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Defining the RNA-binding glycine-rich (RBG) gene superfamily: new insights into nomenclature, phylogeny, and evolutionary trends obtained by genome-wide comparative analysis of Arabidopsis, Chinese cabbage, rice and maize genomes

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Abstract

RNA-binding glycine-rich (RBG) proteins play diverse roles in plant growth, development, protection and genome organization. An overly broad definition for class IV glycine-rich proteins (GRPs), namely RNA-binding activity and a glycine-rich C-terminus, has resulted in many distantly related and/or non-related proteins being grouped into this class of RBGs. This definition has hampered the study of RBG evolution. In this study, we used a comparative genomic approach consisting of ortholog, homolog, synteny and phylogenetic analyses to legitimately exclude all distantly/non-related proteins from class IV GRPs and to identify 15, 22, 12 and 18 RBG proteins in Arabidopsis, Chinese cabbage, rice and maize genomes, respectively. All identified RBGs could be divided into three subclasses, namely RBGA, RBGB and RBGD, which may be derived from a common ancestor. We assigned RBGs excluded from class IV GRPs to a separate RBG superfamily. RBGs have evolved and diversified in different species via different mechanisms; segmental duplication and recombination have had major effects, with tandem duplication, intron addition/deletion and domain recombination/deletion playing minor roles. Loss and retention of duplicated RBGs after polyploidization has been species and subclass specific. For example, following recent whole-genome duplication and triplication in maize and Chinese cabbage, respectively, most duplicated copies of RBGA have been lost in maize while RBGD duplicates have been retained; in Chinese cabbage, in contrast, RBGA duplicates have been retained while RBGD duplicates have been lost. Our findings reveal fundamental information and shed new light on the structural characteristics and evolutionary dynamics of RBGs.

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Acknowledgments

This study was supported by the Postdoctoral Fellowship Program of the National Academy of Agricultural Science, the Rural Program for Agricultural Science and Technology Development (Project No.: PJ01002503) and by the Next-Generation Biogreen 21 Program (Project No.: PJ01116603), Rural Development Administration, Korea.

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  1. Department of Agricultural Biotechnology, National Academy of Agricultural Science (NAAS), Jeonju, 560-500, Korea

    Panneerselvam Krishnamurthy, Jin A Kim, Mi-Jeong Jeong & Soo In Lee

  2. Division of Applied Life Science and PMBBRC, Gyeongsang National University, Jinju, 660-701, Korea

    Chang Ho Kang

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  1. Panneerselvam Krishnamurthy
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Correspondence to Soo In Lee.

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Communicated by S. Hohmann.

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Krishnamurthy, P., Kim, J.A., Jeong, MJ. et al. Defining the RNA-binding glycine-rich (RBG) gene superfamily: new insights into nomenclature, phylogeny, and evolutionary trends obtained by genome-wide comparative analysis of Arabidopsis, Chinese cabbage, rice and maize genomes. Mol Genet Genomics 290, 2279–2295 (2015). https://doi.org/10.1007/s00438-015-1080-0

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