Abstract
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.
Highlights
Duplicate genes rarely exhibit de novo functions; more usually, the functions of the original gene are split into multiple functions among the duplicate genes [1,2,3,4,5]
To address how duplicate genes have contributed to morphological evolution, we classified Arabidopsis duplicate genes into high, low and no morphological diversification groups based on knock-out data, and examined the divergence rates of both expression pattern and protein sequence among the three morphological diversification groups
To compare the divergence rate of expression pattern with that of protein sequence in paralogous gene pairs associated with morphological diversification, we focused on paralogous gene pairs without morphological diversification because the divergence rate of expression pattern and/or protein sequence in these duplicate genes has little effect on morphological diversification
Summary
Duplicate genes rarely exhibit de novo functions (neofunctionalization); more usually, the functions of the original gene are split into multiple functions among the duplicate genes (subfunctionalization) [1,2,3,4,5] Such functionalization through gene duplication is considered to be an important source of diversification in complex organisms [6]. It is of interest to compare the divergence rate of either expression pattern or protein sequence of duplicate genes of the same age that have and have not undergone functionalization. To address how duplicate genes have contributed to morphological evolution, we classified Arabidopsis duplicate genes into high, low and no morphological diversification groups based on knock-out data, and examined the divergence rates of both expression pattern and protein sequence among the three morphological diversification groups. Abnormal morphological changes were classified into seed, vegetative and reproductive phenotypes on the basis of the definition of Meinke
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