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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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(A) Distribution of rt of WGD pairs with normal curve fitting (mean = 0.3268, SD = 0.1685). (B) Distribution of proportion of sequence identity for WGD pairs and pairs of other paralogs. Because the duplication time of “other paralogs” pairs is unknown, we do not use rt here.
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fig1: (A) Distribution of rt of WGD pairs with normal curve fitting (mean = 0.3268, SD = 0.1685). (B) Distribution of proportion of sequence identity for WGD pairs and pairs of other paralogs. Because the duplication time of “other paralogs” pairs is unknown, we do not use rt here.

Mentions: As we set out to use a set of whole-genome duplication pairs, or WGD pairs for short, we first inspected the variability across WGD pairs in terms of sequence divergence, mutation rates, and other properties. Consider two sequences that have diverged for time t, and let r be the mutation rate per site. Further, assume that the observed normalized distance between the two sequences is p (that is, p is the proportion of sites at which the two sequences differ). Assuming equality of substitution rates among sites and equal amino acid frequencies, we have the relationship (Nei and Kumar 2000)(1−p)=e−2rt.For S. cerevisiae WGD pairs, t is estimated to be approximately 100 million years (Wolfe and Shields 1997). Given that we can compute p from the WGD pairs, we can compute the mutation rate r for each pair of WGD gene sequences asr=−ln(1−p)/(2∗t).Because t is the same for all WGD gene pairs, in this work we will compute rt instead:rt=−ln(1−p)/2.(1)The distribution of rt values of WGD pairs is given in Figure 1.


Evolution after whole-genome duplication: a network perspective.

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

(A) Distribution of rt of WGD pairs with normal curve fitting (mean = 0.3268, SD = 0.1685). (B) Distribution of proportion of sequence identity for WGD pairs and pairs of other paralogs. Because the duplication time of “other paralogs” pairs is unknown, we do not use rt here.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig1: (A) Distribution of rt of WGD pairs with normal curve fitting (mean = 0.3268, SD = 0.1685). (B) Distribution of proportion of sequence identity for WGD pairs and pairs of other paralogs. Because the duplication time of “other paralogs” pairs is unknown, we do not use rt here.
Mentions: As we set out to use a set of whole-genome duplication pairs, or WGD pairs for short, we first inspected the variability across WGD pairs in terms of sequence divergence, mutation rates, and other properties. Consider two sequences that have diverged for time t, and let r be the mutation rate per site. Further, assume that the observed normalized distance between the two sequences is p (that is, p is the proportion of sites at which the two sequences differ). Assuming equality of substitution rates among sites and equal amino acid frequencies, we have the relationship (Nei and Kumar 2000)(1−p)=e−2rt.For S. cerevisiae WGD pairs, t is estimated to be approximately 100 million years (Wolfe and Shields 1997). Given that we can compute p from the WGD pairs, we can compute the mutation rate r for each pair of WGD gene sequences asr=−ln(1−p)/(2∗t).Because t is the same for all WGD gene pairs, in this work we will compute rt instead:rt=−ln(1−p)/2.(1)The distribution of rt values of WGD pairs is given in Figure 1.

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