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

Applications in Plant Sciences

Haley Hale¹  Matthew G. Johnson¹  Lisa Pokorny²  Juan Viruel²  Elliot M. Gardner³ 

[1] Department of Biological Sciences Texas Tech University Lubbock Texas 79409 USA;Royal Botanic Gardens Kew, Richmond Surrey TW9 3DS United Kingdom;The Morton Arboretum Lisle Illinois 60532 USA;

关键词: enzymatic fragmentation;    herbariomics;    high‐throughput workflow implementation;    Hyb‐Seq;    low‐cost sequence capture;    pooling and multiplexing strategies;   

DOI  :  10.1002/aps3.11337

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown