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Andermann T, Torres Jiménez MF, Matos-Maraví P, Batista R, Blanco-Pastor JL, Gustafsson ALS, Kistler L, Liberal IM, Oxelman B, Bacon CD, Antonelli A. A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project. Front Genet 2020; 10:1407. [PMID: 32153629 PMCID: PMC7047930 DOI: 10.3389/fgene.2019.01407] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/24/2019] [Indexed: 12/17/2022] Open
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 effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. 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. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies.
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Affiliation(s)
- Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Maria Fernanda Torres Jiménez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Romina Batista
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, PPG GCBEv–Instituto Nacional de Pesquisas da Amazônia—INPA Campus II, Manaus, Brazil
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, Brazil
| | - José L. Blanco-Pastor
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
| | | | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Isabel M. Liberal
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Christine D. Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond-Surrey, United Kingdom
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