Eukaryotic Evolutionary Transitions Are Associated with Extreme Codon Bias in Functionally-Related Proteins 英文参考文献.docVIP

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Eukaryotic Evolutionary Transitions Are Associated with Extreme Codon Bias in Functionally-Related Proteins 英文参考文献.doc

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Eukaryotic Evolutionary Transitions Are Associated with Extreme Codon Bias in Functionally-Related Proteins 英文参考文献

EukaryoticEvolutionaryTransitionsAreAssociatedwith ExtremeCodonBiasinFunctionally-RelatedProteins NicholasJ.Hudson1*,QuanGu1,2,ShivashankarH.Nagaraj1,Yong-ShengDing2,BrianP.Dalrymple1, AntonioReverter1 1ComputationalandSystemsBiology,CSIRO LivestockIndustries,QueenslandBioscience Precinct,St.Lucia,Brisbane,Queensland,Australia, 2CollegeofInformation SciencesandTechnology,DonghuaUniversity,Shanghai,China Abstract Codon bias in the genome of an organism influences its phenome by changing the speed and efficiency of mRNA translation and hence protein abundance. We hypothesized that differences in codon bias, either between-species differencesinorthologousgenes,orwithin-speciesdifferencesbetweengenes,mayplayanevolutionaryrole.Toexplore thishypothesis,wecomparedthegenome-widecodonbiasinsixspeciesthatoccupyvitalpositionsintheEukaryoticTree ofLife.Weacquiredtheentireproteincodingsequencesfortheseorganisms,computedthecodonbiasforallgenesin each organism and explored the output for relationships between codon bias and protein function, both within- and between-lineages.Wediscoveredfivenotablecoordinatedpatterns,withextremecodonbiasmostpronouncedintraits considered highly characteristic of a given lineage. Firstly, the Homo sapiens genome had stronger codon bias for DNA- binding transcription factors than the Saccharomyces cerevisiae genome, whereas the opposite was true for ribosomal proteins–perhapsunderscoringtranscriptionalregulationintheoriginofcomplexity.Secondly,bothmammalianspecies examined possessed extreme codon bias in genes relating to hair – a tissue unique to mammals. Thirdly, Arabidopsis thalianashowedextremecodonbiasingenesimplicatedincellwallformationandchloroplastfunction–whichareunique to plants. Fourthly, Gallus gallus possessed strong codon bias in a subset of genes encoding mitochondrial proteins – perhapsreflectingtheenhancedbioenergeticefficiencyinbirdsthatco-evolvedwithflight.Andlastly,theG.gallusgenome hadextremecodonbiasfortheCiliaryNeurotr