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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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(Left) Expression levels and (right) fitness levels of single genes as a function of the rt values of WGD pairs. For a given WGD pair, the expression levels and fitness levels of both genes are plotted individually in the corresponding rt value for their containing pair.
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fig4: (Left) Expression levels and (right) fitness levels of single genes as a function of the rt values of WGD pairs. For a given WGD pair, the expression levels and fitness levels of both genes are plotted individually in the corresponding rt value for their containing pair.

Mentions: Further, we correlated divergence at the sequence level with gene expression and fitness levels. For gene expression levels, we used the data from Spellman et al. (1998) and (Tsankov et al. (2010). These data are obtained by different groups using different experimental methods, and we apply our analysis to both data sets to validate our results. For gene fitness levels, the data are obtained from Giaever et al. (2002), who use five different media under 31 different conditions. We used the normal conditions (condition 18 and 19 in Giaever et al.2002) and computed the average fitness values in the five media. Plots of rt values vs. expression and fitness levels of WGD pairs are given in Figure 4.


Evolution after whole-genome duplication: a network perspective.

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

(Left) Expression levels and (right) fitness levels of single genes as a function of the rt values of WGD pairs. For a given WGD pair, the expression levels and fitness levels of both genes are plotted individually in the corresponding rt value for their containing pair.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig4: (Left) Expression levels and (right) fitness levels of single genes as a function of the rt values of WGD pairs. For a given WGD pair, the expression levels and fitness levels of both genes are plotted individually in the corresponding rt value for their containing pair.
Mentions: Further, we correlated divergence at the sequence level with gene expression and fitness levels. For gene expression levels, we used the data from Spellman et al. (1998) and (Tsankov et al. (2010). These data are obtained by different groups using different experimental methods, and we apply our analysis to both data sets to validate our results. For gene fitness levels, the data are obtained from Giaever et al. (2002), who use five different media under 31 different conditions. We used the normal conditions (condition 18 and 19 in Giaever et al.2002) and computed the average fitness values in the five media. Plots of rt values vs. expression and fitness levels of WGD pairs are given in Figure 4.

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