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Comparative genomic analysis of CIPK gene family in Arabidopsis and Populus

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Abstract

Calcium serves as a second messenger in various signal transduction pathways in plants. CBL-interacting protein kinases (CIPKs), which have a variety of functions, are involved in calcium signal transduction. Previous, the studies on CIPK family members focused on Arabidopsis and rice. Here, we present a comparative genomic analysis of the CIPK gene family in Arabidopsis and poplar, a model tree species. Twenty-seven potential CIPKs were identified from poplar using genome-wide analysis. Like the CIPK gene family from Arabidopsis, CIPK genes from poplar were also divided into intron-free and intron-harboring groups. In the intron-harboring group, the intron distribution of CIPKs is rather conserved during the genome evolutionary process. Many homologous gene pairs were found in the CIPK gene family, indicating duplication events might contribute to the amplification of this gene family. The phylogenetic comparison of CIPKs in combination with intron distribution analysis revealed that CIPK genes from both Arabidopsis and poplar might have an ancient origin, which formed earlier than the separation of these two eudicot species. Our genomic and bioinformatic analysis will provide an important foundation for further functional dissection of the CBL-CIPK signaling network in poplars.

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Abbreviations

ABA:

Abscisic acid

CBL:

Calcineurin B-like protein

CIPK:

CBL-interacting protein kinase

AtCIPK:

Arabidopsis thaliana CIPK

PtCIPK:

Populus trichocarpa CIPK

CaM:

Calmodulin

CDPK:

Calcium-dependent protein kinase

SOS:

Salt overly sensitive

PKS:

SOS2-like protein kinase

UTR:

Untranslated region

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Acknowledgements

We thank the colleagues in our laboratory for their helpful discussions. This research was supported by National Natural Science Foundation of China (No. 30271096, No. 30371143, No. 30460015 and No. 30571472) and National R&D Key Project of China (2006BAD03A01).

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Authors and Affiliations

  1. College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Qinghua East Road, Haidian District, Beijing, 100083, People’s Republic of China

    Yanhua Yu, Xinli Xia, Weilun Yin & Hechen Zhang

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  1. Yanhua Yu
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  2. Xinli Xia
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  3. Weilun Yin
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  4. Hechen Zhang
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Corresponding authors

Correspondence to Xinli Xia or Weilun Yin.

Electronic supplementary material

Supplemental Fig. 1

Alignment of all the poplar CIPK protein sequences ESM1 (JPG 1372 KB)

Supplemental Fig. 2

Alignment of all the poplar and Arabidopsis CIPK protein se quences ESM2 (JPG 3349 KB)

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Yu, Y., Xia, X., Yin, W. et al. Comparative genomic analysis of CIPK gene family in Arabidopsis and Populus . Plant Growth Regul 52, 101–110 (2007). https://doi.org/10.1007/s10725-007-9165-3

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  • DOI: https://doi.org/10.1007/s10725-007-9165-3

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