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Evolution of the number of LRRs in plant disease resistance genes

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Abstract

The largest group of plant resistance (R) genes contain the regions that encode the nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains (NBS-LRR genes). To gain new resistance, amino acid substitutions and changes in number of the LRRs that recognize the presence of pathogens are considered important. In this study, we focus on the evolution of the number of LRRs and analyze the genome data of five plant species, Arabidopsis thaliana, Oryza sativa, Medicago truncatula, Lotus japonicus and Populus trichocarpa. We first categorized the NBS-LRR genes in each species into groups and subgroups based on the phylogenetic relationships of their NBS domain sequences. Then we estimated the evolutionary rate of the number of LRRs relative to the synonymous divergence in the NBS domain sequences by a maximum likelihood method assuming the single stepwise mutation model. The estimates ranged from 4.5 to 600 and differed between groups in the same species or between species. This indicated different roles played by different groups of the NBS-LRR genes within a species or the effects of various life history characteristics, such as generation time, of the species. We also tested the fit of the model to the data using the variance of number of LRRs in each subgroup. In some subgroups in some plants (16 out of 174 subgroups), the results of simulation using the estimated rates significantly deviated from the observed data. Those subgroups may have undergone different modes of selection from the other subgroups.

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Acknowledgments

This study was partially supported by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (nos. 19370099 and 22370083) and by Program for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry (BRAIN). We thank two anonymous referees for their constructive comments on the earlier draft of the manuscript. We also thank Chris Wood for his critical reading and helpful comments regarding the English manuscript.

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Authors and Affiliations

  1. Graduate School of Systems Life Sciences, Kyushu University, 6-10-1 Hakozaki, Fukuoka, 812-8581, Japan

    Miho Tamura

  2. Department of Biology, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Fukuoka, 812-8581, Japan

    Hidenori Tachida

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  1. Miho Tamura
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  2. Hidenori Tachida
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Correspondence to Hidenori Tachida.

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Communicated by Y. Van de Peer.

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Tamura, M., Tachida, H. Evolution of the number of LRRs in plant disease resistance genes. Mol Genet Genomics 285, 393–402 (2011). https://doi.org/10.1007/s00438-011-0615-2

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  • DOI: https://doi.org/10.1007/s00438-011-0615-2

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