简介：DNAcompositiondynamicsacrossgenomesofdiversetaxonomyisamajorsubjectofgenomeanalyses.DNAcompositionchangesarecharacteristicsofbothreplicationandrepairmachineries.Weinvestigated3,611,007singlenucleotidepolymorphisms(SNPs)generatedbycomparingtwosequencedricegenomesfromdistantinbredlines(subspecies),includingthosefrom242,811intronsand45,462protein-codingsequences(CDSs).Neighboring-nucleotideeffects(NNEs)oftheseSNPsarediverse,dependingonstructuralcontent-basedclassifications(genomewide,intronic,andCDS)andsequencecontext-basedcategories(A/C,A/G,A/T,C/G,C/T,andG/Tsubstitutions)oftheanalyzedSNPs.StrongandevidentNNEsandnucleotideproportionbiasessurroundingtheanalyzedSNPswereobservedin1-3bpsequencesonbothsidesofanSNP.Strongbiaseswereobservedaroundneighboringnucleotidesofprotein-codingSNPs,whichexhibitaperiodicityofthreeinnucleotidecontent,constrainedbyacombinedeffectofcodon-relatedrulesandDNArepairmechanisms.Unlikeapreviousfindinginthehumangenome,wefoundnegativecorrelationbetweenGCcontentsofchromosomesandthemagnitudeofcorrespondingbiasofnucleotideCat-1siteandGat+1site.Theseresultswillfurtherourunderstandingofthemutationmechanisminriceaswellasitsevolutionaryimplications.