Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments.
chimpanzees
conservation genomics
faecal samples
molecular complexity
noninvasive samples
target capture
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Apr 2021
Apr 2021
Historique:
received:
10
03
2020
revised:
15
10
2020
accepted:
13
11
2020
pubmed:
21
11
2020
medline:
18
8
2021
entrez:
20
11
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 33217149
doi: 10.1111/1755-0998.13300
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
745-761Subventions
Organisme : H2020 European Research Council
ID : 864203
Organisme : FPI (Formación de Personal Investigador) Ministerio de Ciencia, Universidades e Investigación
ID : PRE2018-083966
Organisme : CERCA Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya
ID : GRC 2017 SGR 880
Organisme : Agencia Estatal de Investigación (AEI)
ID : "Unidad María de Maeztu"
Organisme : Secretaria d'Universitats i Recerca
Organisme : Howard Hughes International Early Career
Organisme : "La Caixa" doctoral fellowship program
Organisme : MINECO/FEDER, UE
ID : BFU2017-86471-P
Organisme : MINECO/FEDER, UE
ID : CGL2017-82654-P
Organisme : Heinz L. Krekeler Foundation
Organisme : Max Planck Society
Organisme : Obra Social "La Caixa"
Organisme : "La Caixa" Foundation
ID : 100010434
Organisme : Max Planck Society Innovation Fund
Informations de copyright
© 2020 John Wiley & Sons Ltd.
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