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

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...

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Main Authors: Ingrid E. Jordon‐Thaden, James B. Beck, Catherine A. Rushworth, Michael D. Windham, Nicolas Diaz, Jason T. Cantley, Christopher T. Martine, Carl J. Rothfels
Format: Article
Language:English
Published: Wiley 2020-04-01
Series:Applications in Plant Sciences
Subjects:
Online Access:https://doi.org/10.1002/aps3.11344
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spelling doaj-01e686a1632e45d18df9859e5d5b88392020-11-25T03:49:29ZengWileyApplications in Plant Sciences2168-04502020-04-0184n/an/a10.1002/aps3.11344A basic ddRADseq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four generaIngrid E. Jordon‐Thaden0James B. Beck1Catherine A. Rushworth2Michael D. Windham3Nicolas Diaz4Jason T. Cantley5Christopher T. Martine6Carl J. Rothfels7University Herbaria and Department of Integrative Biology University of California Berkeley 3040 Valley Life Sciences Building Berkeley California 94720 USADepartment of Biological Sciences Wichita State University 1845 Fairmount Wichita Kansas 67260 USADepartment of Evolution and Ecology and Center for Population Biology University of California Davis One Shields Avenue Davis California 95616 USADepartment of Biology Duke University 130 Science Drive Durham North Carolina 27708 USADepartment of Biology Bucknell University 1 Dent Drive Lewisburg Pennsylvania 17837 USADepartment of Biology Bucknell University 1 Dent Drive Lewisburg Pennsylvania 17837 USADepartment of Biology Bucknell University 1 Dent Drive Lewisburg Pennsylvania 17837 USAUniversity Herbaria and Department of Integrative Biology University of California Berkeley 3040 Valley Life Sciences Building Berkeley California 94720 USAPremise 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.https://doi.org/10.1002/aps3.11344Boecheradouble‐digest restriction site–associated DNA sequencing (ddRADseq)Drabaherbarium specimensIlexSolidago
collection DOAJ
language English
format Article
sources DOAJ
author Ingrid E. Jordon‐Thaden
James B. Beck
Catherine A. Rushworth
Michael D. Windham
Nicolas Diaz
Jason T. Cantley
Christopher T. Martine
Carl J. Rothfels
spellingShingle Ingrid E. Jordon‐Thaden
James B. Beck
Catherine A. Rushworth
Michael D. Windham
Nicolas Diaz
Jason T. Cantley
Christopher T. Martine
Carl J. Rothfels
A basic ddRADseq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera
Applications in Plant Sciences
Boechera
double‐digest restriction site–associated DNA sequencing (ddRADseq)
Draba
herbarium specimens
Ilex
Solidago
author_facet Ingrid E. Jordon‐Thaden
James B. Beck
Catherine A. Rushworth
Michael D. Windham
Nicolas Diaz
Jason T. Cantley
Christopher T. Martine
Carl J. Rothfels
author_sort Ingrid E. Jordon‐Thaden
title A basic ddRADseq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera
title_short A basic ddRADseq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera
title_full A basic ddRADseq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera
title_fullStr A basic ddRADseq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera
title_full_unstemmed A basic ddRADseq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera
title_sort basic ddradseq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera
publisher Wiley
series Applications in Plant Sciences
issn 2168-0450
publishDate 2020-04-01
description 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.
topic Boechera
double‐digest restriction site–associated DNA sequencing (ddRADseq)
Draba
herbarium specimens
Ilex
Solidago
url https://doi.org/10.1002/aps3.11344
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