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Molecular evolution and sequence divergence of plant chalcone synthase and chalcone synthase-Like genes

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Abstract

Plant chalcone synthase (CHS) and CHS-Like (CHSL) proteins are polyketide synthases. In this study, we evaluated the molecular evolution of this gene family using representative types of CHSL genes, including stilbene synthase (STS), 2-pyrone synthase (2-PS), bibenzyl synthase (BBS), acridone synthase (ACS), biphenyl synthase (BIS), benzalacetone synthase, coumaroyl triacetic acid synthase (CTAS), and benzophenone synthase (BPS), along with their CHS homologs from the same species of both angiosperms and gymnosperms. A cDNA-based phylogeny indicated that CHSLs had diverse evolutionary patterns. STS, ACS, and 2-PS clustered with CHSs from the same species (late diverged pattern), while CTAS, BBS, BPS, and BIS were distant from their CHS homologs (early diverged pattern). The amino-acid phylogeny suggested that CHS and CHSL proteins formed clades according to enzyme function. The CHSs and CHSLs from Polygonaceae and Arachis had unique evolutionary histories. Synonymous mutation rates were lower in late diverged CHSLs than in early diverged ones, indicating that gene duplications occurred more recently in late diverged CHSLs than in early diverged ones. Relative rate tests proved that late diverged CHSLs had unequal rates to CHSs from the same species when using fatty acid synthase, which evolved from the common ancestor with the CHS superfamily, as the outgroup, while the early diverged lineages had equal rates. This indicated that late diverged CHSLs experienced more frequent mutation than early diverged CHSLs after gene duplication, allowing obtaining new functions in relatively short period of time.

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Acknowledgments

This work has been supported by grants from National Natural Science Fundation of China (No. 30900782), Foundation of Chinese Postdoctor (No. 20080440580), Foundation of Postdoctor in Shanghai (No. 09R21411000),and the graduate student education innovation plan of University of Shanghai for Science and Technology, the minimally invasive inspiring innovation fund of University of Shanghai for Science (2013.10).

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Authors and Affiliations

  1. Center of System Biomedical Sciences, College of Medical Appliance and Food Sciences, University of Shanghai for Science and Technology, Jungong Road 516, Yangpu district, Shanghai, 200093, People’s Republic of China

    Yingying Han, Wenwen Zhao, Zhicui Wang, Jingying Zhu & Qisong Liu

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  1. Yingying Han
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  3. Zhicui Wang
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Correspondence to Yingying Han.

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Han, Y., Zhao, W., Wang, Z. et al. Molecular evolution and sequence divergence of plant chalcone synthase and chalcone synthase-Like genes. Genetica 142, 215–225 (2014). https://doi.org/10.1007/s10709-014-9768-3

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  • DOI: https://doi.org/10.1007/s10709-014-9768-3

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