Dataset Information

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.

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.

SUBMITTER: Andermann T

PROVIDER: S-EPMC7047930 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.

Andermann Tobias T Torres Jiménez Maria Fernanda MF Matos-Maraví Pável P Batista Romina R Blanco-Pastor José L JL Gustafsson A Lovisa S ALS Kistler Logan L Liberal Isabel M IM Oxelman Bengt B Bacon Christine D CD Antonelli Alexandre A

Frontiers in genetics 20200221

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 phyl ...[more]

PMID: 32153629

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Dataset Information

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.

Publications

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.

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