Andermann Tobias, Torres Jiménez Maria Fernanda, Matos-Maraví Pável, Batista Romina, Blanco-Pastor José L, Gustafsson A Lovisa S, Kistler Logan, Liberal Isabel M, Oxelman Bengt, Bacon Christine D, Antonelli Alexandre
Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.
Front Genet. 2020 Feb 21;10:1407. doi: 10.3389/fgene.2019.01407. eCollection 2019.
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.
高通量DNA测序技术能够实现对基因组大部分区域进行经济高效的测序。许多系统发育研究并非对整个基因组进行测序和注释，而是将测序工作集中在大量预先选择的基因座上，这在增加覆盖范围的同时进一步降低了成本和生物信息学挑战。一种在测序前富集基因座的常用方法通常被称为目标序列捕获。该技术已被证明适用于进化深度差异极大的系统发育研究。此外，它已被证明能产生适用于系统发育分析的强大的多位点DNA序列数据集。然而，目标捕获需要仔细考虑，这可能会极大地影响实验的成功率。在这里，我们提供了一个设计系统发育基因组目标捕获实验的简单流程图。我们讨论了从目标基因座的识别到序列数据最终生物信息学处理的必要决策。我们概述了与目标捕获项目的分类范围、样本质量和可用基因组资源相关的挑战及解决方案。我们希望这篇综述能为设计和开展成功的系统发育目标捕获研究提供有用的路线图。
