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

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