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Genome-wide analysis and expression of the calcium-dependent protein kinase gene family in cucumber

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Abstract

Calcium-dependent protein kinases (CDPKs) are multi-functional proteins that combine calcium-binding and signaling capabilities within a single gene product. Current studies have shown that the CDPKs regulate numerous growth and developmental processes and biotic and abiotic stress responses. Nonetheless, knowledge concerning the specific expression patterns and evolutionary history of the CDPK family in cucumber (Cucumis sativus L.) remains very limited. We, therefore, investigated the phylogenetic relationships and expression profiles of the 19 CDPK genes identified in the cucumber genome sequence, resolving them into four subfamilies based on a phylogenetic tree and gene structures. Tissue-specific expression profiles suggest that cucumber CDPK genes are involved in cucumber tissue development. An expression analysis based on qRT-PCR indicated that cucumber CDPK genes are extensively involved in abscisic acid, salt, cold, drought, heat, and waterlogging responses, possibly by different mechanisms. The fates of two paralogs after divergence were also investigated, suggesting subfunctionalization and neofunctionalization during evolution. These observations lay an important foundation for functional and evolutionary analyses of the CDPK gene family in cucurbitaceae species.

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Abbreviations

CsCDPK:

Cucumis sativus calcium-dependent protein kinase

BLAST:

The basic local alignment search tool

SMART:

Simple modular architecture research tool

HMM:

Hidden markov model

NJ:

The neighbor-joining

MEGA:

Molecular evolutionary genetics analysis

GSDS:

Gene structure display server

pI:

Isoelectric point

M.W.:

Molecular weight

qRT-PCR:

Quantitative real-time PCR

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Acknowledgments

The authors thank Martin Agyei Yeboah (West Africa Centre for Crop Improvement WACCI) for his critical reading of the manuscript. This research was supported by the National Natural Science Foundation of China (Nos. 31372087 and 31201640).

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    1. School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China

      Xuewen Xu, Min Liu, Lu Lu, Min He, Wenqin Qu, Qiang Xu, Xiaohua Qi & Xuehao Chen

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    1. Xuewen Xu
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    2. Min Liu
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    3. Lu Lu
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    Correspondence to Xuehao Chen.

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    Communicated by L. Xiong.

    X. Xu and M. Liu have contributed equally to this work.

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    Xu, X., Liu, M., Lu, L. et al. Genome-wide analysis and expression of the calcium-dependent protein kinase gene family in cucumber. Mol Genet Genomics 290, 1403–1414 (2015). https://doi.org/10.1007/s00438-015-1002-1

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