Journal
APPLICATIONS IN PLANT SCIENCES
Volume 8, Issue 4, Pages -Publisher
WILEY
DOI: 10.1002/aps3.11337
Keywords
enzymatic fragmentation; herbariomics; high-throughput workflow implementation; Hyb-Seq; low-cost sequence capture; pooling and multiplexing strategies
Categories
Funding
- Texas Tech University College of Arts and Sciences
- National Science Foundation [NSF-DEB 1753800]
- Garfield Weston Foundation (Global Tree Seed Bank Project)
- EU-SYNTHESYS [NL-TAF-6894]
- National Science Foundation Postdoctoral Research Fellowship [1711391]
- Marie SklodowskaCurie Individual Fellowship [704464-YAMNOMICS-MSCA-IFEF-ST]
- RBGK
- Direct For Biological Sciences
- Div Of Biological Infrastructure [1711391] Funding Source: National Science Foundation
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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.
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