An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications 英文参考文献.docVIP

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An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications 英文参考文献.doc

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An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications 英文参考文献

AnAtlasoftheSpeedofCopyNumberChangesin AnimalGeneFamiliesandItsImplications DengPan1,LiqingZhang1,2* 1Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America, 2Program in Genetics, Bioinformatics, and Computational Biology, Blacksburg,Virginia,UnitedStatesofAmerica Abstract The notion that gene duplications generating new genes and functions is commonly accepted in evolutionary biology. However, this assumption is more speculative from theory rather than well proven in genome-wide studies. Here, we generatedanatlasoftherateofcopynumberchanges(CNCs)inallthegenefamiliesoftenanimalgenomes.Wegrouped thegenefamilieswithsimilarCNCdynamicsintoratepatterngroups(RPGs)andannotatedtheirfunctionusinganovel bottom-upapproach.BycomparingCNCratepatterns,weshowedthatmostofthespecies-specificCNCratesgroupsare formedbygeneduplicationratherthangeneloss,andmostofthechangesinratesofCNCsmaybetheresultofadaptive evolution.WealsofoundthatthefunctionsofmanyRPGsmatchtheirbiologicalsignificancewell.Ourworkconfirmedthe roleofgeneduplicationingeneratingnovelphenotypes,andtheresultscanserveasaguideforresearcherstoconnectthe phenotypicfeaturestocertaingeneduplications. Citation: Pan D, Zhang L (2009) An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications. PLoS ONE 4(10): e7342. doi:10.1371/journal.pone.0007342 Editor:PawelMichalak,UniversityofTexasArlington,UnitedStatesofAmerica ReceivedJune23,2009;AcceptedAugust28,2009;PublishedOctober23,2009 Copyright: ? 2009 Pan, Zhang. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:NSFgrantsIIS-0710945.Thefundershadnoroleinstudydesign,datacollectionandanalysis,decisiontopublish,orpreparationofthemanuscript. CompetingInterests:Theauthorshavedeclaredthatnocompetinginterestsexist. *E-mail:lqzhang@ Introduction