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.
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DOI：
10.1371/journal.pgen.1000781
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发表时间：
2009-12
期刊：
影响因子：
4.5
通讯作者：
Shinozaki K
中科院分区：
文献类型：
--
作者：
Hanada K;Kuromori T;Myouga F;Toyoda T;Shinozaki K
基因表达和蛋白质功能的差异被认为是重要的重复基因的功能化的机制。然而，它还没有解决是否重复基因的表达或蛋白质差异是更大的那些基因经历了功能化相比，那些没有。我们研究了共492旁系同源基因对与植物模式生物（拟南芥）的形态多样化。将这些旁系同源基因对分为高、低和无形态多样化组，基于敲除数据，我们发现，与无形态多样化组相比，在高或低形态多样化组中基因表达和蛋白质序列的趋异率显著更高。这些结果表明，表达和蛋白质序列的差异是重复基因形态多样性的重要来源。虽然这两种机制并不相互排斥，但我们的分析表明，表达模式的变化起次要作用（33%-41%），蛋白质序列的变化起主要作用（59%-67%）。最后，我们研究了重复基因在多大程度上与表达或蛋白质分歧在全基因组水平上发挥形态多样化。有趣的是，从A. thaliana没有经历导致形态多样化的表达或蛋白质分歧。这些结果表明，大多数重复基因经历了轻微的功能化。形态进化与分子进化之间的关系是理解真核生物进化的核心问题。特别是，在进化过程中，重复的基因如何促进形态多样化，这一点引起了人们的极大兴趣。作为重复基因功能化的机制，基因表达和蛋白质功能的分化被认为是重要的。虽然已经报道了表达和蛋白质差异都倾向于随着重复年龄的增加而增加，但尚不清楚重复基因中的表达或蛋白质差异是否在经历功能化的那些基因中比那些没有经历功能化的基因更大。在这里，我们研究了492个重复的基因对与不同程度的形态多样化的拟南芥。利用这些数据，我们发现表达和蛋白质序列的差异是重复基因形态多样性的重要来源。虽然这两种机制并不相互排斥，但我们的分析表明，表达差异是次要因素，蛋白质差异是形态多样化的主要因素。然而，随机选择的重复基因的表达或蛋白质序列并没有显示出导致形态多样化的显着分歧。这些结果表明，大多数重复基因在基因组中经历了轻微的功能化。
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. The relationship between morphological and molecular evolution is a central issue to the understanding of eukaryote evolution. In particular, there is much interest in how duplicate genes have contributed to morphological diversification during evolution. As a mechanism of functionalization of duplicate genes, differentiation of both gene expression and protein function are believed to be important. Although it has been reported that both expression and protein divergence tend to increase as a duplication ages, it is unclear whether expression or protein divergence in duplicate genes is greater in those genes that have undergone functionalization compared with those that have not. Here, we studied 492 duplicate gene pairs associated with various degrees of morphological diversification in Arabidopsis thaliana. Using these data, we found that the divergence of both expression and protein sequence were important sources for morphological diversification of duplicate genes. Although both mechanisms are not mutually exclusive, our analysis suggested that expression divergence is the minor contributor and protein divergence is the major contributor to morphological diversification. However, the expression or protein sequence of randomly chosen duplicate genes did not show significant divergence that resulted in morphological diversification. These results indicate that most duplicate genes experienced minor functionalization in the genome.
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影响因子：
56.9
作者：
Gao, LZ;Innan, H
通讯作者：
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影响因子：
7.2
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作者：
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