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, 5 (12), e1000781

Increased Expression and Protein Divergence in Duplicate Genes Is Associated With Morphological Diversification


Increased Expression and Protein Divergence in Duplicate Genes Is Associated With Morphological Diversification

Kousuke Hanada et al. PLoS Genet.


The differentiation of both gene expression and protein function is thought to be important as a mechanism of the functionalization of duplicate genes. However, it has not been addressed whether expression or protein divergence of duplicate genes is greater in those genes that have undergone functionalization compared with those that have not. We examined a total of 492 paralogous gene pairs associated with morphological diversification in a plant model organism (Arabidopsis thaliana). Classifying these paralogous gene pairs into high, low, and no morphological diversification groups, based on knock-out data, we found that the divergence rate of both gene expression and protein sequences were significantly higher in either high or low morphological diversification groups compared with those in the no morphological diversification group. These results strongly suggest that the divergence of both expression and protein sequence are important sources for morphological diversification of duplicate genes. Although both mechanisms are not mutually exclusive, our analysis suggested that changes of expression pattern play the minor role (33%-41%) and that changes of protein sequence play the major role (59%-67%) in morphological diversification. Finally, we examined to what extent duplicate genes are associated with expression or protein divergence exerting morphological diversification at the whole-genome level. Interestingly, duplicate genes randomly chosen from A. thaliana had not experienced expression or protein divergence that resulted in morphological diversification. These results indicate that most duplicate genes have experienced minor functionalization.

Conflict of interest statement

The authors have declared that no competing interests exist.


Figure 1
Figure 1. Paralogous gene pairs with high, low, and no morphological diversification.
(A) Paralogous gene pairs with different knock-out phenotypes are defined to have high morphological diversification. (B) Paralogous gene pairs with similar or identical knock-out phenotypes are defined to have low morphological diversification. (C) Paralogous gene pairs in which morphological changes are observed only upon the deletion of multiple paralogous genes but not by the deletion of each gene individually are defined to have no morphological diversification.
Figure 2
Figure 2. Divergence rate of expression and protein sequence in paralogous gene pairs.
(A) Relationship between expression divergence (Ed) and morphological diversification (defined in the main text). Ed is log ((1−R)/(1+R))/Ks, where R is the correlation coefficient of paralogous gene pairs among different experimental conditions and Ks is synonymous distance. (B) Relationship between ratio of Ka (nonsynonymous distance) to Ks in paralogous gene pairs and morphological diversification. (C) Relationship between ratio of Kr (radical nonsynonymous distance) to Kc (conservative nonsynonymous distance) and morphological diversification. The random sample included 1,000 pairs of paralogs. The distributions of Ed, Ka/Ks ratio and Kr/Kc ratio are shown as box plots with the solid horizontal line indicating the median value, the box representing the inter quartile range (25%–75%), and the dotted line indicating the first to the 99th percentile.

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