A guide to carrying out a phylogenomic target sequence capture project
A peer-reviewed article of this Preprint also exists.
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Abstract
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing efforts on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing sequencing depth. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth and has proven to produce powerful, large multi-locus DNA sequence datasets of selected loci, suitable for phylogenetic analyses. However, target capture requires careful theoretical and practical considerations, which will greatly affect the success of the experiment. Here we provide an easy-to-follow flowchart for adequately designing phylogenomic target capture experiments, and we discuss necessary considerations and decisions from the first steps in the lab to the final bioinformatic processing of the sequence data. We particularly discuss issues and challenges related to the taxonomic scope, sample quality, and available genomic resources of target capture projects and how these issues affect all steps from bait design to the bioinformatic processing of the data. Altogether this review outlines a roadmap for future target capture experiments and is intended to assist researchers with making informed decisions for designing and carrying out successful phylogenetic target capture studies
Cite this as
2019. A guide to carrying out a phylogenomic target sequence capture project. PeerJ Preprints 7:e27968v1 https://doi.org/10.7287/peerj.preprints.27968v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
Author comment
This manuscript provides an easy-to-follow workflow for adequately designing phylogenomic target capture experiments. We discuss issues and challenges related to target capture design, lab protocols, and data analysis.
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Competing Interests
The authors declare no conflicts of interest. In particular, we do not have any relation to any of the companies or their products listed here, and the opinions expressed in this review are based on our own experiences and interpretations.
Author Contributions
Tobias Andermann prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft, literature review.
Maria Fernanda Torres Jimenez prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft, literature review.
Pável Matos-Maraví authored or reviewed drafts of the paper, approved the final draft, literature review.
Romina Batista authored or reviewed drafts of the paper, approved the final draft.
José L Blanco-Pastor authored or reviewed drafts of the paper, approved the final draft.
A. Lovisa S Gustafsson authored or reviewed drafts of the paper, approved the final draft.
Logan Kistler authored or reviewed drafts of the paper, approved the final draft.
Isabel M Liberal authored or reviewed drafts of the paper, approved the final draft.
Bengt Oxelman authored or reviewed drafts of the paper, approved the final draft.
Christine D Bacon authored or reviewed drafts of the paper, approved the final draft.
Alexandre Antonelli authored or reviewed drafts of the paper, approved the final draft.
Data Deposition
The following information was supplied regarding data availability:
No data or code were generated for or during this project.
Funding
M.F.T. and C.D.B. were funded by the Swedish Research Council (2017-04980). PMM was funded by the European Union’s Horizon 2020 Programme under the Marie Skłodowska-Curie (MARIPOSAS-704035). R.B received a Doctoral Fellowship and a Fellowship for Internship abroad from Coordination for the Improvement of Higher Education Personnel (CAPES, Processo 99999.000566/2015-02). T.A. and A.A. were funded by a Wallenberg Academy Fellowship. A.A. was further funded by the Swedish Research Council (B0569601), the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013, ERC Grant Agreement n. 331024), and the Swedish Foundation for Strategic Research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.