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Patterns of molecular evolution and predicted function in thaumatin-like proteins of Populus trichocarpa

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Abstract

Some pathogenesis-related proteins (PR proteins) are subject to positive selection, while others are under negative selection. Here, we report the patterns of molecular evolution in thaumatin-like protein (TLP, PR5 protein) genes of Populus trichocarpa. Signs of positive selection were found in 20 out of 55 Populus TLPs using the likelihood ratio test and ML-based Bayesian methods. Due to the connection between the acidic cleft and the antifungal activity, the secondary structure and three-dimensional structure analyses predicted antifungal activity β-1,3-glucanase activities in these TLPs. Moreover, the coincidence with variable basic sites in the acidic cleft and positively selected sites suggested that fungal diseases may have been the main environmental stress that drove rapid adaptive evolution in Populus.

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Abbreviations

PR proteins:

Pathogenesis-related proteins

TLPs:

Thaumatin-like proteins

ML:

Maximum likelihood

JTT:

Jones–Taylor–Thornton

AIC:

Akaike information criterion

LRT:

Likelihood ratio test

BEB:

Bayes empirical Bayesian

NEB:

Naive empirical Bayes

ABA:

Abscisic acid

SA:

Salicylate acid

JA:

Jasmonic acid

ET:

Ethylene

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Acknowledgments

This work was financially supported by National Natural Science Foundation of China (No. 30872048), and Chinese Natural Science & Technology Resources Sharing Programs (No. 2005DKA21207-14) and National Science & Technology Basic Program of China (No. 2009FY210100).

Author information

Correspondence to Jia Ping Zhao.

Additional information

X. H. Su contributed equally to this work.

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Zhao, J.P., Su, X.H. Patterns of molecular evolution and predicted function in thaumatin-like proteins of Populus trichocarpa . Planta 232, 949–962 (2010). https://doi.org/10.1007/s00425-010-1218-6

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Keywords

  • Antifungal activity
  • Glucanase activity
  • Homology modeling
  • Molecular evolution
  • Positive selection