Examination of Genome Homogeneity in Prokaryotes Using Genomic Signatures 英文参考文献.docVIP

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Examination of Genome Homogeneity in Prokaryotes Using Genomic Signatures 英文参考文献.doc

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Examination of Genome Homogeneity in Prokaryotes Using Genomic Signatures 英文参考文献

ExaminationofGenomeHomogeneityinProkaryotes UsingGenomicSignatures JonBohlin*,EysteinSkjerve DepartmentofFoodSafetyandInfectionBiology,NorwegianSchoolofVeterinaryScience,Oslo,Norway Abstract Background: DNA word frequencies, normalized for genomic AT content, are remarkably stable within prokaryotic genomesandarethereforesaidtoreflecta‘‘genomicsignature.’’Thegenomicsignaturescanbeusedtophylogenetically classifyorganismsfromarbitrarysampledDNA.Genomicsignaturescanalsobeusedtosearchforhorizontallytransferred DNAorDNAregionssubjectedtospecialselectionforces.Thus,thestabilityofthegenomicsignaturecanbeusedasa measureofgenomichomogeneity.Thefactorsassociatedwiththestabilityofthegenomicsignaturesarenotknown,and this motivated us to investigate further. We analyzed the intra-genomic variance of genomic signatures based on AT contentnormalization(0thorderMarkovmodel)aswellasgenomicsignaturesnormalizedbysmallerDNAwords(1st and 2nd order Markov models) for 636 sequenced prokaryotic genomes. Regression models were fitted, with intra-genomic signature variance as the response variable, to a set of factors representing genomic properties such as genomic AT content, genome size, habitat, phylum, oxygen requirement, optimal growth temperature and oligonucleotide usage variance (OUV, a measure of oligonucleotide usage bias), measured as the variance between genomic tetranucleotide frequenciesandMarkovchainapproximatedtetranucleotidefrequencies,aspredictors. Principal Findings: Regression analysis revealed that OUV was the most important factor (p,0.001) determining intra- genomichomogeneityasmeasuredusinggenomicsignatures.Thismeansthatthelessrandomtheoligonucleotideusage isinthesenseofhigherOUV,themorehomogeneousthegenomeisintermsofthegenomicsignature.Theotherfactors influencingvarianceinthegenomicsignature(p,0.001)weregenomicATcontent,phylumandoxygenrequirement. Conclusions:GenomichomogeneityinprokaryotesisintimatelylinkedtogenomicGCcontent,oligonucleotideusagebias (OUV) and aero