Duplication and Gene Conversion in the Drosophila melanogaster Genome 英文参考文献.docVIP

DuplicationandGeneConversionintheDrosophila melanogasterGenome NaokiOsada1,2,HidekiInnan1,2 * 1NationalInstituteofBiomedicalInnovation,Osaka,Japan,2GraduateUniversityforAdvancedStudies,Hayama,Japan Abstract UsingthegenomicsequencesofDrosophilamelanogastersubgroup,thepatternofgeneduplicationswasinvestigatedwith special attention to interlocus gene conversion. Our fine-scale analysis with careful visual inspections enabled accurate identificationofanumberofduplicatedblocks(genomicregions).Theorthologouspartsofthoseduplicatedblockswere alsoidentifiedintheD.simulansandD.sechelliagenomes,bywhichwewereabletoclearlyclassifytheduplicatedblocks into post- and pre-speciation blocks. We found 31 post-speciation duplicated genes, from which the rate of gene duplication(fromonecopytotwocopies)isestimatedtobe1.061029persingle-copygeneperyear.Theroleofinterlocus gene conversion was observed in several respects in our data: (1) synonymous divergence between a duplicated pair is overallverylow.Consequently,thegeneduplicationratewouldbeseriouslyoverestimatedbycountingduplicatedgenes withlowdivergence;(2)thesizesofyoungduplicatedblocksaregenerallylarge.Wepostulatethatthedegenerationof gene conversion around the edges could explain the shrinkage of ‘‘identifiable’’ duplicated regions; and (3) elevated paralogous divergence is observed around the edges in many duplicated blocks, supporting our gene conversion– degeneration model. Our analysis demonstrated that gene conversion between duplicated regions is a common and genome-widephenomenonintheDrosophilagenomes,andthatitsroleshouldbeespeciallysignificantintheearlystages of duplicated genes. Based on a population genetic prediction, we applied a new genome-scan method to test for signaturesofselectionforneofunctionalizationandfoundastrongsignatureinapairoftransportergenes. Citation: Osada N, Innan H (2008) Duplication and Gene Conversion in the Drosophila melanogaster Genome. PLoS Genet 4(12): e1000305. doi:10.1371/ journal.pgen.100030