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A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

Journal article
Authors Tobias Andermann
Maria Fernanda Torres Jimenez
Pável Matos-Maraví
R. Batista
José Luis Blanco-Pastor
A. L. S. Gustafsson
L. Kistler
Isabel M. Liberal
Bengt Oxelman
Christine D. Bacon
Alexandre Antonelli
Published in Frontiers in Genetics
Volume 10
Pages 20
ISSN 1664-8021
Publication year 2020
Published at Department of Biological and Environmental Sciences
Pages 20
Language en
Keywords anchored enrichment, bait, high throughput sequencing, Hyb-Seq, Illumina, NGS, molecular phylogenetics, probe, DNA extraction methods, ultraconserved elements, genome sequence, software package, museum specimens, exon capture, enrichment, evolutionary, loci, hybridization, Genetics & Heredity
Subject categories Biological Sciences


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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