Genome-wide analysis of the putative AP2/ERF family genes in Vitis vinifera

Zhuang, Jing; Peng, Ri‐He; Cheng, Zong‐Ming; Zhang, Jian; Cai, Bin; Zhang, Zhen; Gao, Feng; Zhu, Bo; Fu, Xin; Jin, Xiaofeng; Chen, Jianmin; Qiao, Yu; Xiong, Ai‐Sheng; Yao, Qizheng

doi:10.1016/j.scienta.2009.08.002

Cited by 100 publications

(77 citation statements)

References 63 publications

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“…We also searched the database using amino acid sequences, such as RAV, AP2, and the soloist gene At4g13040, of the AP2/ERF domain of members of the Arabidopsis AP2/ERF family as the query to confirm that the search was exhaustive (Zhuang and others 2009). In addition, the same sequences that were obtained with MELONOMICS by hidden Markov model (HMM) analysis with Pfam number PF00847, which contains a typical AP2/ERF domain (Wang and others 2010).…”

Section: Identification Of Erf Family Genes In Melon Genomementioning

confidence: 99%

Genome-Wide Identification and Phylogenetic Analysis of the ERF Gene Family in Melon

Zhang

Bade

et al. 2014

J Plant Growth Regul

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Members of the ERF transcription factor family have significant functions in regulating gene expression in response to biotic and abiotic stresses. In melon (Cucumis melo L.), however, few ERF genes have been studied. In this study, we performed a comprehensive computational analysis of 119 ERF family genes and identified 136 ERF superfamily genes in melon. We present a complete overview of ERF family gene in melon, including the phylogeny, gene structures, and putative conserved motifs of melon ERF family proteins, as well as a comparative analysis between ERF subfamily genes in cucumber. The AP2/ERF gene superfamily in melon can be classified into three families, ERF (ethylene-responsive factor), RAV (related to ABI3/VP1), and AP2 (APETALA2), which comprise 119, 4, and 13 members, respectively. The ERF family in melon was divided into 11 groups, designated I to XI, as in tomato. Our motif analysis indicated that most conserved motifs outside of the AP2/ERF domain are distributed between different clades in the phylogenetic tree. Most ERF family genes have no introns. Based on the observation that 11 of these groups existed in melon, we concluded that the chief functional diversification in the ERF family predated the divergence between monocots and dicots. In our analysis of expression patterns, ERF subfamily genes were distributed widely throughout melon plant tissues and most of the ERF subfamily genes were detected in all seven types of tissues. Some ERF subfamily genes show expression patterns characteristic of tissuespecific expression, implying their probability of performing various roles in growth and development in melon.

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Section: Identification Of Erf Family Genes In Melon Genomementioning

confidence: 99%

Genome-Wide Identification and Phylogenetic Analysis of the ERF Gene Family in Melon

Zhang

Bade

et al. 2014

J Plant Growth Regul

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“…The AP2/ERF transcription factors are related to stress response in plant under biotic and abiotic stresses. Up to now, AP2/ERF genes have been isolated from wheat [15], Oryza sativa, cotton [16], soybean [17], maize, Arabidopsis thaliana, Brassica napus [18], Hevea brasiliensis [19], tobacco, grape [20], poplar, and their functions have been analyzed.…”

Section: Ap2/erf In Plant Stress Resistancementioning

confidence: 99%

Research Advances of AP2/ERF Transcription Factors

Wang¹,

Li²

2018

Proceedings of the 2017 2nd International Conference on Biological Sciences and Technology (BST 2017)

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Abstract. The AP2/ERF transcription factor family is one of the largest transcription factor groups in plants and it plays very important roles in growth, development, biotic and abiotic stress response. In this study, we summarized the research advances on AP2/ERF transcription factor involved in plant growth, development, stress resistance, regulation of secondary metabolites and the current research status in poplar, in order to provide reference for plant-breeding applications. IntroductionTranscription factor (TF), also known as trans-acting factor, is a kind of protein that can specifically bind to the cis-acting element in the promoter of eukaryotes. It plays a role as a switch in initiating downstream gene expression via interaction between transcription factor and proteins [1]. With the completion of genome sequences in plants and the development of bioinformatics analysis, a variety of transcription factors, which are associated with drought, high salinity, cold, hormone, pathogen response, growth and development, have been isolated from higher plants since Paz-Ares first reported the TF from Zea mays in 1987 [2].The AP2/ERF (APETALA 2/ethylene-responsive element binding factor, AP2/ERF) family is one of the largest TF families in plants. It accounts for nearly 9% of the TFs in plants and contains a 58 or 59 amino acid conserved domain. The AP2/ERF TF is widely involved in regulation of growth, development and various stress responses in plant [3]. According to the characteristics and number of AP2/ERF domain, it can be divided into 3 families: AP2, RAV, and ERF. The AP2 family contains two repeated AP2/ERF domains, and this family plays a very important role in plant developmental processes [4]. The RAV family contains one AP2/ERF domain and a B3 domain, which plays an important role in response to ethylene, brassinolide, biotic and abiotic stress [5]. The ERF family contains one AP2/ERF domain and it can be divided into two subfamilies: CBF/DREB subfamily and ERF subfamily. The differences between the two subfamilies are the 14th and 19th amino acid. The 14th and 19th amino acids of DREB are valine and glutamic acid, while the corresponding amino acids in ERF are alanine and aspartic acid. DREB and ERF transcription factors are mainly involved in plant response to hormone [6] and environmental stresses [7].In this review, we analyzed the functions of AP2/ERF TFs in plant growth, development, stress resistance, regulation of secondary metabolites in medicinal plant and the current research status in poplar, in order to provide reference for plant-breeding applications.

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“…There are rapid accumulations of information on soybean transcription factors and their putative functions related to osmotic stresses (Tian et al, 2004;Mochida et al, 2009;Schmutz et al, 2010;Wang et al, 2010b). A summary of the recent findings is presented below and in Table 1. AP2/ERF AP2/ERF transcription factors can be classified into 5 subfamilies including the AP2 (APETALA2), ERF (ethylene-responsive transcription factor), DREB (dehydration-responsive element-binding protein), RAV (related to ABI3/VP1), and Soloist (Sakuma et al, 2002;Zhuang et al, 2009) depending on the number of AP2/EFR domain. More than 380 AP2/ERF genes are present in the soybean genome (Mochida et al, 2009;Wang et al, 2010b) while only a few of them have been characterized (Gao et al, 2005;Li et al, 2005;Chen et al, 2006;Chen et al, 2007;Mazarei et al, 2007;Wang et al, 2008;Zhang et al, 2008b;Chen et al, 2009a;Zhang et al, 2009a;Zhang et al, 2009b;Zhuang et al, 2009;El Ouakfaoui et al, 2010;Jin et al, 2010).…”

Section: Transcription Factors Participated In Osmotic Stress Signallmentioning

confidence: 99%

“…A summary of the recent findings is presented below and in Table 1. AP2/ERF AP2/ERF transcription factors can be classified into 5 subfamilies including the AP2 (APETALA2), ERF (ethylene-responsive transcription factor), DREB (dehydration-responsive element-binding protein), RAV (related to ABI3/VP1), and Soloist (Sakuma et al, 2002;Zhuang et al, 2009) depending on the number of AP2/EFR domain. More than 380 AP2/ERF genes are present in the soybean genome (Mochida et al, 2009;Wang et al, 2010b) while only a few of them have been characterized (Gao et al, 2005;Li et al, 2005;Chen et al, 2006;Chen et al, 2007;Mazarei et al, 2007;Wang et al, 2008;Zhang et al, 2008b;Chen et al, 2009a;Zhang et al, 2009a;Zhang et al, 2009b;Zhuang et al, 2009;El Ouakfaoui et al, 2010;Jin et al, 2010). More than 10 members of the gene family encoding DREB transcription factors present in the soybean genome (Phang et al, 2008), and 7 of the GmDREB genes are induced by ABA, salt, drought, and/or cold stress (Table 1) (Gao et al, 2005;Li et al, 2005;Chen et al, 2006;Chen et al, 2007;Chen et al, 2009a;Jin et al, 2010).…”

Section: Transcription Factors Participated In Osmotic Stress Signallmentioning

confidence: 99%