Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses

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dc.contributor.author Woods, Shane
dc.contributor.author Coghlan, Avril
dc.contributor.author Rivers, David
dc.contributor.author Warnecke, Tobias
dc.contributor.author Jeffries, Sean J.
dc.contributor.author Kwon, Taejoon
dc.contributor.author Rogers, Anthony
dc.contributor.author Hurst, Laurence D.
dc.contributor.author Ahringer, Julie
dc.date.accessioned 2016-02-17T11:46:18Z
dc.date.available 2016-02-17T11:46:18Z
dc.date.issued 2013
dc.identifier.citation Woods S, Coghlan A, Rivers D, Warnecke T, Jeffries SJ, Kwon T, et al. (2013) Duplication and Retention Biases of Essential and Non-Essential Genes Revealed by Systematic Knockdown Analyses. PLoS Genet 9(5): e1003330. doi:10.1371/journal.pgen.1003330 en
dc.identifier.volume 9 en
dc.identifier.issued 5 en
dc.identifier.issn 1553-7390
dc.identifier.uri http://hdl.handle.net/10468/2381
dc.identifier.doi 10.1371/journal.pgen.1003330
dc.description.abstract When a duplicate gene has no apparent loss-of-function phenotype, it is commonly considered that the phenotype has been masked as a result of functional redundancy with the remaining paralog. This is supported by indirect evidence showing that multi-copy genes show loss-of-function phenotypes less often than single-copy genes and by direct tests of phenotype masking using select gene sets. Here we take a systematic genome-wide RNA interference approach to assess phenotype masking in paralog pairs in the Caenorhabditis elegans genome. Remarkably, in contrast to expectations, we find that phenotype masking makes only a minor contribution to the low knockdown phenotype rate for duplicate genes. Instead, we find that non-essential genes are highly over-represented among duplicates, leading to a low observed loss-of-function phenotype rate. We further find that duplicate pairs derived from essential and non-essential genes have contrasting evolutionary dynamics: whereas non-essential genes are both more often successfully duplicated (fixed) and lost, essential genes are less often duplicated but upon successful duplication are maintained over longer periods. We expect the fundamental evolutionary duplication dynamics presented here to be broadly applicable. en
dc.description.sponsorship Gates Cambridge Scholarship; Royal Society Wolfson Research Merit Award; Wellcome Trust Senior Research Fellowship (054523); Wellcome Trust; Wissenschaftskolleg zu Berlin; MRC; NIH National Center for Research Resources (NCRR) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Public Library of Science en
dc.rights © 2013 Woods et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited en
dc.rights.uri http://creativecommons.org/licenses/by/4.0/ en
dc.subject C. elegans chromosome-I en
dc.subject Caenorhabditis elegans en
dc.subject RNA interference en
dc.subject Phylogenetic trees en
dc.subject Copy number en
dc.subject C. elegans en
dc.subject Yeast en
dc.subject Redundancy en
dc.subject Evolution en
dc.subject Families en
dc.title Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Avril Coghlan, Microbiology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: a.coghlan@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.internal.wokid WOS:000320030000001
dc.contributor.funder Gates Cambridge Scholarship programme en
dc.contributor.funder Royal Society, United Kingdom en
dc.contributor.funder Wellcome Trust, United Kingdom en
dc.contributor.funder Wissenschaftskolleg zu Berlin de
dc.contributor.funder National Institutes of Health, United States en
dc.description.status Peer reviewed en
dc.identifier.journaltitle PLOS GENETICS en
dc.internal.IRISemailaddress a.coghlan@ucc.ie en
dc.identifier.articleid UNSP e1003330


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© 2013 Woods et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Except where otherwise noted, this item's license is described as © 2013 Woods et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
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