Multiple Mechanisms Promote the Retained Expression of Gene Duplicates in the Tetraploid Frog Xenopus laevis 英文参考文献.docVIP

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Multiple Mechanisms Promote the Retained Expression of Gene Duplicates in the Tetraploid Frog Xenopus laevis 英文参考文献.doc

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Multiple Mechanisms Promote the Retained Expression of Gene Duplicates in the Tetraploid Frog Xenopus laevis 英文参考文献

MultipleMechanismsPromotetheRetained ExpressionofGeneDuplicates intheTetraploidFrogXenopuslaevis Fre′de′ricJ.J.Chain[,Ben J.Evans[* CenterforEnvironmentalGenomics,DepartmentofBiology,McMasterUniversity,Hamilton,Ontario,Canada Gene duplication provides a window of opportunity for biological variants to persist under the protection of a co- expressed copy with similar or redundant function. Duplication catalyzes innovation (neofunctionalization), subfunction degeneration (subfunctionalization), and genetic buffering (redundancy), and the genetic survival of each paralog is triggered by mechanisms that add, compromise, or do not alter protein function. We tested the applicabilityofthreetypesofmechanismsforpromotingtheretainedexpressionofduplicatedgenesin290expressed paralogsofthetetraploidclawedfrog,Xenopuslaevis.Testswerebasedonexplicitexpectationsconcerningtheka/ks ratio,andthenumberandlocationofnonsynonymoussubstitutionsafterduplication.Functionalconstraintsonthe majorityofparalogsarenotsignificantlydifferentfromasingletonortholog.However,werecoverstrongsupportthat some of them have an asymmetric rate of nonsynonymous substitution: 6% match predictions of the neo- functionalization hypothesis in that (1) each paralog accumulated nonsynonymous substitutions at a significantly differentrateand(2)theonethatevolvesfasterhasahigherka/ksratiothantheotherparalogandthanasingleton ortholog.Fewerparalogs(3%)exhibitacomplementarypatternofsubstitutionattheproteinlevelthatispredictedby enhancement or degradation of different functional domains, and the remaining 13% have a higher average ka/ks ratioinbothparalogsthatisconsistentwithalteredfunctionalconstraints,diversifyingselection,oractivity-reducing mutations after duplication. We estimate that these paralogs have been retained since they originated by genome duplicationbetween21and41millionyearsago.Multiplemechanismsoperatetopromotetheretainedexpressionof duplicates in the same genome, in genes in the same functional