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Fishing for DNA? Designing baits for population genetics in target enrichment experiments: guidelines, considerations and the new tool supeRbaits
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  • Belen Jimenez Mena,
  • Hugo Flávio,
  • Romina Henriques,
  • Alice Manuzzi,
  • Miguel Ramos,
  • Dorte Meldrup,
  • Janette Edson,
  • Snaebjorn Palsson,
  • Guðbjörg Ásta Ólafsdóttir,
  • Jennifer Ovenden,
  • Einar Nielsen
Belen Jimenez Mena
Technical University of Denmark
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Hugo Flávio
Technical University of Denmark
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Romina Henriques
Technical University of Denmark
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Alice Manuzzi
Technical University of Denmark
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Miguel Ramos
University of Porto
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Dorte Meldrup
Technical University of Denmark
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Janette Edson
The University of Queensland
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Snaebjorn Palsson
University of Iceland
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Guðbjörg Ásta Ólafsdóttir
University of Iceland
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Jennifer Ovenden
The University of Queensland
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Einar Nielsen
Technical University of Denmark
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Abstract

Targeted sequencing is an increasingly popular Next Generation Sequencing (NGS) approach for studying populations, through 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 encompass our considerations and guidelines for bait design to benefit 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

Peer review status:UNDER REVIEW

25 Jun 2021Submitted to Molecular Ecology Resources
08 Jul 2021Assigned to Editor
08 Jul 2021Submission Checks Completed
12 Jul 2021Reviewer(s) Assigned