Simple Structural Differences between Coding and Noncoding DNA 英文参考文献.docVIP

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Simple Structural Differences between Coding and Noncoding DNA 英文参考文献.doc

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Simple Structural Differences between Coding and Noncoding DNA 英文参考文献

SimpleStructuralDifferencesbetweenCodingand NoncodingDNA KennethJ.Locey1*,EthanP.White1,2 1DepartmentofBiology,UtahStateUniversity,Logan,Utah,UnitedStatesofAmerica,2TheEcologyCenter,UtahStateUniversity,Logan,Utah,UnitedStatesofAmerica Abstract Background: The study of large-scale genome structure has revealed patterns suggesting the influence of evolutionary constraintsongenomeevolution.However,theresultsofthesestudiescanbedifficulttointerpretduetotheconceptual complexity of the analyses. This makes it difficult to understand how observed statistical patterns relate to the physical distributionofgenomicelements.Weuseasimplerandmoreintuitiveapproachtoevaluatepatternsofgenomestructure. Methodology/Principal Findings: We used randomization tests based on Morisita’s Index of aggregation to examine average differences in the distribution of purines and pyrimidines among coding and noncoding regions of 261 chromosomesfrom223microbialgenomesrepresenting21phylumlevelgroups.Purinesandpyrimidineswereaggregated inthenoncodingDNAof86%ofgenomes,butwereonlyaggregatedinthecodingregionsof52%ofgenomes.Codingand noncodingDNAdifferedinaggregationin94%ofgenomes.Noncodingregionsweremoreaggregatedthancodingregions in91%ofthesegenomes.Genomelengthappearstolimitaggregation,butchromosomelengthdoesnot.Chromosomes from the same species are similarly aggregated despite substantial differences in length. Aggregation differed among taxonomic groups, revealing support for a previously reported pattern relating genome structure to environmental conditions. Conclusions/Significance: Our approach revealed several patterns of genome structure among different types of DNA, different chromosomes of the same genome, and among different taxonomic groups. Similarity in aggregation among chromosomesofvaryinglengthfromthesamegenomesuggeststhatindividualchromosomestructurehasnotevolved independentlyofthegeneralconstraintsongenomestructureasawhole.Thesepatternsweredetectedusingsimpleand readilyinterpretable