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Genome Biology and Evolution Advance Access originally published online on October 29, 2009
Genome Biology and Evolution (2009) Vol. 2009:409; doi:10.1093/gbe/evp043 published on November 18, 2009
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© 2009 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Evolutionary Persistence of Functional Compensation by Duplicate Genes in Arabidopsis

Kousuke Hanada*,{dagger},1, Takashi Kuromori*,1, Fumiyoshi Myouga*, Tetsuro Toyoda{dagger}, Wen-Hsiung Li{ddagger} and Kazuo Shinozaki*

* Gene Discovery Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
{dagger} Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
{ddagger} Department of Ecology and Evolution, University of Chicago

E-mail: whli{at}uchicago.edu; kohanada{at}psc.riken.jp.


  Abstract

Knocking out a gene from a genome often causes no phenotypic effect. This phenomenon has been explained in part by the existence of duplicate genes. However, it was found that in mouse knockout data duplicate genes are as essential as singleton genes. Here, we study whether it is also true for the knockout data in Arabidopsis. From the knockout data in Arabidopsis thaliana obtained in our study and in the literature, we find that duplicate genes show a significantly lower proportion of knockout effects than singleton genes. Because the persistence of duplicate genes in evolution tends to be dependent on their phenotypic effect, we compared the ages of duplicate genes whose knockout mutants showed less severe phenotypic effects with those with more severe effects. Interestingly, the latter group of genes tends to be more anciently duplicated than the former group of genes. Moreover, using multiple-gene knockout data, we find that functional compensation by duplicate genes for a more severe phenotypic effect tends to be preserved by natural selection for a longer time than that for a less severe effect. Taken together, we conclude that duplicate genes contribute to genetic robustness mainly by preserving compensation for severe phenotypic effects in A. thaliana.

Keywords: duplicate, Arabidopsis thaliana, phenotypic effect, functional compensation, selection pressure and genetic robustness

Accepted October 21, 2009

1 These authors contributed equally to this work.

Marta Wayne, Associate Editor


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