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Genome-wide identification, classification, and expression analysis of CDPK and its closely related gene families in poplar (Populus trichocarpa)

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Abstract

Calcium-dependent protein kinases (CDPKs) are Ca2+-binding proteins known to play crucial roles in Ca2+ signal transduction pathways which have been identified throughout plant kingdom and in certain types of protists. Genome-wide analysis of CDPKs have been carried out in Arabidopsis, rice and wheat, and quite a few of CDPKs were proved to play crucial roles in plant stress responsive signature pathways. In this study, a comprehensive analysis of Populus CDPK and its closely related gene families was performed, including phylogeny, chromosome locations, gene structures, and expression profiles. Thirty Populus CDPK genes and twenty closely related kinase genes were identified, which were phylogenetically clustered into eight distinct subfamilies and predominately distributed across fifteen linkage groups (LG). Genomic organization analyses indicated that purifying selection has played a pivotal role in the retention and maintenance of Populus CDPK gene family. Furthermore, microarray analysis showed that a number of Populus CDPK and its closely related genes differentially expressed across disparate tissues and under various stresses. The expression profiles of paralogous pairs were also investigated to reveal their evolution fates. In addition, quantitative real-time RT-PCR was performed on nine selected CDPK genes to confirm their responses to drought stress treatment. These observations may lay the foundation for future functional analysis of Populus CDPK and its closely related gene families to unravel their biological roles.

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Acknowledgments

This study was supported by grants from the National Basic Research Program of China (2012CB114501), the National High-Tech Research and Development Program of China (2011AA100209), the National Natural Science Foundation of China (31070272, 31000311 and 30901157), the Program of 100 Distinguished Young Scientists of the Chinese Academy of Sciences (to Gongke Zhou), the Promotive Research Fund for Young and Middle-aged Scientists of Shandong Province (BS2011SW055), and the Qingdao Municipal Science and Technology Plan Project (11-2-4-8-(1)-jch, 11-2-4-8-(2)-jch and 12-1-4-9-(2)-jch). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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  1. CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and BioProcess Technology, Chinese Academy of Sciences, Qingdao, Shandong, People’s Republic of China

    Ran Zuo, Ruibo Hu, Guohua Chai, Meiling Xu, Guang Qi & Gongke Zhou

  2. Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA

    Yingzhen Kong

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  1. Ran Zuo
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  2. Ruibo Hu
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Correspondence to Yingzhen Kong or Gongke Zhou.

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Zuo, R., Hu, R., Chai, G. et al. Genome-wide identification, classification, and expression analysis of CDPK and its closely related gene families in poplar (Populus trichocarpa). Mol Biol Rep 40, 2645–2662 (2013). https://doi.org/10.1007/s11033-012-2351-z

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