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Genome-wide analysis of the RING finger gene family in apple

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Abstract

The RING finger protein family plays a crucial role in plant growth and development and in response to biotic and abiotic stresses. However, no detailed information concerning this family is available for apple (Malus × domestica L. Borkh) due to the limited information on whole genome sequences. In this study, 688 RING domains in 663 predicted proteins were identified in apple. Based on the spacing between metal ligands or substitutions at one or more of the metal ligand positions, nine RING types were identified: RING-H2, RING-HC, RING-C2, RING-v, RING-D, RING-S/T, RING-G, RING-mH2, and RING-mHC, in which the first seven types were described previously in Arabidopsis, while the latter two were newly identified in apple. Proteins containing RING finger motifs were further classified into 57 groups according to the different known or unknown domains outside the RING domains. A total of 643 retrieved proteins appear to be distributed over all 17 linkage groups with different densities. Microarray and expressed sequence tag data revealed that only a few of these RING finger proteins may be involved in fruit development. As a first step towards genome-wide analyses of the RING-containing genes in apple, our results provide valuable information for understanding the classification and putative functions of the RING finger gene family in higher plants.

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Acknowledgments

This work was supported by the National Natural Science Foundation (Grant No. 30970230) and the Genetically Modified Organisms Breeding Major Projects (2009ZX08009-092B) in China.

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Authors and Affiliations

  1. State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, People’s Republic of China

    Yanze Li, Bingjiang Wu, Guodong Yang, Changai Wu & Chengchao Zheng

  2. Maize Institute, Shandong Academy of Agricultural Sciences/National Maize Improvement Sub-Center, Jinan, 250100, People’s Republic of China

    Yanli Yu

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  1. Yanze Li
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  2. Bingjiang Wu
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  3. Yanli Yu
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  4. Guodong Yang
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Correspondence to Chengchao Zheng.

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Communicated by P. Westhoff.

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Li, Y., Wu, B., Yu, Y. et al. Genome-wide analysis of the RING finger gene family in apple. Mol Genet Genomics 286, 81–94 (2011). https://doi.org/10.1007/s00438-011-0625-0

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