A Basic ddRADseq Two‐Enzyme Protocol Performs Well with Herbarium and Silica‐Dried Tissues across Four Genera

Authors

Ingrid E. Jordon‐Thaden, University of California Berkeley
James B. Beck, Wichita State University
Catherine A. Rushworth, University of California Davis
Michael D. Windham, Duke University
Nick Diaz, Portland State University
Jason T. Cantley, Bucknell University
Christopher T. Martine, Bucknell University
Carl J. Rothfels, University of California Berkeley

Sponsor

Support included a WSU ARCS award (to J.B.B.), a K-INBRE Bioinformatics Core Facility Award (P20 GM103418) (J.B.B.), a National Science Foundation Award (DEB-1556323) (J.B.B.), a David Burpee Endowment (C.T.M. and I.E.J.T.), backers of Experiment.com (I.E.J.T.), and the Heckard Fund of the Jepson Herbarium (I.E.J.T.).

Published In

Applications in Plant Sciences

Document Type

Article

Publication Date

1-2020

Subjects

DNA sequencing -- Research

Abstract

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 herbariumbased ddRADseq projects that minimize the expenses associated with fieldwork and sample evaluation.

Rights

© 2020 Jordon‐Thaden et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America

This work is licensed under a Creative Commons Attribution 4.0 International License.

Locate the Document

https://doi.org/10.1002/aps3.11344

DOI

10.1002/aps3.11344

Persistent Identifier

https://archives.pdx.edu/ds/psu/32830

Citation Details

Jordon‐Thaden, I. E., Beck, J. B., Rushworth, C. A., Windham, M. D., Diaz, N., Cantley, J. T., ... & Rothfels, C. J. (2020). A basic dd RAD seq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera. Applications in Plant Sciences, e11344.