Table_1_A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.xlsx

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.

高吞吐量 DNA 测序技术使得对基因组较大片段进行快速且经济的测序成为可能。在众多系统发育研究中，研究者们不再致力于整个基因组的测序与注释，而是聚焦于大量预先选定的位点进行测序，此举不仅进一步降低了成本和生物信息学挑战，同时提升了测序覆盖率。在测序前对位点进行富集的常见方法通常被称为靶向序列捕获。该技术已被证明适用于广泛进化深度的系统发育研究。此外，它已证实能够产生强大的、大规模多位点 DNA 序列数据集，非常适合进行系统发育分析。然而，靶向捕获需要仔细考虑，这可能会极大地影响实验的成功率。在此，我们提供了一个简单的流程图，用于设计系统发育学靶向捕获实验。我们讨论了从目标位点的识别到序列数据的最终生物信息学处理的必要决策。我们概述了与靶向捕获项目分类学范围、样本质量和可用基因组资源相关的问题及解决方案。我们希望这篇综述能为设计和实施成功的系统发育学靶向捕获研究提供一份实用的路线图。