A basic ddRADseq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera

• Published in: Applications in plant sciences Vol. 8; no. 4; pp. e11344 - n/a
• Main Authors: Jordon‐Thaden, Ingrid E., Beck, James B., Rushworth, Catherine A., Windham, Michael D., Diaz, Nicolas, Cantley, Jason T., Martine, Christopher T., Rothfels, Carl J.
• Format: Journal Article
• Language: English
• Published: United States John Wiley and Sons Inc 01.04.2020; Wiley
• Subjects: Application; Boechera; double‐digest restriction site–associated DNA sequencing (ddRADseq); Draba; herbarium specimens; Ilex; Solidago; herbarium specimens; Draba; Boechera; Solidago; Ilex; double‐digest restriction site–associated DNA sequencing (ddRADseq)
• ISSN: 2168-0450; 2168-0450
• DOI: 10.1002/aps3.11344

Premise The ability to sequence genome‐scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double‐digest restriction site–associated DNA sequencing (ddRADseq) protocol using DNAs from four genera extracted from both silica‐dried and herbarium tissue. Methods DNAs from Draba, Boechera, Solidago, and Ilex were processed with a ddRADseq protocol. The effects of DNA degradation, taxon, and specimen age were assessed. Results Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were obtained from the majority of samples. Discussion These results suggest that herbarium samples can be incorporated into ddRADseq project designs, and that specimen age can be used as a rapid on‐site guide for sample choice. The detailed protocol we provide will allow users to pursue herbarium‐based ddRADseq projects that minimize the expenses associated with fieldwork and sample evaluation.