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Genome-wide identification and expression analysis of rice cell cycle genes

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Abstract

Cyclins, cyclin-dependent kinases, and a number of other proteins control the progression of plant cell cycle. Although extensive studies have revealed the roles of some cell cycle regulators and the underlying mechanisms in Arabidopsis, relatively a small number of cell cycle regulators were functionally analyzed in rice. In this study, we describe 41 regulators in the rice genome. Our results indicate that the rice genome contains a less number of the core cell cycle regulators than the Arabidopsis one does, although the rice genome is much larger than the Arabidopsis one. Eight groups of CDKs similar to those in Arabidopsis were identified in the rice genome through phylogenetic analysis, and the corresponding members in the different groups include E2F, CKI, Rb, CKS and Wee. The structures of the core cell regulators were relatively conserved between the rice and Arabidopsis genomes. Furthermore, the expression of the majority of the core cell cycle genes was spatially regulated, and the most closely related ones showed very similar patterns of expression, suggesting functional redundancy and conservation between the highly similar core cell cycle genes in rice and Arabidopsis. Following auxin or cytokinin treatment, the expression of the core cell cycle genes was either upregulated or downregulated, suggesting that auxin and/or cytokinin may directly regulate the expression of the core cell cycle genes. Our results provide basic information to understand the mechanism of cell cycle regulation and the functions of the rice cell cycle genes.

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Acknowledgements

This research was supported by the Major State Basic Research Program of the People’s Republic of China (2005CB120803).

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  1. Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China

    Jing Guo, Jian Song, Fang Wang & Xian Sheng Zhang

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  1. Jing Guo
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  2. Jian Song
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  3. Fang Wang
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Correspondence to Xian Sheng Zhang.

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Fig. S1

Expression profiles of the rice core cell cycle genes in seedlings after auxin treatment. The transcript levels of these genes were analyzed over a 24-h period after 10 μM IAA treatment. The rice actin gene was used as an internal control. (A) Cyclins; (B) CDKs and CKS; (C) KRPs; (D) E2F/DPs; (E) Rbs. ↑, upregulation; ↓, downregulation (JPG 615 kb)

Fig. S2

Expression profiles of the rice core cell cycle genes in seedlings after cytokinin treatment. The transcript levels of these genes were analyzed over 4-h period in response to 5 μM exogenous 6-BA. The rice actin gene was used as an internal control. (A) Cyclins; (B) CDKs and CKS; (C) KRP; (D) E2F/DPs; (E) Rbs. ↑, upregulation; ↓, downregulation (JPG 724 kb)

Table S1

A list of rice core cell cycle genes (DOC 227 kb)

Table S2

Sequences of rice core cell cycle genes (XLS 235 kb)

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Guo, J., Song, J., Wang, F. et al. Genome-wide identification and expression analysis of rice cell cycle genes. Plant Mol Biol 64, 349–360 (2007). https://doi.org/10.1007/s11103-007-9154-y

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