Evolution After Whole-genome Duplication: A Network Perspective

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dc.citation.journalTitleG3: Genes, Genomes, Genetics Early Onlineen_US
dc.contributor.authorZhu, Yunen_US
dc.contributor.authorLin, Zhenguoen_US
dc.contributor.authorNakhleh, Luayen_US
dc.date.accessioned2013-09-25T17:19:03Zen_US
dc.date.available2013-09-25T17:19:03Zen_US
dc.date.issued2013en_US
dc.description.abstractGene 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 paper, 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 tness data. We nd 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, we nd that divergence of WGD pairs correlates strongly with gene expression and tness data. Owing to 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 nd 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 nd 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.en_US
dc.embargo.termsnoneen_US
dc.identifier.citationZhu, Yun, Lin, Zhenguo and Nakhleh, Luay. "Evolution After Whole-genome Duplication: A Network Perspective." <i>G3: Genes, Genomes, Genetics Early Online,</i> (2013) Genetics Society of America: http://dx.doi.org/10.1534/g3.113.008458.en_US
dc.identifier.doihttp://dx.doi.org/10.1534/g3.113.008458en_US
dc.identifier.urihttps://hdl.handle.net/1911/72111en_US
dc.language.isoengen_US
dc.publisherGenetics Society of Americaen_US
dc.rightsThis is an author's peer-reviewed final manuscript, as accepted by the publisher.en_US
dc.subject.keywordwhole-genome duplicationen_US
dc.subject.keywordprotein networksen_US
dc.subject.keywordyeasten_US
dc.subject.keywordduplication rateen_US
dc.titleEvolution After Whole-genome Duplication: A Network Perspectiveen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpost-printen_US
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