Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants

• Published in: Applications in plant sciences Vol. 8; no. 4; pp. e11337 - n/a
• Main Authors: Hale, Haley, Gardner, Elliot M., Viruel, Juan, Pokorny, Lisa, Johnson, Matthew G.
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.04.2020; John Wiley and Sons Inc; Wiley
• Subjects: Automation; Cost control; Deoxyribonucleic acid; DNA; DNA sequencing; enzymatic fragmentation; genes; Genomics; herbaria; herbariomics; high‐throughput workflow implementation; Hyb‐Seq; Laboratories; low‐cost sequence capture; metagenomics; Methods; Nitrogen; Phylogeny; Plant sciences; pooling and multiplexing strategies; Quality; Review; California; United States > US; Germany; New Jersey; herbariomics; low‐cost sequence capture; high‐throughput workflow implementation; Hyb‐Seq; pooling and multiplexing strategies; enzymatic fragmentation
• ISSN: 2168-0450; 2168-0450
• DOI: 10.1002/aps3.11337

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.