Characterizing restriction enzyme‐associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom‐designed RNA probes

摘要: Population genetic studies of non-model organisms frequently employ reduced representation library (RRL) methodologies, many which rely on protocols in genomic DNA is digested by one or more restriction enzymes. However, because high molecular weight recommended for these protocols, samples with degraded are generally unsuitable RRL methods. Given that ancient and historic specimens can provide key temporal perspectives to evolutionary questions, we explored how custom-designed RNA probes could enrich loci (Restriction Enzyme-Associated Loci baits, REALbaits). Starting Genotyping-by-Sequencing (GBS) data generated modern common ragweed (Ambrosia artemisiifolia L.) specimens, designed 20,000 target well-characterized herbarium voucher dating from 1835–1913. Compared shotgun sequencing, observed enrichment the targeted at 19–151-fold. Using our GBS capture pipeline a dataset 38 samples, discovered 22,813 SNPs, providing sufficient resolution distinguish geographic populations. For found dilution REALbaits 10% their original concentration still yielded downstream analyses sequencing depth ~7M reads was characterize most without wasting capacity. In addition, had highly variable rates success, primarily attribute similarity between loci, trait ultimately interferes unambiguous read mapping. Our findings help researchers design experiments thereby an efficient means integrate into existing datasets. This article protected copyright. All rights reserved.