Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments

Noninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive...

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Detalles Bibliográficos
Autores: Fontseré Alemany, Clàudia, 1992-, Alvarez-Estape, Marina, Kuhlwilm, Martin, Marquès i Bonet, Tomàs, 1975-, Lizano González, Esther, 1974-
Tipo de recurso: artículo
Estado:Versión aceptada para publicación
Fecha de publicación:2021
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/52338
Acceso en línea:http://hdl.handle.net/10230/52338
http://dx.doi.org/10.1111/1755-0998.13300
Access Level:acceso abierto
Palabra clave:Chimpanzees
Conservation genomics
Faecal samples
Molecular complexity
Noninvasive samples
Target capture
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spelling Maximizing the acquisition of unique reads in noninvasive capture sequencing experimentsFontseré Alemany, Clàudia, 1992-Alvarez-Estape, MarinaKuhlwilm, MartinMarquès i Bonet, Tomàs, 1975-Lizano González, Esther, 1974-ChimpanzeesConservation genomicsFaecal samplesMolecular complexityNoninvasive samplesTarget captureNoninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive samples, such as faeces, but its sensitivity has not yet been extensively studied. Coping with faecal samples with an endogenous DNA content below 1% is a common problem when prior selection of samples from a large collection is not possible. However, samples classified as unfavourable for target capture sequencing might be the only representatives of unique specific geographical locations, or to answer the question of interest. To explore how library complexity may be increased without repeating DNA extractions and generating new libraries, in this study we captured the exome of 60 chimpanzees (Pan troglodytes) using faecal samples with very low proportions of endogenous content (<1%). Our results indicate that by performing additional hybridizations of the same libraries, the molecular complexity can be maintained to achieve higher coverage. Also, whenever possible, the starting DNA material for capture should be increased. Finally, we specifically calculated the sequencing effort needed to avoid exhausting the library complexity of enriched faecal samples with low endogenous DNA content. This study provides guidelines, schemes and tools for laboratories facing the challenges of working with noninvasive samples containing extremely low amounts of endogenous DNA.The Pan African Programme: The Cultured Chimpanzee (PanAf) is generously funded by the Max Planck Society, the Max Planck Society Innovation Fund and the Heinz L. Krekeler Foundation. E.L is supported by CGL2017-82654-P (MINECO/FEDER,UE). M.K. is supported by “la Caixa” Foundation (ID 100010434), fellowship code LCF/BQ/PR19/11700002. T.M.-B is supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 864203), BFU2017-86471-P (MINECO/FEDER, UE), “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018-000792-M), Howard Hughes International Early Career, Obra Social "La Caixa" and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880).Wiley20222021info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/52338http://dx.doi.org/10.1111/1755-0998.13300reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésMol Ecol Resour. 2021;21(3):745-61info:eu-repo/grantAgreement/EC/H2020/864203info:eu-repo/grantAgreement/ES/2PE/BFU2017‐86471‐Pinfo:eu-repo/grantAgreement/ES/2PE/CGL2017‐82654‐PThis is the peer reviewed version of the following article: Fontsere C, Alvarez-Estape M, Lester J, Arandjelovic M, Kuhlwilm M, Dieguez P et al. Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments. Mol Ecol Resour. 2021;21(3):745-61. DOI: 10.1111/1755-0998.13300, which has been published in final form at http://dx.doi.org/10.1111/1755-0998.13300. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.info:eu-repo/semantics/openAccessoai:recercat.cat:10230/523382026-05-29T05:05:01Z
dc.title.none.fl_str_mv Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments
title Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments
spellingShingle Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments
Fontseré Alemany, Clàudia, 1992-
Chimpanzees
Conservation genomics
Faecal samples
Molecular complexity
Noninvasive samples
Target capture
title_short Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments
title_full Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments
title_fullStr Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments
title_full_unstemmed Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments
title_sort Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments
dc.creator.none.fl_str_mv Fontseré Alemany, Clàudia, 1992-
Alvarez-Estape, Marina
Kuhlwilm, Martin
Marquès i Bonet, Tomàs, 1975-
Lizano González, Esther, 1974-
author Fontseré Alemany, Clàudia, 1992-
author_facet Fontseré Alemany, Clàudia, 1992-
Alvarez-Estape, Marina
Kuhlwilm, Martin
Marquès i Bonet, Tomàs, 1975-
Lizano González, Esther, 1974-
author_role author
author2 Alvarez-Estape, Marina
Kuhlwilm, Martin
Marquès i Bonet, Tomàs, 1975-
Lizano González, Esther, 1974-
author2_role author
author
author
author
dc.subject.none.fl_str_mv Chimpanzees
Conservation genomics
Faecal samples
Molecular complexity
Noninvasive samples
Target capture
topic Chimpanzees
Conservation genomics
Faecal samples
Molecular complexity
Noninvasive samples
Target capture
description Noninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive samples, such as faeces, but its sensitivity has not yet been extensively studied. Coping with faecal samples with an endogenous DNA content below 1% is a common problem when prior selection of samples from a large collection is not possible. However, samples classified as unfavourable for target capture sequencing might be the only representatives of unique specific geographical locations, or to answer the question of interest. To explore how library complexity may be increased without repeating DNA extractions and generating new libraries, in this study we captured the exome of 60 chimpanzees (Pan troglodytes) using faecal samples with very low proportions of endogenous content (<1%). Our results indicate that by performing additional hybridizations of the same libraries, the molecular complexity can be maintained to achieve higher coverage. Also, whenever possible, the starting DNA material for capture should be increased. Finally, we specifically calculated the sequencing effort needed to avoid exhausting the library complexity of enriched faecal samples with low endogenous DNA content. This study provides guidelines, schemes and tools for laboratories facing the challenges of working with noninvasive samples containing extremely low amounts of endogenous DNA.
publishDate 2021
dc.date.none.fl_str_mv 2021
2022
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/52338
http://dx.doi.org/10.1111/1755-0998.13300
url http://hdl.handle.net/10230/52338
http://dx.doi.org/10.1111/1755-0998.13300
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Mol Ecol Resour. 2021;21(3):745-61
info:eu-repo/grantAgreement/EC/H2020/864203
info:eu-repo/grantAgreement/ES/2PE/BFU2017‐86471‐P
info:eu-repo/grantAgreement/ES/2PE/CGL2017‐82654‐P
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 Wiley
publisher.none.fl_str_mv Wiley
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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