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Recent duplications dominate NBS-encoding gene expansion in two woody species

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Abstract

Most disease resistance genes in plants encode NBS-LRR proteins. However, in woody species, little is known about the evolutionary history of these genes. Here, we identified 459 and 330 respective NBS-LRRs in grapevine and poplar genomes. We subsequently investigated protein motif composition, phylogenetic relationships and physical locations. We found significant excesses of recent duplications in perennial species, compared with those of annuals, represented by rice and Arabidopsis. Consequently, we observed higher nucleotide identity among paralogs and a higher percentage of NBS-encoding genes positioned in numerous clusters in the grapevine and poplar. These results suggested that recent tandem duplication played a major role in NBS-encoding gene expansion in perennial species. These duplication events, together with a higher probability of recombination revealed in this study, could compensate for the longer generation time in woody perennial species e.g. duplication and recombination could serve to generate novel resistance specificities. In addition, we observed extensive species-specific expansion in TIR-NBS-encoding genes. Non-TIR-NBS-encoding genes were poly- or paraphyletic, i.e. genes from three or more plant species were nested in different clades, suggesting different evolutionary patterns between these two gene types.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (30570987 and 30470122), Pre-program for NBRPC (2005CCA02100) and 111 project to D. T., or J-Q. C.

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Authors and Affiliations

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

    Sihai Yang, Xiaohui Zhang, Jia-Xing Yue, Dacheng Tian & Jian-Qun Chen

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  1. Sihai Yang
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  2. Xiaohui Zhang
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  3. Jia-Xing Yue
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  4. Dacheng Tian
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  5. Jian-Qun Chen
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Corresponding authors

Correspondence to Dacheng Tian or Jian-Qun Chen.

Additional information

Communicated by A. Tyagi.

Sihai Yang and Xiaohui Zhang contributed equally to this work.

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Yang, S., Zhang, X., Yue, JX. et al. Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol Genet Genomics 280, 187–198 (2008). https://doi.org/10.1007/s00438-008-0355-0

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