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Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes

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Abstract

A complete set of candidate disease resistance ( R) genes encoding nucleotide-binding sites (NBSs) was identified in the genome sequence of japonica rice ( Oryza sativa L. var. Nipponbare). These putative R genes were characterized with respect to structural diversity, phylogenetic relationships and chromosomal distribution, and compared with those in Arabidopsis thaliana. We found 535 NBS-coding sequences, including 480 non-TIR (Toll/IL-1 receptor) NBS-LRR (Leucine Rich Repeat) genes. TIR NBS-LRR genes, which are common in A. thaliana, have not been identified in the rice genome. The number of non-TIR NBS-LRR genes in rice is 8.7 times higher than that in A. thaliana, and they account for about 1% of all of predicted ORFs in the rice genome. Some 76% of the NBS genes were located in 44 gene clusters or in 57 tandem arrays, and 16 apparent gene duplications were detected in these regions. Phylogenetic analyses based both NBS and N-terminal regions classified the genes into about 200 groups, but no deep clades were detected, in contrast to the two distinct clusters found in A. thaliana. The structural and genetic diversity that exists among NBS-LRR proteins in rice is remarkable, and suggests that diversifying selection has played an important role in the evolution of R genes in this agronomically important species. (Supplemental material is available online at http://gattaca.nju.edu.cn.)

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Acknowledgements

We thank J. J. Emerson for useful discussions, the Japan Society for the Promotion of Science for Young Scientists for the award of Research Fellowships to H. A., Nanjing University for the generous initial funding of D.T., and IBM for a SUR grant

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Authors and Affiliations

  1. State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, 210093, Nanjing, China

    T. Zhou, Y. Wang, J.-Q. Chen, Z. Jing, K. Jiang, J. Shen & D. Tian

  2. Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA

    H. Araki

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  1. T. Zhou
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  2. Y. Wang
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  3. J.-Q. Chen
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  4. H. Araki
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  5. Z. Jing
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  6. K. Jiang
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  7. J. Shen
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  8. D. Tian
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Corresponding author

Correspondence to D. Tian.

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Communicated by R. Hagemann

The first three authors contributed equally to this work

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Zhou, T., Wang, Y., Chen, JQ. et al. Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. Mol Genet Genomics 271, 402–415 (2004). https://doi.org/10.1007/s00438-004-0990-z

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  • DOI: https://doi.org/10.1007/s00438-004-0990-z

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