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Diversification, phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize ARF genes

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Abstract

Auxin response factors (ARFs), member of the plant-specific B3 DNA binding superfamily, target specifically to auxin response elements (AuxREs) in promoters of primary auxin-responsive genes and heterodimerize with Aux/IAA proteins in auxin signaling transduction cascade. In previous research, we have isolated and characterized maize Aux/IAA genes in whole-genome scale. Here, we report the comprehensive analysis of ARF genes in maize. A total of 36 ARF genes were identified and validated from the B73 maize genome through an iterative strategy. Thirty-six maize ARF genes are distributed in all maize chromosomes except chromosome 7. Maize ARF genes expansion is mainly due to recent segmental duplications. Maize ARF proteins share one B3 DNA binding domain which consists of seven-stranded β sheets and two short α helixes. Twelve maize ARFs with glutamine-rich middle regions could be as activators in modulating expression of auxin-responsive genes. Eleven maize ARF proteins are lack of homo- and heterodimerization domains. Putative cis-elements involved in phytohormones and light signaling responses, biotic and abiotic stress adaption locate in promoters of maize ARF genes. Expression patterns vary greatly between clades and sister pairs of maize ARF genes. The B3 DNA binding and auxin response factor domains of maize ARF proteins are primarily subjected to negative selection during selective sweep. The mixed selective forces drive the diversification and evolution of genomic regions outside of B3 and ARF domains. Additionally, the dicot-specific proliferation of ARF genes was detected. Comparative genomics analysis indicated that maize, sorghum and rice duplicate chromosomal blocks containing ARF homologs are highly syntenic. This study provides insights into the distribution, phylogeny and evolution of ARF gene family.

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Acknowledgments

We are grateful to editors and reviewers for their helpful comments. This work is supported partly by the Nature Science Foundation of Universities in Jiangsu Province (No. 09KJB180010) and the High-Level Personnel Foundation of Yangzhou University (No. nxy5286).

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  1. Key Laboratory of Jiangsu Province for Crop Genetics and Physiology, Key Laboratory of Ministry of Education for Plant Functional Genomics, College of Agriculture, Yangzhou University, Yangzhou, 225009, China

    Yijun Wang, Dexiang Deng, Yating Shi, Nan Miao, Yunlong Bian & Zhitong Yin

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11033_2011_991_MOESM6_ESM.tif

Fig. S1 Phylogeny of maize and rice ARF proteins. Ten sister pairs of maize ARF genes were emphasized in red. Scale bar 0.05 showed 0.05 amino acid substitution per site (TIFF 240 kb)

Fig. S2 Domains of maize ARF proteins 7 (TIFF 1820 kb)

Fig. S3 Motifs distribution in maize ARF proteins 8 (XLS 64 kb)

11033_2011_991_MOESM9_ESM.tif

Fig. S4 Heat map of expression patterns of ten sister pairs of maize ARF genes. SR, seedling root; SS, seedling shoot; R: root; L, leaf; T, tassel; P: pollen; E: ear 9 (TIFF 175 kb)

11033_2011_991_MOESM10_ESM.tif

Fig. S5 Phylogenesis of maize and sorghum ARF proteins. Evolutional branches of ten sister pairs of maize ARF genes except ZmARF1/ZmARF2 and their sorghum orthologs were marked in green 10 (TIFF 70 kb)

Fig. S6 Synteny of maize and rice duplicate genomic blocks containing ARF homologs 11 (TIFF 425 kb)

Supplementary text file Sequence information of all ARF genes from eleven species 12 (TXT 209 kb)

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Wang, Y., Deng, D., Shi, Y. et al. Diversification, phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize ARF genes. Mol Biol Rep 39, 2401–2415 (2012). https://doi.org/10.1007/s11033-011-0991-z

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