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Investigating ancient duplication events in the Arabidopsis genome

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Journal of Structural and Functional Genomics

Abstract

The complete genomic analysis of Arabidopsis thaliana has shown that a major fraction of the genome consists of paralogous genes that probably originated through one or more ancient large-scale gene or genome duplication events. However, the number and timing of these duplications still remains unclear, and several different hypotheses have been put forward recently. Here, we reanalyzed duplicated blocks found in the Arabidopsis genome described previously and determined their date of divergence based on silent substitution estimations between the paralogous genes and, where possible, by phylogenetic reconstruction. We show that methods based on averaging protein distances of heterogeneous classes of duplicated genes lead to unreliable conclusions and that a large fraction of blocks duplicated much more recently than assumed previously. We found clear evidence for one large-scale gene or even complete genome duplication event somewhere between 70 to 90 million years ago. Traces pointing to a much older (probably more than 200 million years) large-scale gene duplication event could be detected. However, for now it is impossible to conclude whether these old duplicates are the result of one or more large-scale gene duplication events. abbreviations dA, fraction of amino acid substitutions; Kn, number of nonsynonymous substitutions per nonsynonymous site; Ks, number of synonymous substitutions per synonymous site; MYA, million years ago

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  1. Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, K.L. Ledeganckstraat 35, B−9000, Gent, Belgium

    Cedric Simillion, Yvan Saeys & Yves Van de Peer

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  1. Jeroen Raes
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  2. Klaas Vandepoele
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  3. Cedric Simillion
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Correspondence to Yves Van de Peer.

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Raes, J., Vandepoele, K., Simillion, C. et al. Investigating ancient duplication events in the Arabidopsis genome. J Struct Func Genom 3, 117–129 (2003). https://doi.org/10.1023/A:1022666020026

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