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Likelihood Analysis of the Chalcone Synthase Genes Suggests the Role of Positive Selection in Morning Glories (Ipomoea)

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Abstract

Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoides, which are important for the pigmentation of flowers and act as attractants to pollinators. Genes encoding CHS constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. In morning glories (Ipomoea), five functional CHS genes (A–E) have been described. Phylogenetic analysis of the Ipomoea CHS gene family revealed that CHS A, B, and C experienced accelerated rates of amino acid substitution relative to CHS D and E. To examine whether the CHS genes of the morning glories underwent adaptive evolution, maximum-likelihood models of codon substitution were used to analyze the functional sequences in the Ipomoea CHS gene family. These models used the nonsynonymous/synonymous rate ratio (ω = d N /d S ) as an indicator of selective pressure and allowed the ratio to vary among lineages or sites. Likelihood ratio test suggested significant variation in selection pressure among amino acid sites, with a small proportion of them detected to be under positive selection along the branches ancestral to CHS A, B, and C. Positive Darwinian selection appears to have promoted the divergence of subfamily ABC and subfamily DE and is at least partially responsible for a rate increase following gene duplication.

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Acknowledgements

We thank two anonymous reviewers for comments. This study was supported by National Natural Science Foundation of China Grant 39830020 to H.G., and HFSP Grant Y0055/2001-M and BBSRC Grant 31/G14969 to Z.Y.

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  1. College of Life Sciences, Peking, University, Beijing, 100871, China

    Ji Yang & Hongya Gu

  2. Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, England

    Ziheng Yang

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  2. Hongya Gu
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Correspondence to Ziheng Yang.

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Yang, J., Gu, H. & Yang, Z. Likelihood Analysis of the Chalcone Synthase Genes Suggests the Role of Positive Selection in Morning Glories (Ipomoea) . J Mol Evol 58, 54–63 (2004). https://doi.org/10.1007/s00239-003-2525-3

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