Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits

Belén Jiménez-Mena; Hugo Flávio; Romina Henriques; Alice Manuzzi; Miguel Ramos; Dorte Meldrup; Janette Edson; Snæbjörn Pálsson; Guðbjörg Ásta Ólafsdóttir; Jennifer R. Ovenden; Einar Eg Nielsen

doi:10.1111/1755-0998.13598

Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits

Belén Jiménez-Mena, Hugo Flávio, Romina Henriques, Alice Manuzzi, Miguel Ramos, Dorte Meldrup, Janette Edson, Snæbjörn Pálsson, Guðbjörg Ásta Ólafsdóttir, Jennifer R. Ovenden, Einar Eg Nielsen

University of Iceland

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English
Pages (from-to)	2105-2119
Number of pages	15
Journal	Molecular Ecology Resources
Volume	22
Issue number	5
DOIs	https://doi.org/10.1111/1755-0998.13598
Publication status	Published - 18 Feb 2022

Bibliographical note

Funding Information: We thank Maj‐Britt Jacobsen, Britta Sønderskov Pedersen, Trine Rohde and Daniel Grundtvig Rosenstand Thomsen for their work at the laboratory processing the samples for the different studies, as well as James Henty Williams, Carl Hutter and two anonymous reviewers for useful comments on the manuscript. We thank Dominic Swift for access to the tiger shark transcriptome. We also thank Alison Devault and Brian Brunelle from Arbor Biosciences for clarifications on the MYBaits workflow and bait design. Figure 3c was created using a script developed by Stephen Turner ( https://gettinggeneticsdone.blogspot.com/2014/03/visualize‐coverage‐exome‐targeted‐ngs‐bedtools.html ). GENOJAWS was funded by the Australian Research Grant (DP170102043) and The Danish Council for Independent Research Grant DFF (6108‐00583). SDPAS project was funded by Innovationsfonden. CodStory was funded by the Icelandic Research Fund. Publisher Copyright: © 2022 DTU. Molecular Ecology Resources published by John Wiley & Sons Ltd.

Other keywords

Animals
DNA/genetics
Genetics, Population
Genomics/methods
High-Throughput Nucleotide Sequencing/methods
Hunting
R-package
Sequence Analysis, DNA/methods
ancient DNA
baits
capture sequencing
genomics
population genetics

Access to Document

10.1111/1755-0998.13598

Cite this

Jiménez-Mena, B., Flávio, H., Henriques, R., Manuzzi, A., Ramos, M., Meldrup, D., Edson, J., Pálsson, S., Ásta Ólafsdóttir, G., Ovenden, J. R., & Nielsen, E. E. (2022). Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits. Molecular Ecology Resources, 22(5), 2105-2119. https://doi.org/10.1111/1755-0998.13598

@article{b4eb2739f9214adc9bfb3481f92650a4,

title = "Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits",

abstract = "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.",

keywords = "Animals, DNA/genetics, Genetics, Population, Genomics/methods, High-Throughput Nucleotide Sequencing/methods, Hunting, R-package, Sequence Analysis, DNA/methods, ancient DNA, baits, capture sequencing, genomics, population genetics",

author = "Bel{\'e}n Jim{\'e}nez-Mena and Hugo Fl{\'a}vio and Romina Henriques and Alice Manuzzi and Miguel Ramos and Dorte Meldrup and Janette Edson and Sn{\ae}bj{\"o}rn P{\'a}lsson and \{{\'A}sta {\'O}lafsd{\'o}ttir\}, Gu{\dh}bj{\"o}rg and Ovenden, \{Jennifer R.\} and Nielsen, \{Einar Eg\}",

note = "Funding Information: We thank Maj‐Britt Jacobsen, Britta S{\o}nderskov Pedersen, Trine Rohde and Daniel Grundtvig Rosenstand Thomsen for their work at the laboratory processing the samples for the different studies, as well as James Henty Williams, Carl Hutter and two anonymous reviewers for useful comments on the manuscript. We thank Dominic Swift for access to the tiger shark transcriptome. We also thank Alison Devault and Brian Brunelle from Arbor Biosciences for clarifications on the MYBaits workflow and bait design. Figure 3c was created using a script developed by Stephen Turner ( https://gettinggeneticsdone.blogspot.com/2014/03/visualize‐coverage‐exome‐targeted‐ngs‐bedtools.html ). GENOJAWS was funded by the Australian Research Grant (DP170102043) and The Danish Council for Independent Research Grant DFF (6108‐00583). SDPAS project was funded by Innovationsfonden. CodStory was funded by the Icelandic Research Fund. Publisher Copyright: {\textcopyright} 2022 DTU. Molecular Ecology Resources published by John Wiley \& Sons Ltd.",

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doi = "10.1111/1755-0998.13598",

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Jiménez-Mena, B, Flávio, H, Henriques, R, Manuzzi, A, Ramos, M, Meldrup, D, Edson, J, Pálsson, S , Ásta Ólafsdóttir, G, Ovenden, JR & Nielsen, EE 2022, 'Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits', Molecular Ecology Resources, vol. 22, no. 5, pp. 2105-2119. https://doi.org/10.1111/1755-0998.13598

TY - JOUR

T1 - Fishing for DNA? Designing baits for population genetics in target enrichment experiments

T2 - Guidelines, considerations and the new tool supeRbaits

AU - Jiménez-Mena, Belén

AU - Flávio, Hugo

AU - Henriques, Romina

AU - Manuzzi, Alice

AU - Ramos, Miguel

AU - Meldrup, Dorte

AU - Edson, Janette

AU - Pálsson, Snæbjörn

AU - Ásta Ólafsdóttir, Guðbjörg

AU - Ovenden, Jennifer R.

AU - Nielsen, Einar Eg

N1 - Funding Information: We thank Maj‐Britt Jacobsen, Britta Sønderskov Pedersen, Trine Rohde and Daniel Grundtvig Rosenstand Thomsen for their work at the laboratory processing the samples for the different studies, as well as James Henty Williams, Carl Hutter and two anonymous reviewers for useful comments on the manuscript. We thank Dominic Swift for access to the tiger shark transcriptome. We also thank Alison Devault and Brian Brunelle from Arbor Biosciences for clarifications on the MYBaits workflow and bait design. Figure 3c was created using a script developed by Stephen Turner ( https://gettinggeneticsdone.blogspot.com/2014/03/visualize‐coverage‐exome‐targeted‐ngs‐bedtools.html ). GENOJAWS was funded by the Australian Research Grant (DP170102043) and The Danish Council for Independent Research Grant DFF (6108‐00583). SDPAS project was funded by Innovationsfonden. CodStory was funded by the Icelandic Research Fund. Publisher Copyright: © 2022 DTU. Molecular Ecology Resources published by John Wiley & Sons Ltd.

PY - 2022/2/18

Y1 - 2022/2/18

N2 - 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.

AB - 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.

KW - Animals

KW - DNA/genetics

KW - Genetics, Population

KW - Genomics/methods

KW - High-Throughput Nucleotide Sequencing/methods

KW - Hunting

KW - R-package

KW - Sequence Analysis, DNA/methods

KW - ancient DNA

KW - baits

KW - capture sequencing

KW - genomics

KW - population genetics

UR - https://www.scopus.com/pages/publications/85125542748

U2 - 10.1111/1755-0998.13598

DO - 10.1111/1755-0998.13598

M3 - Article

C2 - 35178874

SN - 1755-098X

VL - 22

SP - 2105

EP - 2119

JO - Molecular Ecology Resources

JF - Molecular Ecology Resources

IS - 5

ER -

Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits

Abstract

Bibliographical note

Other keywords

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Cite this