Atypical AT Skew in Firmicute Genomes Results from Selection and Not from Mutation 英文参考文献.docVIP

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Atypical AT Skew in Firmicute Genomes Results from Selection and Not from Mutation 英文参考文献.doc

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Atypical AT Skew in Firmicute Genomes Results from Selection and Not from Mutation 英文参考文献

AtypicalATSkewinFirmicuteGenomesResultsfrom SelectionandNotfromMutation CatherineA.Charneski1,FrankHonti1,2,JosephineM.Bryant1,3,LaurenceD.Hurst1.*,EdwardJ.Feil1. * 1DepartmentofBiologyandBiochemistry,UniversityofBath,Bath,UnitedKingdom,2MedicalResearchCouncilFunctionalGenomicsUnit,DepartmentofPhysiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom, 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom Abstract The second parity rule states that, if there is no bias in mutation or selection, then within each strand of DNA complementarybasesarepresentatapproximatelyequalfrequencies.Inbacteria,however,thereiscommonlyanexcessof G(overC)and,toalesserextent,T(overA)inthereplicatoryleadingstrand.ThelowG+CFirmicutes,suchasStaphylococcus aureus,areunusualindisplayinganexcessofAoverTontheleadingstrand.Asmutationhasbeenestablishedasamajor force in the generation of such skews across various bacterial taxa, this anomaly has been assumed to reflect unusual mutationbiasesinFirmicutegenomes.Hereweshowthatthisisnotthecaseandthatmutationbiasdoesnotexplainthe atypicalATskewseeninS.aureus.First,recentlyarisenintergenicSNPspredicttheclassicalreplication-derivedequilibrium enrichmentofTrelativetoA,contrarytowhatisobserved.Second,sitespredictedtobeunderweakpurifyingselection displayonlyweakATskew.Third,ATskewisprimarilyassociatedwithlargelynon-synonymousfirstandsecondcodonsites andisseenwithrespecttotheirsensedirection,notwhichreplicatingstrandtheylieon.TheatypicalATskewweshowto be a consequence of the strong bias for genes to be co-oriented with the replicating fork, coupled with the selective avoidanceofbothstopcodonsandcostlyaminoacids,whichtendtohaveT-richcodons.Thatintergenicsequencehas moreAthanT,whileatmutationalequilibriumapreponderanceofTisexpected,pointstoapossiblefurtherunresolved selectivesourceofskew. Citation:CharneskiCA,HontiF,BryantJM,HurstLD,FeilEJ(2011)AtypicalATSkewinFirmicuteGenomesResultsfromSelectionan