Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura.docVIP

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Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura.doc

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Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura

MacdonaldandLongGenomeBiology2006,7:R67 /2006/7/7/R67 RESEARCH OpenAccess Finescalestructuralvariantsdistinguishthe genomesofDrosophilamelanogasterand D.pseudoobscura StuartJMacdonald*andAnthonyDLong Abstract Background:Aprimaryobjectiveofcomparativegenomicsistoidentifygenomicelementsoffunctional significancethatcontributetophenotypicdiversity.Complexchangesingenomestructure(insertions,duplications, rearrangements,translocations)maybewidespread,andhaveimportanteffectsonorganismaldiversity.Anysurvey ofgenomicvariationisincompletewithoutanassessmentofstructuralchanges. Results:Were-examinethegenomesequencesofthedivergedspeciesDrosophilamelanogasterandD. pseudoobscuratoidentifyfine-scalestructuralfeaturesthatdistinguishthegenomes.Wedetect95largeinsertion/ deletioneventsthatoccurwithintheintronsoforthologousgenepairs,themajorityofwhichrepresentinsertion oftransposableelements.Wealsoidentify143microinversionsbelow5kbinsize.Thesemicroinversionsreside withinintronsorjustupstreamordownstreamofgenes,andinvertconservedDNAsequence.Thesequence conservationwithinmicroinversionssuggeststheymaybeenrichedforfunctionalgeneticelements,andtheir positionwithrespecttoknowngenesimplicatesthemintheregulationofgeneexpression.Althoughwefounda distinctpatternofGCcontentacrossmicroinversions,thiswasindistinguishablefromthepatternobservedacross blocksofconservednon-codingsequence. Conclusion:Drosophilahaslongbeenknownasagenusharboringavarietyoflargeinversionsthatdisrupt chromosomecolinearity.Herewedemonstratethatmicroinversions,manyofwhicharebelow1kbinlength, locatedin/neargenesmayalsobeanimportantsourceofgeneticvariationinDrosophila.Furtherexaminationof otherDrosophilagenomesequenceswilllikelyidentifyanarrayofnovelmicroinversionevents. Background large deletions segregating within the human genome Amajoraimofcomparativeandpopulationgenomicsis [5-8],polymorphicinversionsinhumans[5,9],aswellas toelucidatetheinter-andintraspecificgeneticvariation structural genome differences between