Fragmentation of contaminant and endogenous dna in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics

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 th...

ver descrição completa

Detalhes bibliográficos
Autores: García Garcerà, Marc, Gigli, Elena, 1978-, Sánchez Quinto, Federico A, 1985-, Ramírez, Oscar, Calafell i Majó, Francesc, Civit, Sergi, Lalueza Fox, Carles, 1965-
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2011
País:España
Recursos:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/23509
Acesso em linha:http://hdl.handle.net/10230/23509
http://dx.doi.org/10.1371/journal.pone.0024161
Access Level:acceso abierto
Palavra-chave:Genètica animal
ADN fòssil
id ES_687ccc85b7f4c301e4487c67a5265d4e
oai_identifier_str oai:repositori.upf.edu:10230/23509
network_acronym_str ES
network_name_str España
repository_id_str
spelling Fragmentation of contaminant and endogenous dna in ancient samples determined by shotgun sequencing; prospects for human palaeogenomicsGarcía Garcerà, MarcGigli, Elena, 1978-Sánchez Quinto, Federico A, 1985-Ramírez, OscarCalafell i Majó, FrancescCivit, SergiLalueza Fox, Carles, 1965-Genètica animalADN fòssilBackground: 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.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 manuscriptPublic Library of Science (PLoS)201520152011info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/23509http://dx.doi.org/10.1371/journal.pone.0024161reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésPLoS ONE. 2011;6(8):e24161info:eu-repo/grantAgreement/ES/3PN/BFU2009-06974© 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 creditedinfo:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/235092026-06-12T07:21:37Z
dc.title.none.fl_str_mv Fragmentation of contaminant and endogenous dna in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics
title Fragmentation of contaminant and endogenous dna in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics
spellingShingle Fragmentation of contaminant and endogenous dna in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics
García Garcerà, Marc
Genètica animal
ADN fòssil
title_short Fragmentation of contaminant and endogenous dna in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics
title_full Fragmentation of contaminant and endogenous dna in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics
title_fullStr Fragmentation of contaminant and endogenous dna in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics
title_full_unstemmed Fragmentation of contaminant and endogenous dna in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics
title_sort Fragmentation of contaminant and endogenous dna in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics
dc.creator.none.fl_str_mv García Garcerà, Marc
Gigli, Elena, 1978-
Sánchez Quinto, Federico A, 1985-
Ramírez, Oscar
Calafell i Majó, Francesc
Civit, Sergi
Lalueza Fox, Carles, 1965-
author García Garcerà, Marc
author_facet García Garcerà, Marc
Gigli, Elena, 1978-
Sánchez Quinto, Federico A, 1985-
Ramírez, Oscar
Calafell i Majó, Francesc
Civit, Sergi
Lalueza Fox, Carles, 1965-
author_role author
author2 Gigli, Elena, 1978-
Sánchez Quinto, Federico A, 1985-
Ramírez, Oscar
Calafell i Majó, Francesc
Civit, Sergi
Lalueza Fox, Carles, 1965-
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Genètica animal
ADN fòssil
topic Genètica animal
ADN fòssil
description 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.
publishDate 2011
dc.date.none.fl_str_mv 2011
2015
2015
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/23509
http://dx.doi.org/10.1371/journal.pone.0024161
url http://hdl.handle.net/10230/23509
http://dx.doi.org/10.1371/journal.pone.0024161
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv PLoS ONE. 2011;6(8):e24161
info:eu-repo/grantAgreement/ES/3PN/BFU2009-06974
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science (PLoS)
publisher.none.fl_str_mv Public Library of Science (PLoS)
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869409963516887040
score 15,812455

Registos relacionados