Fragmentation of Contaminant and Endogenous DNA in Ancient Samples Determined by Shotgun Sequencing; Prospects for Human Palaeogenomics 英文参考文献.docVIP

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Fragmentation of Contaminant and Endogenous DNA in Ancient Samples Determined by Shotgun Sequencing; Prospects for Human Palaeogenomics 英文参考文献.doc

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Fragmentation of Contaminant and Endogenous DNA in Ancient Samples Determined by Shotgun Sequencing; Prospects for Human Palaeogenomics 英文参考文献

FragmentationofContaminantandEndogenousDNAin AncientSamplesDeterminedbyShotgunSequencing; ProspectsforHumanPalaeogenomics MarcGarc?′a-Garcera`1.,ElenaGigli1.,FedericoSanchez-Quinto1,OscarRamirez1,FrancescCalafell1, SergiCivit2,CarlesLalueza-Fox1* 1InstitutdeBiologiaEvolutiva,CSIC-UPF,Barcelona,Spain,2DepartmentdeBioestad?′stica,UniversitatdeBarcelona,Barcelona,Spain Abstract Background: Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequencedatageneratedonhigh-throughputsequencingplatformsindicatethatfragmentationofancientDNAsequences isacharacteristictraitprimarilyarisingduetodepurinationprocessesthatcreateabasicsitesleadingtoDNAbreaks. Methodology/Principals Findings: To investigate whether this pattern is present in ancient remains from a temperate environment,wehave454-FLXpyrosequenceddifferentsamplesdatedbetween5,500and49,000yearsago:abonefrom an extinct goat (Myotragus balearicus) that was treated with a depurinating agent (bleach), an Iberian lynx bone not subjectedtoanytreatment,ahumanNeolithicsamplefromBarcelona(Spain),andaNeandertalsamplefromtheElSidro′n site(Asturias,Spain).Theefficiencyofretrievalofendogenoussequencesisbelow1%inallcases.Wehaveusedthenon- humansamplestoidentifyhumansequences(0.35and1.4%,respectively),thatwepositivelyknowarecontaminants. Conclusions: We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resultingcontaminantsequencesthatisindistinguishablefrompreviouslydescribedendogenoussequences.Furthermore, thenucleotidecompositionpatternobservedin59and39endsofcontaminantsequencesismuchmorecomplexthanthe flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminanthistoriesisneeded,ourresultssuggestthatendogenousandcontaminantsequencescannotbedistinguished bythefr