TY - JOUR
T1 - Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants
AU - Hale, Haley
AU - Gardner, Elliot M.
AU - Viruel, Juan
AU - Pokorny, Lisa
AU - Johnson, Matthew G.
N1 - Publisher Copyright:
© 2020 Hale et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America
Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.
PY - 2020/4/1
Y1 - 2020/4/1
N2 - 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.
AB - 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.
KW - Hyb-Seq
KW - enzymatic fragmentation
KW - herbariomics
KW - high-throughput workflow implementation
KW - low-cost sequence capture
KW - pooling and multiplexing strategies
UR - http://www.scopus.com/inward/record.url?scp=85083446011&partnerID=8YFLogxK
U2 - 10.1002/aps3.11337
DO - 10.1002/aps3.11337
M3 - Review article
AN - SCOPUS:85083446011
VL - 8
JO - Applications in Plant Sciences
JF - Applications in Plant Sciences
SN - 2168-0450
IS - 4
M1 - e11337
ER -