinshen, Zou Yulan, Liu Zixia, Wen Feng
School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
Funct Integr Genomics. 2018 Nov;18(6):709-724. doi: 10.1007/s10142-018-0622-z. Epub 2018 Jun 20.
Auxin response factors (ARFs) are one type of essential family of transcription factors that bind with auxin response elements (AuxRE), and play vital roles in variety of plant development and physiological processes. Brachypodium distachyon, related to the major cereal grain species, were recently developed to be a good model organism for functional genomics research. So far, genome-wide overview of the ARF gene family in B. distachyon was not available. Here, a systemic analysis of ARF gene family members in B. distachyon was performed. A comprehensive overview of the characterization of the BdARFs was obtained by multiple bioinformatics analyses, including the gene and protein structure, chromosome locations, conserved motifs of proteins, phylogenetic analysis, and cis-elements in promoters of BdARF. Results showed that all BdARFs contained conserved DBD, MR, and CTD could be divided into four classes, Ia, IIa, IIb, and III. Expression profiles of BdARF genes indicated that they were expressed across various tissues and organs, which could be clustered into three main expression groups, and most of BdARF genes were involved in phytohormone signal transduction pathways and regulated physiological process in responding to multiple environmental stresses. And predicted regulatory network between B. distachyon ARFs and IAAs was also discussed. Our genomics analysis of BdARFs could yield new insights into the complexity of the control of BdARF genes and lead to potential applications in the investigation of the accurate regulatory mechanisms of ARFs in herbaceous plants.
生长素响应因子（ARFs）是一类重要的转录因子家族，它们与生长素响应元件（AuxRE）结合，并在多种植物发育和生理过程中发挥重要作用。与主要谷物物种相关的二穗短柄草最近被开发成为功能基因组学研究的良好模式生物。到目前为止，尚未有二穗短柄草ARF基因家族的全基因组概述。在此，对二穗短柄草ARF基因家族成员进行了系统分析。通过多种生物信息学分析，包括基因和蛋白质结构、染色体定位、蛋白质保守基序、系统发育分析以及二穗短柄草ARF启动子中的顺式元件，获得了对二穗短柄草ARFs特征的全面概述。结果表明，所有二穗短柄草ARFs都包含保守的DBD、MR和CTD，可分为四类，即Ia、IIa、IIb和III。二穗短柄草ARF基因的表达谱表明它们在各种组织和器官中表达，可聚类为三个主要表达组，并且大多数二穗短柄草ARF基因参与植物激素信号转导途径并在响应多种环境胁迫时调节生理过程。此外，还讨论了二穗短柄草ARFs与IAA之间预测的调控网络。我们对二穗短柄草ARFs的基因组学分析可以为二穗短柄草ARF基因控制的复杂性提供新的见解，并导致在草本植物中ARFs精确调控机制研究中的潜在应用。
