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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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For the set of WGD pairs, the lengths of gene sequences, the number of copies within the families, and the degree of the genes, respectively, are shown against rt.
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fig2: For the set of WGD pairs, the lengths of gene sequences, the number of copies within the families, and the degree of the genes, respectively, are shown against rt.

Mentions: As we stated previously, it seems that the mutation rates are not very different for the different WGD pairs. Still, variability exists in the rates, and the question is: what factors play a role in this variability? To answer this question, we correlated the divergence rates of WGD pairs with three metrics: the length of gene sequences, the number of gene copies in the family, and the degree of the gene in the PPI network. The results are shown in Figure 2.


Evolution after whole-genome duplication: a network perspective.

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

For the set of WGD pairs, the lengths of gene sequences, the number of copies within the families, and the degree of the genes, respectively, are shown against rt.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: For the set of WGD pairs, the lengths of gene sequences, the number of copies within the families, and the degree of the genes, respectively, are shown against rt.
Mentions: As we stated previously, it seems that the mutation rates are not very different for the different WGD pairs. Still, variability exists in the rates, and the question is: what factors play a role in this variability? To answer this question, we correlated the divergence rates of WGD pairs with three metrics: the length of gene sequences, the number of gene copies in the family, and the degree of the gene in the PPI network. The results are shown in Figure 2.

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