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Analysis of Brassica napus ESTs: gene discovery and expression patterns of AP2/ERF-family transcription factors

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Abstract

Starting from expressed sequence tag sequences and using the conserved amino acid sequence of the Arabidopsis thaliana AP2/ERF domain as a probe, we used in silico cloning to identify 87 genes that encode putative AP2/ERF transcription factors (TFs) from the Brassica napus. Almost all of the putative AP2/ERF factors from B. napus were similar to genes previously defined as AP2/ERF genes from A. thaliana. Based on the number of AP2-domains and the function of the genes, the AP2/ERF TFs from B. napus were classified into four subfamilies, named the AP2, DREB, ERF, and RAV subfamilies. We then predicted and analyzed cDNA sequences and amino acid sequences, amino acid compositions, physical and chemical characteristics, phylogenetic trees, conserved domain sequences, functional domains, molecular models, and folding states of the proteins they are predicted to encode. Expression analysis showed that four factors, which belonged to the ERF and DREB subfamilies, were induced by abiotic stresses, as well as by hormone treatment. This suggests that those AP2/ERF factors may be involved in signaling pathways responsive to abiotic and biotic stresses. The results from this study, reported herein, form a basis for future functional analyses of B. napus TFs that belong to the AP2/ERF family.

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Abbreviations

TF:

Transcription factor

ABA:

Abscisic acid

AP2:

APETALA2 factor

CBF:

C-repeat binding factor

DREB:

Dehydration responsive element binding factor

ERF:

Ethylene responsive element binding factor

RAV:

Related to ABI3/VP

PEG:

Polyethylene glycol

WT:

Wild-type

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Acknowledgments

The research was supported by the National Natural Science Foundation of China (31200520), Jiangsu Natural Science Foundation (BK2012774), China Postdoctoral Science Foundation (2013M541686) and the Ph.D Programs Foundation of Ministry of Education of China (20120097120031).

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  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China

    Jing Zhuang & Bo Zhu

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  1. Jing Zhuang
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Correspondence to Jing Zhuang.

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Zhuang, J., Zhu, B. Analysis of Brassica napus ESTs: gene discovery and expression patterns of AP2/ERF-family transcription factors. Mol Biol Rep 41, 45–56 (2014). https://doi.org/10.1007/s11033-013-2836-4

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