Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa

Zhuang, Jing; Cai, Bin; Peng, Ri‐He; Zhu, Bo; Jin, Xiaofeng; Xue, Yong; Gao, Feng; Fu, Xin; Tian, Yong‐Sheng; Wang, Zhao; Qiao, Yu; Zhang, Zhen; Xiong, Ai‐Sheng; Yao, Qizheng

doi:10.1016/j.bbrc.2008.04.087

Cited by 278 publications

(257 citation statements)

References 19 publications

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“…Phylogenetic tree was constructed using the Neighbor-Joining (NJ) method and diagrams of the trees were drawn with the help of MEGA software (20). The sequence analysis and the construction of a phylogenetic tree were done essentially as described (21). The Arabidopsis AP2/ERF family sequences were downloaded from DATF, which is maintained by Beijing University (http://datf.cbi.pku.edu.cn/).…”

Section: Ap2/erf-b3 Tf Cloning From B Napus L Huyou15mentioning

confidence: 99%

Optimizing the binding activity of the AP2/ERF transcription factor with the GCC box element from Brassica napus by directed evolution

Jin

Zhu²,

Peng³

et al. 2010

BMB Reports

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In this study, we cloned the ERF-B3 subfamily transcription factor gene BnaERF-B3-hy15 from Brassica napus L. Huyou15. This 600 bp gene encodes a 199 amino acid classic ethylene responsive factor (ERF), which shown no binding or very weak binding GCC box-binding activity by the yeast one-hybrid assay. We used gene shuffling and the yeast one-hybrid system to obtain three mutated sequences that can bind to the GCC box. Sequence analysis indicated that two residues, Gly156 in the AP2 domain and Phe62 at the N-terminal domain were mutated to arginine and serine, respectively. Changes of Gly156 to arginine and Phe62 to serine increased the GCCbinding activity of BnaERF-B3-hy15 and the alter of Gly156 to arginine changed the AP2-domain structure of BnaERF-B3-hy15. [BMB reports 2010; 43(8): 567-572]

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Section: Ap2/erf-b3 Tf Cloning From B Napus L Huyou15mentioning

confidence: 99%

Optimizing the binding activity of the AP2/ERF transcription factor with the GCC box element from Brassica napus by directed evolution

Jin

Zhu²,

Peng³

et al. 2010

BMB Reports

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“…Phytochromes are light-sensing proteins that respond to red and far-red light cues, and phytochrome B2 (PHYB2) has been associated with daylength-driven budset in P. tremula (Ma et al, 2010). AP2/ERF is a large family of 200 genes in Populus that are involved in a number of stress responses (Zhuang et al, 2008) and potentially in dormancy induction (Rohde et al, 2007). In P. euphratica, expression of an AP2/ERF locus is induced by cold and drought (Chen et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

“…In P. euphratica, expression of an AP2/ERF locus is induced by cold and drought (Chen et al, 2009). Ethylene-responsive factor 61 (ERF61 = EBB1 = PtERF-B1-2) contains a typical AP2/ERF-binding domain (Zhuang et al, 2008), and has been implicated in date of leaf flush in Populus based on activation tagging (Yordanov et al, 2014). Because of their role in tree development, we hypothesized that these phenology candidate genes would show evidence of divergent selection.…”

Section: Introductionmentioning

confidence: 99%

Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

et al. 2015

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Studies of genetic variation can clarify the role of geography and spatio-temporal variation of climate in shaping demography, particularly in temperate zone tree species with large latitudinal ranges. Here, we examined genetic variation in narrowleaf cottonwood, Populus angustifolia, a dominant riparian tree. Using multi-locus surveys of polymorphism in 363 individuals across the species' 1800 km latitudinal range, we found that, first, P. angustifolia has stronger neutral genetic structure than many forest trees (simple sequence repeat (SSR) F ST = 0.21), with major genetic groups corresponding to large apparent geographical barriers to gene flow. Second, using SSRs and putatively neutral sequenced loci, coalescent simulations indicated that populations diverged before the last glacial maximum (LGM), suggesting the presence of population structure before the LGM. Third, the LGM and subsequent warming appear to have had different influences on each of these distinct populations, with effective population size reduction in the southern extent of the range but major expansion in the north. These results are consistent with the hypothesis that climate and geographic barriers have jointly affected the demographic history of P. angustifolia, and point the importance of both factors as being instrumental in shaping genetic variation and structure in widespread forest trees.

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“…The entire ERF family has been identified in some plants, and contains 147 and 157 genes in Arabidopsis and rice, respectively (Sakuma et al, 2002;Nakano et al, 2006). To date, 98 and 200 AP2/ERF genes have been indentified in soybean and Populus trichocarpa, respectively (Zhuang et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

A genome-wide analysis of the ERF gene family in sorghum

Yan¹,

Hong²,

Zhou³

et al. 2013

Genet. Mol. Res.

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ABSTRACT. The ethylene response factor (ERF) family are members of the APETALA2 (AP2)/ERF transcription factor superfamily; they are known to play an important role in plant adaptation to biotic and abiotic stress. ERF genes have been studied in Arabidopsis, rice, grape, and maize; however, there are few reports of ERF genes in sorghum. We identified 105 sorghum ERF (SbERF) genes, which were categorized into 12 groups (A-1 to A-6 and B-1 to B-6) based on their sequence similarity, and this new method of classification for ERF genes was then further characterized. A comprehensive bioinformatic analysis of SbERF genes was performed using a sorghum genomic database, to analyze the phylogeny of SbERF genes, identify other conserved motifs apart from the AP2/ERF domain, map SbERF genes to the 10 sorghum chromosomes, and determine the tissue-specific expression patterns of SbERF genes. Gene clustering indicates that SbERF genes were generated by tandem duplications. Comparison of SbERF genes with maize ERF homologs suggests lateral gene transfer between monocot species. These results can contribute to our understanting of ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 12 (2): 2038-2055 (2013 Analysis of the ERF gene family in sorghum 2039 the evolution of the ERF gene family.

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Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa

Cited by 278 publications

References 19 publications

Optimizing the binding activity of the AP2/ERF transcription factor with the GCC box element from Brassica napus by directed evolution

Optimizing the binding activity of the AP2/ERF transcription factor with the GCC box element from Brassica napus by directed evolution

Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

A genome-wide analysis of the ERF gene family in sorghum

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