title: Diversification, phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize ARF genes.
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.
authors.affiliation: 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. yjwang61@163.com
authors.forename: Yijun
authors.initials: Y
authors.lastname: Wang
authors.forename: Dexiang
authors.initials: D
authors.lastname: Deng
authors.forename: Yating
authors.initials: Y
authors.lastname: Shi
authors.forename: Nan
authors.initials: N
authors.lastname: Miao
authors.forename: Yunlong
authors.initials: Y
authors.lastname: Bian
authors.forename: Zhitong
authors.initials: Z
authors.lastname: Yin
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology; D019143:Evolution, Molecular; D017343:Genes, Plant / Q000235:genetics*; D014644:Genetic Variation; D007210:Indoleacetic Acids / Q000378:metabolism; D008957:Models, Genetic; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D013045:Species Specificity; D026801:Synteny / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D003313:Zea mays / Q000235:genetics*
chemical_list: D007210:Indoleacetic Acids; D014157:Transcription Factors