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A genome-wide analysis of the expansin genes in Malus × Domestica

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Abstract

Expansins were first identified as cell wall-loosening proteins; they are involved in regulating cell expansion, fruits softening and many other physiological processes. However, our knowledge about the expansin family members and their evolutionary relationships in fruit trees, such as apple, is limited. In this study, we identified 41 members of the expansin gene family in the genome of apple (Malus × Domestica L. Borkh). Phylogenetic analysis revealed that expansin genes in apple could be divided into four subfamilies according to their gene structures and protein motifs. By phylogenetic analysis of the expansins in five plants (Arabidopsis, rice, poplar, grape and apple), the expansins were divided into 17 subgroups. Our gene duplication analysis revealed that whole-genome and chromosomal-segment duplications contributed to the expansion of Mdexpansins. The microarray and expressed sequence tag (EST) data showed that 34 Mdexpansin genes could be divided into five groups by the EST analysis; they may also play different roles during fruit development. An expression model for MdEXPA16 and MdEXPA20 showed their potential role in developing fruit. Overall, our study provides useful data and novel insights into the functions and regulatory mechanisms of the expansin genes in apple, as well as their evolution and divergence. As the first step towards genome-wide analysis of the expansin genes in apple, our results have established a solid foundation for future studies on the function of the expansin genes in fruit development.

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Abbreviations

BLAST:

The basic local alignment search tool

SMART:

A simple modular architecture research tool

HMM:

Hidden Markov model

NJ:

The neighbour-joining

MEGA:

Molecular evolutionary genetics analysis

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Acknowledgments

This work was supported by the National Research Center for Apple Engineering and Technology, the Open Project Program of the State Key Laboratory of Crop Biology (Grant No. 2013KF07), the Open Project Program of Key laboratory of Biology and Molecular Biology in University of Shandong (Weifang University) (Grant No. 2012SWKF01) and Program of Science and Technology Development of Weifang (Grant No. 20121305) in China.

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Authors and Affiliations

  1. State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, College of Horticulture Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, People’s Republic of China

    Shizhong Zhang, Zheng Gao, Changtian Chen, Zesheng Jiang & Huairui Shu

  2. Key Laboratory of Biology and Molecular Biology in University of Shandong, Weifang University, Weifang, Shandong, 261061, People’s Republic of China

    Ruirui Xu

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  1. Shizhong Zhang
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  2. Ruirui Xu
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  3. Zheng Gao
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  4. Changtian Chen
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  5. Zesheng Jiang
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  6. Huairui Shu
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Correspondence to Huairui Shu.

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Communicated by S. Hohmann.

S. Zhang and R. Xu contributed equally to this work.

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Zhang, S., Xu, R., Gao, Z. et al. A genome-wide analysis of the expansin genes in Malus × Domestica . Mol Genet Genomics 289, 225–236 (2014). https://doi.org/10.1007/s00438-013-0796-y

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