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

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.

Project(s)

Global Tree Seed Bank Project

Funder

Funder name	Awards
Texas Tech University College of Arts and Sciences
National Science Foundation, United States	NSF-DEB 1753800 - Postdoctoral Research Fellowship (1711391)
Garfield Weston Foundation, United States	Global Tree Seed Bank Project
Synthesys, European Union	NL-TAF-6894
H2020 Marie Skłodowska-Curie Actions, European Union	Individual Fellowship (704464–YAMNOMICS–MSCA-IF-EF-ST)
Royal Botanic Gardens, Kew, United Kingdom	Pilot study (YAMAGASY)