Identification, characterization, and expression analysis of auxin response factor (ARF) gene family in Brachypodium distachyon
- 290 Downloads
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.
KeywordsAuxin response factors Phytohormones Abiotic stresses Expression analysis Brachypodium distachyon
We want to thank the contributors of the JGI and PlantGDB, which were convenient tools used to search for ARF genes. We are grateful to Peng Li from Shanghai Chenshan Botanic Garden for careful and thorough editing of this manuscript. We especially appreciate the conversation with the members of our group in developing some of the ideas presented in this study.
This work was supported by the National Natural Science Foundation of China [31560075, 31460046], Natural Science Foundation of Jiangxi Province [20151BAB214003, 20161BAB214149], and Foundation of Chinese medicine research of health and family planning commission of Jiangxi province [2015A075].
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
- Budak H, Hernandez P, Schulman AH (2014) Analysis and exploitation of cereal genomes with the aid of Brachypodium. Genomics Plant Genet Resour:585–613Google Scholar
- Li SB, OuYang WZ, Hou XJ, Xie LL, Hu CG, Zhang JZ (2015b) Genome-wide identification, isolation and expression analysis of auxin response factor (ARF) gene family in sweet orange (Citrus sinensis). Front Plant Sci 6:119. https://doi.org/10.3389/fpls.2015.00119 CrossRefPubMedPubMedCentralGoogle Scholar
- Liu K, Yuan C, Li H, Lin W, Yang Y, Shen C, Zheng X (2015) Genome-wide identification and characterization of auxin response factor (ARF) family genes related to flower and fruit development in papaya (Carica papaya L.). BMC Genomics 16:901. https://doi.org/10.1186/s12864-015-2182-0 CrossRefPubMedPubMedCentralGoogle Scholar
- Liu K, Wang J, Li H, Zhong J, Feng S, Pan Y, Yuan C (2016) Identification, expression and IAA-amide synthetase activity analysis of Gretchen Hagen 3 in papaya fruit (Carica papaya L.) during postharvest process. Front Plant Sci 7:1555. https://doi.org/10.3389/fpls.2016.01555 CrossRefPubMedPubMedCentralGoogle Scholar
- Oh E, Zhu JY, Bai MY, Arenhart RA, Sun Y, Wang ZY (2014) Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl. eLife 3. doi: https://doi.org/10.7554/eLife.03031
- Powers SK, Strader LC (2016) Up in the air: untethered factors of auxin response. F1000Research 5. doi: https://doi.org/10.12688/f1000research.7492.1
- Sun R, Wang K, Guo T, Jones DC, Cobb J, Zhang B, Wang Q (2015) Genome-wide identification of auxin response factor (ARF) genes and its tissue-specific prominent expression in Gossypium raimondii. Funct Integr Genomics 15:481–493. https://doi.org/10.1007/s10142-015-0437-0 CrossRefPubMedGoogle Scholar