Meeting Abstract
The reduced cost of high-throughput targeted sequencing, along with new “universal” probe sets like Angiosperms353, means genomic-scale data is no longer limited to heavily funded laboratories. However, the feasibility of targeted sequencing for population genetics has not been fully explored. Here, we look at the costs and challenges of producing target-capture datasets from herbarium specimens to answer within-species questions in a variety of flowering plants. We describe best practices for choosing methods for DNA extraction, use of enzymatic fragmentation, high-throughput library preparation, and sequencing platform using the Angiosperms353 probe set for enrichment of hundreds of nuclear genes. Our dataset includes herbarium specimens from 24 angiosperm species collected during a survey of Guadalupe Mountains National Park between 1971 and 1974. The variety and age of the specimens brings their own challenges to large scale processing, especially DNA extraction due to the presence of different foliar or floral compounds as well as the diverse tissue composition used. Using Angiosperms353, we observed a 15-20% median enrichment efficiency and that 25000 reads on target was enough to recover over 200 genes. We also consistently recovered the same genes within species. In addition to the targeted genes, we successfully captured flanking noncoding regions, effectively doubling the amount of variable characters that have potential use for population level studies. By optimizing and generating a detailed protocol and cost calculator for sample processing, we offer a strategy for wide adoption of target capture sequencing for both phylogenetics and population genetics.
