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Evolution after whole-genome duplication: a network perspective.

Zhu Y, Lin Z, Nakhleh L - G3 (Bethesda) (2013)

Bottom Line: We find that molecular interactions involving WGD genes evolve at rates that are three orders of magnitude slower than the rates of evolution of the corresponding sequences.Further epistasis analysis of WGD pairs categorized by their inferred evolutionary fates demonstrated the utility of these techniques.Finally, we find that WGD pairs and other pairs of paralogous genes of small-scale duplication origin share similar properties, giving good support for generalizing our results from WGD pairs to evolution after gene duplication in general.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Rice University, Houston, Texas 77005.

ABSTRACT
Gene duplication plays an important role in the evolution of genomes and interactomes. Elucidating how evolution after gene duplication interplays at the sequence and network level is of great interest. In this work, we analyze a data set of gene pairs that arose through whole-genome duplication (WGD) in yeast. All these pairs have the same duplication time, making them ideal for evolutionary investigation. We investigated the interplay between evolution after WGD at the sequence and network levels and correlated these two levels of divergence with gene expression and fitness data. We find that molecular interactions involving WGD genes evolve at rates that are three orders of magnitude slower than the rates of evolution of the corresponding sequences. Furthermore, we find that divergence of WGD pairs correlates strongly with gene expression and fitness data. Because of the role of gene duplication in determining redundancy in biological systems and particularly at the network level, we investigated the role of interaction networks in elucidating the evolutionary fate of duplicated genes. We find that gene neighborhoods in interaction networks provide a mechanism for inferring these fates, and we developed an algorithm for achieving this task. Further epistasis analysis of WGD pairs categorized by their inferred evolutionary fates demonstrated the utility of these techniques. Finally, we find that WGD pairs and other pairs of paralogous genes of small-scale duplication origin share similar properties, giving good support for generalizing our results from WGD pairs to evolution after gene duplication in general.

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Three fates of a duplicated gene from a network perspective.
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fig6: Three fates of a duplicated gene from a network perspective.

Mentions: After gene duplication, duplicates can have different functional fates, such as maintaining the same function as the ancestral single-copy gene, developing a new function, etc. Given our previous results regarding the use of shared neighborhoods of WGD pairs to estimate the rate of divergence, we here use the neighborhoods of WGD pairs as proxies of their functional fates. For CF, the two genes in a WGD pair maintain exactly the same set of neighbors; in SF, each gene in a WGD pair maintains a subset of original neighbors, whereas the union of their neighbors equals the original set. Finally, in NF, one gene in the WGD pair develops a new set of neighbors while losing all of the duplicated neighbors. According to this strategy, pure conserved functionalization would result in a normalized shared neighborhood size equal to 1, whereas pure subfunctionalization and neofunctionalization would both result in a normalized shared neighborhood size of 0. Figure 6 illustrates these three categories.


Evolution after whole-genome duplication: a network perspective.

Zhu Y, Lin Z, Nakhleh L - G3 (Bethesda) (2013)

Three fates of a duplicated gene from a network perspective.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3815064&req=5

fig6: Three fates of a duplicated gene from a network perspective.
Mentions: After gene duplication, duplicates can have different functional fates, such as maintaining the same function as the ancestral single-copy gene, developing a new function, etc. Given our previous results regarding the use of shared neighborhoods of WGD pairs to estimate the rate of divergence, we here use the neighborhoods of WGD pairs as proxies of their functional fates. For CF, the two genes in a WGD pair maintain exactly the same set of neighbors; in SF, each gene in a WGD pair maintains a subset of original neighbors, whereas the union of their neighbors equals the original set. Finally, in NF, one gene in the WGD pair develops a new set of neighbors while losing all of the duplicated neighbors. According to this strategy, pure conserved functionalization would result in a normalized shared neighborhood size equal to 1, whereas pure subfunctionalization and neofunctionalization would both result in a normalized shared neighborhood size of 0. Figure 6 illustrates these three categories.

Bottom Line: We find that molecular interactions involving WGD genes evolve at rates that are three orders of magnitude slower than the rates of evolution of the corresponding sequences.Further epistasis analysis of WGD pairs categorized by their inferred evolutionary fates demonstrated the utility of these techniques.Finally, we find that WGD pairs and other pairs of paralogous genes of small-scale duplication origin share similar properties, giving good support for generalizing our results from WGD pairs to evolution after gene duplication in general.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Rice University, Houston, Texas 77005.

ABSTRACT
Gene duplication plays an important role in the evolution of genomes and interactomes. Elucidating how evolution after gene duplication interplays at the sequence and network level is of great interest. In this work, we analyze a data set of gene pairs that arose through whole-genome duplication (WGD) in yeast. All these pairs have the same duplication time, making them ideal for evolutionary investigation. We investigated the interplay between evolution after WGD at the sequence and network levels and correlated these two levels of divergence with gene expression and fitness data. We find that molecular interactions involving WGD genes evolve at rates that are three orders of magnitude slower than the rates of evolution of the corresponding sequences. Furthermore, we find that divergence of WGD pairs correlates strongly with gene expression and fitness data. Because of the role of gene duplication in determining redundancy in biological systems and particularly at the network level, we investigated the role of interaction networks in elucidating the evolutionary fate of duplicated genes. We find that gene neighborhoods in interaction networks provide a mechanism for inferring these fates, and we developed an algorithm for achieving this task. Further epistasis analysis of WGD pairs categorized by their inferred evolutionary fates demonstrated the utility of these techniques. Finally, we find that WGD pairs and other pairs of paralogous genes of small-scale duplication origin share similar properties, giving good support for generalizing our results from WGD pairs to evolution after gene duplication in general.

Show MeSH