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Genome-wide analysis of AP2/ERF transcription factors in carrot (Daucus carota L.) reveals evolution and expression profiles under abiotic stress

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Abstract

AP2/ERF is a large transcription factor family that regulates plant physiological processes, such as plant development and stress response. Carrot (Daucus carota L.) is an important economical crop with a genome size of 480 Mb; the draft genome sequencing of this crop has been completed by our group. However, little is known about the AP2/ERF factors in carrot. In this study, a total of 267 putative AP2/ERF factors were identified from the whole-genome sequence of carrot. These AP2/ERF proteins were phylogenetically clustered into five subfamilies based on their similarity to the amino acid sequences from Arabidopsis. The distribution and comparative genome analysis of the AP2/ERF factors among plants showed the AP2/ERF factors had expansion during the evolutionary process, and the AP2 domain was highly conserved during evolution. The number of AP2/ERF factors in land plants expanded during their evolution. A total of 60 orthologous and 145 coorthologous AP2/ERF gene pairs between carrot and Arabidopsis were identified, and the interaction network of orthologous genes was constructed. The expression patterns of eight AP2/ERF family genes from each subfamily (DREB, ERF, AP2, and RAV) were related to abiotic stresses. Yeast one-hybrid and β-galactosidase activity assays confirmed the DRE and GCC box-binding activities of DREB subfamily genes. This study is the first to identify and characterize the AP2/ERF transcription factors in carrot using whole-genome analysis, and the findings may serve as references for future functional research on the transcription factors in carrot.

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Acknowledgments

The research was supported by the New Century Excellent Talents in University (NCET-11-0670); Jiangsu Natural Science Foundation (BK20130027); China Postdoctoral Science Foundation (2014M551609), the National Natural Science Foundation of China (31272175), Priority Academic Program Development of Jiangsu Higher Education Institutions.

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The authors declare that there are no competing interests.

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This article does not contain any studies with human participants or animal performed by any of the authors.

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Authors and Affiliations

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

    Meng-Yao Li, Zhi-Sheng Xu, Ying Huang, Chang Tian, Feng Wang & Ai-Sheng Xiong

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  1. Meng-Yao Li
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  2. Zhi-Sheng Xu
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  3. Ying Huang
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  4. Chang Tian
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  5. Feng Wang
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  6. Ai-Sheng Xiong
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Correspondence to Ai-Sheng Xiong.

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Communicated by S. Hohmann.

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438_2015_1061_MOESM1_ESM.tif

Supplementary material 1 (TIFF 339 kb). Fig. S1 The highly conserved domain in each subfamilies of AP2/ERF family transcription factor

438_2015_1061_MOESM2_ESM.tif

Supplementary material 2 (TIFF 325 kb). Fig. S2 Sequence alignment of each DREB protein between the two carrot varieties. The white and cyan backgrounds represent the different amino acid residues

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Li, MY., Xu, ZS., Huang, Y. et al. Genome-wide analysis of AP2/ERF transcription factors in carrot (Daucus carota L.) reveals evolution and expression profiles under abiotic stress. Mol Genet Genomics 290, 2049–2061 (2015). https://doi.org/10.1007/s00438-015-1061-3

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