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Genome-wide identification and characterization of aquaporin genes (AQPs) in Chinese cabbage (Brassica rapa ssp. pekinensis)

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Abstract

Aquaporins (AQPs) are members of a superfamily of integral membrane proteins and play a significant role in the transportation of small molecules across membranes. However, currently little is known about the AQP genes in Chinese cabbage (Brassica rapa ssp. pekinensis). In this study, a genome-wide analysis was carried out to identify the AQP genes in Chinese cabbage. In total, 53 non-redundant AQP genes were identified that were located on all of the 10 chromosomes. The number of AQP genes in Chinese cabbage was greater than in Arabidopsis. They were classified into four subfamilies, including PIP, TIP, NIP, and SIP. Thirty-three groups of AQP orthologous genes were identified between Chinese cabbage and Arabidopsis, but orthologs corresponding to AtNIP1;1 and AtPIP2;8 were not detected. Seventeen groups of paralogous genes were identified in Chinese cabbage. Three-dimensional models of the AQPs of Chinese cabbage were constructed using Phyre2, and ar/R selectivity filters were analyzed comparatively between Chinese cabbage and Arabidopsis. Generally, gene structure was conserved within each subfamily, especially in the SIP subfamily. Intron loss events have occurred during the evolution of the PIP, TIP, and NIP subfamilies. The expression of AQP genes in Chinese cabbage was analyzed in different organs. Most AQP genes were downregulated in response to salt stress. This work shows that the AQP genes of Chinese cabbage have undergone triplication and subsequent biased gene loss.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (31301788, 31372058), the Grand Science and Technology Special Project of Zhejiang Province (2012C12903-3-8), and the China Postdoctoral Science Foundation (2013M540500).

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Authors and Affiliations

  1. Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China

    Peng Tao, Xinmin Zhong, Biyuan Li, Wuhong Wang, Zhichen Yue, Juanli Lei & Xiaoyun Huang

  2. Zhejiang Institute of Communication and Media, Hangzhou, 310018, China

    Weiling Guo

  3. College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China

    Xiaoyun Huang

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  1. Peng Tao
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  2. Xinmin Zhong
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Correspondence to Xinmin Zhong.

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Tao, P., Zhong, X., Li, B. et al. Genome-wide identification and characterization of aquaporin genes (AQPs) in Chinese cabbage (Brassica rapa ssp. pekinensis). Mol Genet Genomics 289, 1131–1145 (2014). https://doi.org/10.1007/s00438-014-0874-9

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