The reduced cost of high‐throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per‐sample cost, which can be inflated when using off‐the‐shelf kits or reagents not purchased in bulk. Here, we discuss methods to reduce per‐sample costs in high‐throughput targeted sequencing projects. We review the minimal equipment and consumable requirements for targeted sequencing while comparing several alternatives to reduce bulk costs in DNA extraction, library preparation, target enrichment, and sequencing. We consider how each of the workflow alterations may be affected by DNA quality (e.g., fresh vs. herbarium tissue), genome size, and the phylogenetic scale of the project. We provide a cost calculator for researchers considering targeted sequencing to use when designing projects, and identify challenges for future development of low‐cost sequencing in non‐model plant systems.

中文翻译：

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降低植物系统基因组学和群体基因组学目标捕获测序中每个样本成本的策略。


高通量测序成本的降低和具有广泛系统发育适用性的基因集的开发导致序列捕获方法的兴起，作为植物系统发育学和群体基因组学的合理平台。大型靶向测序项目的一个重要考虑因素是每个样本的成本，当使用现成的试剂盒或非批量购买的试剂时，每个样本的成本可能会增加。在这里，我们讨论降低高通量靶向测序项目中每个样本成本的方法。我们审查了靶向测序的最低设备和耗材要求，同时比较了几种替代方案，以降低 DNA 提取、文库制备、靶标富集和测序方面的批量成本。我们考虑每个工作流程的改变可能如何受到 DNA 质量（例如，新鲜组织与植物标本室组织）、基因组大小和项目系统发育规模的影响。我们为研究人员在设计项目时考虑使用靶向测序提供了一个成本计算器，并确定了非模型植物系统中低成本测序未来发展的挑战。