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.

Genome-wide identification, characterization and expression analysis of the auxin response factor gene family in Vitis vinifera

“…The availability of genomic resources such as ESTs and genome sequences has provided an opportunity to look for the members of ARF gene family. Until now, 23 Arabidopsis ARFs, 25 rice ARFs, 39 poplar ARFs, 13 Physcomitrella patens ARFs, 17 tomato ARFs, 10 Selaginella moellendorfiri ARFs and 22 maize ARFs have been deduced based on genomic resources, respectively (Hagen and Guilfoyle 2002;Wang et al 2007;Kalluri et al 2007;Rensing et al 2008;Kumar et al 2011;Banks et al 2011;Wang et al 2012). Finet et al (2013) also reported the information on ARF gene families in other 15 plant species including 19 ARF genes in grapevine.…”

Current perspectives on the hormonal control of seed development in Arabidopsis and maize: a focus on auxin

“…Genome-wide analyses on the maize reference genome were performed to identify the Aux/IAA (Wang et al, 2010b) and ARF gene families in maize (Liu et al, 2011; Xing et al, 2011; Wang et al, 2012). The 31 identified ZmAux/IAA genes showed a putative expression (based on EST mining) in different tissues and organs that suggests a temporal and spatial pattern of regulation.…”

“…The 31 identified ZmAux/IAA genes showed a putative expression (based on EST mining) in different tissues and organs that suggests a temporal and spatial pattern of regulation. The 31–36 ZmARF are also known to have a tissue-specificity that changes during plant development (Wang et al, 2010b, 2012; Liu et al, 2011; Xing et al, 2011). Each ZmARF possesses a sister pair due to chromosomal duplication of the maize genome, and they are distributed in all the chromosomes except chromosome 7 (Xing et al, 2011; Wang et al, 2012).…”

Genome-wide identification of the auxin response factor (ARF) gene family and expression analysis of its role associated with pistil development in Japanese apricot (Prunus mume Sieb. et Zucc)

“…Until now, based on reported genomic sequences, 23 ARFs have been identified in Arabidopsis, 25 in rice, 39 in poplar, 13 in Physcomitrella patens, 17 in tomato, 10 in Selaginella moellendorfiri, 36 in maize, 15 in cucumber and 19 in grape (Banks et al 2011;Hagen and Guilfoyle 2002;Kalluri et al 2007;Kumar et al 2011;Liu and Hu 2013a;Rensing et al 2008;Wan et al 2014;Wang et al 2007Wang et al , 2012. It is believed that the multi-member phenomenon of a specific gene family in a particular organism is caused by the frequent emergence of extensive genomic duplication and diversification in the evolutionary history of organisms.…”