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

Premise of the study: The ability to sequence genome-scale data from herbarium specimens would allow for the economical development of broad datasets with taxonomic and geographic sampling not otherwise possible. Here we evaluate the utility of a basic restriction site-associated DNA (ddRADseq) protocol with DNAs from four genera extracted from both silica-dried and herbarium tissue.

Methods: DNAs from Draba, Boechera, Solidago, and Ilex were processed with a double-digest restriction-site associated DNA sequencing (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 datasets were obtained from the majority of the 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 RADseq projects that minimize expenses associated with fieldwork and sample evaluation.

Methods

DNAs from Draba, Boechera, Solidago, and Ilex were processed with a double-digest restriction-site associated DNA sequencing (ddRADseq) protocol. The effects of DNA degradation, taxon, and specimen age were assessed. Raw data was processed with PyRAD, PEAR, R, and Garli on CIPRES.