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

Jordon-Thaden, Ingrid, University of Wisconsin-Madison, https://orcid.org/0000-0001-6225-6034

Beck, James, Wichita State University

Rushworth, Catherine, University of California, Davis

Windham, Michael, Duke University

Diaz, Nicolas, Bucknell University

Cantley, Jason, San Francisco State University

Martine, Chris, Bucknell University

Rothfels, Carl, University of California, Berkeley

jordonthaden@wisc.edu, james.beck@wichita.edu, crushworth@ucdavis.edu, mdw26@duke.edu, nicdiaz@pdx.edu, cantley@sfsu.edu, ctm015@bucknell.edu, crothfels@berkeley.edu

Published Apr 23, 2020 on Dryad. https://doi.org/10.5061/dryad.rbnzs7h80

Cite this dataset

Jordon-Thaden, Ingrid et al. (2020). A basic ddRADseq two-enzyme protocol performs well in herbarium and silica-dried tissues across four genera [Dataset]. Dryad. https://doi.org/10.5061/dryad.rbnzs7h80

Abstract

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.

Funding

WSU ARCS award

K-INBRE Bioinformatics Core Facility Award, Award: P20 GM103418

National Science Foundation, Award: DEB-1556323

David Burpee Endowment

Heckard Fund of the Jepson Herbarium

WSU ARCS award

K-INBRE Bioinformatics Core Facility Award, Award: P20 GM103418

David Burpee Endowment

Heckard Fund of the Jepson Herbarium