Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster 英文参考文献.docVIP

SequencingofPooledDNASamples(Pool-Seq)Uncovers ComplexDynamicsofTransposableElementInsertions inDrosophilamelanogaster RobertKofler.,AndreaJ.Betancourt.,ChristianSchlo¨tterer* Institutfu¨rPopulationsgenetik,VetmeduniVienna,Wien,Austria Abstract Transposableelements(TEs)aremobilegeneticelementsthatparasitizegenomesbysemi-autonomouslyincreasingtheir own copy number within the host genome. While TEs are important for genome evolution, appropriate methods for performingunbiasedgenome-widesurveysofTEvariationinnaturalpopulationshavebeenlacking.Here,wedescribea novelandcost-effectiveapproachforestimatingpopulationfrequenciesofTEinsertionsusingpaired-endIlluminareads from a pooled population sample. Importantly, the method treats insertions present in and absent from the reference genomeidentically, allowingunbiased TEpopulation frequencyestimates.We applythismethodtodatafromanatural Drosophila melanogaster population from Portugal. Consistent with previous reports, we show that low recombining genomic regions harbor more TE insertions and maintain insertions at higher frequencies than do high recombining regions.Weconservativelyestimatethattherearealmosttwiceasmany‘‘novel’’TEinsertionsitesassitesknownfromthe referencesequenceinourpopulationsample(6,824novelversus3,639referencesites,withonaveragea31-foldcoverage per insertion site). Different families of transposable elements show large differences in their insertion densities and populationfrequencies.OuranalysessuggestthatthehistoryofTEactivitysignificantlycontributestothispattern,with recentlyactivefamiliessegregatingatlowerfrequenciesthanthoseactiveinthemoredistantpast.Finally,usingourhigh- resolutionTEabundancemeasurements,weidentified13candidatepositivelyselectedTEinsertionsbasedontheirhigh populationfrequenciesandonlowTajima’sDvaluesintheirneighborhoods. Citation: KoflerR, Betancourt AJ, Schlo¨tterer C(2012) Sequencing ofPooledDNA Samples (Pool-Seq) UncoversComplexDynamics ofTransposable Element InsertionsinDroso