Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments

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• dc.contributor.author Fontseré Alemany, Clàudia, 1992-
• dc.contributor.author Alvarez-Estape, Marina
• dc.contributor.author Kuhlwilm, Martin
• dc.contributor.author Marquès i Bonet, Tomàs, 1975-
• dc.contributor.author Lizano González, Esther, 1974-
• dc.date.accessioned 2022-01-27T07:48:18Z
• dc.date.issued 2021
• dc.description.abstract 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.
• dc.description.sponsorship 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).
• dc.format.mimetype application/pdf
• dc.identifier.citation 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
• dc.identifier.doi http://dx.doi.org/10.1111/1755-0998.13300
• dc.identifier.issn 1755-098X
• dc.identifier.uri http://hdl.handle.net/10230/52338
• dc.language.iso eng
• dc.publisher Wiley
• dc.relation.ispartof Mol Ecol Resour. 2021;21(3):745-61
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/864203
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017‐86471‐P
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/CGL2017‐82654‐P
• dc.rights This 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.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.subject.keyword Chimpanzees
• dc.subject.keyword Conservation genomics
• dc.subject.keyword Faecal samples
• dc.subject.keyword Molecular complexity
• dc.subject.keyword Noninvasive samples
• dc.subject.keyword Target capture
• dc.title Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/acceptedVersion