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Relative evolutionary rates of NBS-encoding genes revealed by soybean segmental duplication

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Abstract

It is well known that nucleotide binding site (NBS)-encoding genes are duplicate-rich and fast-evolving genes. However, there is little information on the relative importance of tandem and segmental NBS duplicates and their exact evolutionary rates. The two rounds of large-scale duplication that have occurred in soybean provide a unique opportunity to investigate these issues. Comparison of NBS and non-NBS genes on segments of syntenic homoeologs shows that NBS-encoding genes evolve at least 1.5-fold faster (~1.5-fold higher synonymous and ~2.3-fold higher nonsynonymous substitution rates) and lose their genes ~twofold faster than the flanking non-NBS genes. Compared with segmental duplicates, tandem NBS duplicates are more abundant in soybean, suggesting that tandem duplication is the major driving force in the expansion of NBS genes. Notably, significant sequence exchanges along with significantly positive selection were detected in most tandem-duplicated NBS gene families. The results suggest that the rapid evolution of NBS genes may be due to the combined effects of diversifying selection and frequent sequence exchanges. Interestingly, TIR–NBS–LRR genes (TNLs) have a higher nucleotide substitution rate than non-TNLs, indicating that these types of NBS genes may have a rather different evolutionary pattern. It is important to determine the exact relative evolutionary rates of TNL, non-TNL, and non-NBS genes in order to understand how fast the host plant can adjust its response to rapidly evolving pathogens in a coevolutionary context.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (30930008, 30970198 and J0730641) and National Key Project for Gene Transform in China (2009ZX08009-27B). Two anonymous reviewers provided helpful comments.

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Authors and Affiliations

  1. State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China

    Xiaohui Zhang, Ying Feng, Dacheng Tian, Sihai Yang & Jian-Qun Chen

  2. National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

    Hao Cheng

Authors
  1. Xiaohui Zhang
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  2. Ying Feng
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  3. Hao Cheng
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  4. Dacheng Tian
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  5. Sihai Yang
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  6. Jian-Qun Chen
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Corresponding authors

Correspondence to Sihai Yang or Jian-Qun Chen.

Additional information

Communicated by Y. Van de Peer.

X. Zhang and Y. Feng contributed equally to this work.

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Zhang, X., Feng, Y., Cheng, H. et al. Relative evolutionary rates of NBS-encoding genes revealed by soybean segmental duplication. Mol Genet Genomics 285, 79–90 (2011). https://doi.org/10.1007/s00438-010-0587-7

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  • DOI: https://doi.org/10.1007/s00438-010-0587-7

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