Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits.
R-package
ancient DNA
baits
capture sequencing
genomics
population genetics
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Jul 2022
Jul 2022
Historique:
revised:
24
01
2022
received:
25
06
2021
accepted:
07
02
2022
pubmed:
19
2
2022
medline:
9
6
2022
entrez:
18
2
2022
Statut:
ppublish
Résumé
Targeted sequencing is an increasingly popular next-generation sequencing (NGS) approach for studying populations that involves focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three diverse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern samples. The workflow used for designing these three bait sets has been implemented in the R-package supeRbaits, which encompasses our considerations and guidelines for bait design for the benefit of researchers and practitioners. The supeRbaits R-package is user-friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: https://github.com/BelenJM/supeRbaits.
Identifiants
pubmed: 35178874
doi: 10.1111/1755-0998.13598
pmc: PMC9313901
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2105-2119Subventions
Organisme : The Icelandic Research Fund
ID : "CODSTORY"
Organisme : Innovationsfonden: Udvikling af den danske laksebestand - større populationer, genetiske ressourcer og rekreativt fiskeri"
ID : "SDPAS
Organisme : The Danish Council for Independent Research Grant DFF
ID : 6108-00583
Organisme : Australian Research Grant
ID : DP170102043
Informations de copyright
© 2022 DTU. Molecular Ecology Resources published by John Wiley & Sons Ltd.
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