Abstract
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.
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Acknowledgements
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.
Funding
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].
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Supplementary Fig. 1
Sequence logos for the conserved motifs of ARF proteins in B. distachyon. (PNG 1074 kb)
Supplementary Fig. 2
Protein sequences alignment and domain analysis of BdARF family proteins. (PNG 8164 kb)
Supplementary Fig. 3
Phylogenetic analysis of Arabidopsis, maize, rice and B. distachyon ARF proteins. (PNG 3946 kb)
Supplementary Fig. 4
Predicted co-expression network of BdARFs in B. distachyon. (PNG 89 kb)
Supplementary Table 1
The CDS and protein sequence of BdARFs. (DOC 146 kb)
Supplementary Table 2
The list of qRT-PCR primers of BdARF genes. (DOC 45 kb)
Supplementary Table 3
Expression data of BdARF genes after phytohormone treatment and abiotic stresses. (DOC 170 kb)
Supplementary Table 4
Promoter analysis of BdARF genes. (DOC 117 kb)
Supplementary Table 5
ARF genes in 54 ecotypes proteome of B. distachyon. (XLS 64 kb)
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Zhou, X., Wu, X., Li, T. et al. Identification, characterization, and expression analysis of auxin response factor (ARF) gene family in Brachypodium distachyon. Funct Integr Genomics 18, 709–724 (2018). https://doi.org/10.1007/s10142-018-0622-z
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DOI: https://doi.org/10.1007/s10142-018-0622-z