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Selection-Driven Divergence After Gene Duplication in Arabidopsis thaliana

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Abstract

Gene duplications are one of the most important mechanisms for the origin of evolutionary novelties. Even though various models of the fate of duplicated genes have been established, current knowledge about the role of divergent selection after gene duplication is rather limited. In this study, we analyzed sequence divergence in response to neo- and subfunctionalization of segmentally duplicated genes in the genome of Arabidopsis thaliana. We compared the genomes of A. thaliana and the poplar Populus trichocarpa to identify orthologous pairs of genes and their corresponding inparalogs. Maximum-likelihood analyses of the nonsynonymous and synonymous substitution rate ratio \( \left( {\omega = d_{\rm{N}} /d_{\rm{S}} } \right) \) of pairs of A. thaliana inparalogs were used to detect differences in the evolutionary rates of protein coding sequences. We analyzed 1,924 A. thaliana paralogous pairs and our results indicate that around 6.9% show divergent ω values between the lineages for a fraction of sites. We observe an enrichment of regulatory sequences, a reduced level of co-expression and an increased number of substitutions that can be attributed to positive selection based on an McDonald–Kreitman type of analysis. Taken together, these results show that selection after duplication contributes substantially to gene novelties and hence functional divergence in plants.

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Acknowledgments

The authors are grateful to the bioinformatics group of the IPK Gatersleben as well as Christian Kauhaus at University of Jena for access to the computer clusters. Matthias Höffken provided useful hints on Python scripting and contributed Python code for statistical analyses. The authors thank Adam Eyre-Walker for discussion on the MK analysis of inparalogs. The authors also thank D. Tian and two anonymous referees for their valuable comments on the manuscript. The study was supported by an undergraduate scholarship by the Studienstiftung des deutschen Volkes to TG and IPK core funding to KS.

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  1. Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany

    Toni I. Gossmann & Karl J. Schmid

  2. Life Sciences, University of Sussex, Brighton, BN1 9QG, UK

    Toni I. Gossmann

  3. Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany

    Karl J. Schmid

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Gossmann, T.I., Schmid, K.J. Selection-Driven Divergence After Gene Duplication in Arabidopsis thaliana . J Mol Evol 73, 153–165 (2011). https://doi.org/10.1007/s00239-011-9463-2

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