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Adapterama IV: Sequence Capture of Dual-digest RADseq Libraries with Identifiable Duplicates (RADcap)

Sandra L. Hoffberg, Troy J. Kieran, Julian M. Catchen, Alison Devault, View ORCID ProfileBrant C. Faircloth, Rodney Mauricio, View ORCID ProfileTravis C Glenn
doi: https://doi.org/10.1101/044651
Sandra L. Hoffberg
1Department of Genetics, University of Georgia, Athens, GA 30602, USA
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  • For correspondence: sandra@hoffberg.org travisg@uga.edu
Troy J. Kieran
2Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
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Julian M. Catchen
3Department of Animal Biology, University of Illinois, Urbana, IL 61801, USA
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Alison Devault
4MycroArray, 5692 Plymouth Rd., Ann Arbor, MI 48105, USA
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Brant C. Faircloth
5Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
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Rodney Mauricio
1Department of Genetics, University of Georgia, Athens, GA 30602, USA
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Travis C Glenn
1Department of Genetics, University of Georgia, Athens, GA 30602, USA
2Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
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  • ORCID record for Travis C Glenn
  • For correspondence: sandra@hoffberg.org travisg@uga.edu
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Abstract

Molecular ecologists seek to genotype hundreds to thousands of loci from hundreds to thousands of individuals at minimal cost per sample. Current methods such as restriction site associated DNA sequencing (RADseq) and sequence capture are constrained by costs associated with inefficient use of sequencing data and sample preparation, respectively. Here, we demonstrate RADcap, an approach that combines the major benefits of RADseq (low cost with specific start positions) with those of sequence capture (repeatable sequencing of specific loci) to significantly increase efficiency and reduce costs relative to current approaches. The RADcap approach uses a new version of dual-digest RADseq (3RAD) to identify candidate SNP loci for capture bait design, and subsequently uses custom sequence capture baits to consistently enrich candidate SNP loci across many individuals. We combined this approach with a new library preparation method for identifying and removing PCR duplicates from 3RAD libraries, which allows researchers to process RADseq data using traditional pipelines, and we tested the RADcap method by genotyping sets of 96 to 384 Wisteria plants. Our results demonstrate that our RADcap method: 1) can methodologically reduce (to <5%) and computationally remove PCR duplicate reads from data; (2) achieves 80-90% reads-on-target in 11 of 12 enrichments; (3) returns consistent coverage (≥4x) across >90% of individuals at up to 99.9% of the targeted loci; (4) produces consistently high occupancy matrices of genotypes across hundreds of individuals; and (5) is inexpensive, with reagent and sequencing costs totaling <$6/sample and adapter and primer costs of only a few hundred dollars.

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Posted April 20, 2016.
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Adapterama IV: Sequence Capture of Dual-digest RADseq Libraries with Identifiable Duplicates (RADcap)
Sandra L. Hoffberg, Troy J. Kieran, Julian M. Catchen, Alison Devault, Brant C. Faircloth, Rodney Mauricio, Travis C Glenn
bioRxiv 044651; doi: https://doi.org/10.1101/044651
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Adapterama IV: Sequence Capture of Dual-digest RADseq Libraries with Identifiable Duplicates (RADcap)
Sandra L. Hoffberg, Troy J. Kieran, Julian M. Catchen, Alison Devault, Brant C. Faircloth, Rodney Mauricio, Travis C Glenn
bioRxiv 044651; doi: https://doi.org/10.1101/044651

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