Fragmentation of contaminant and endogenous dna in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics
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- dc.contributor.author García Garcerà, Marcca
- dc.contributor.author Gigli, Elena, 1978-ca
- dc.contributor.author Sánchez Quinto, Federico A, 1985-ca
- dc.contributor.author Ramírez, Oscarca
- dc.contributor.author Calafell i Majó, Francescca
- dc.contributor.author Civit, Sergica
- dc.contributor.author Lalueza Fox, Carles, 1965-ca
- dc.date.accessioned 2015-05-04T07:42:54Z
- dc.date.available 2015-05-04T07:42:54Z
- dc.date.issued 2011ca
- dc.description.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 sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. Methodology/Principals Findings: To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus) that was treated with a depurinating agent (bleach), an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain), and a Neandertal sample from the El Sidrón site (Asturias, Spain). The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively), that we positively know are contaminants. Conclusions: We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5′ and 3′ ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.en
- dc.description.sponsorship CL-F, OR and SC are supported by a grant from the Ministerio de Innovación y Ciencia from Spain (BFU2009-06974). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscripten
- dc.format.mimetype application/pdfca
- dc.identifier.citation García-Garcerà M, Gigli E, Sánchez-Quinto F, Ramirez O, Calafell F, Civit S, Lalueza-Fox C. Fragmentation of contaminant and endogenous dna in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics. PLoS ONE. 2011;6(8):e24161. DOI: 10.1371/journal.pone.0024161ca
- dc.identifier.doi http://dx.doi.org/10.1371/journal.pone.0024161
- dc.identifier.issn 1932-6203ca
- dc.identifier.uri http://hdl.handle.net/10230/23509
- dc.language.iso engca
- dc.publisher Public Library of Science (PLoS)ca
- dc.relation.ispartof PLoS ONE. 2011;6(8):e24161
- dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2009-06974
- dc.rights © 2011 García-Garcerà et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedca
- dc.rights.accessRights info:eu-repo/semantics/openAccessca
- dc.subject.other Genètica animalca
- dc.subject.other ADN fòssilca
- dc.title Fragmentation of contaminant and endogenous dna in ancient samples determined by shotgun sequencing; prospects for human palaeogenomicsen
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionca