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A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restrictionsite‐associated DNA sequencing (RAD‐seq) to develop an economical single nucleotide polymorphism (SNP) DNA barcoding system that suffice...

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Autores principales: Fitzek, Elisabeth, Delcamp, Adline, Guichoux, Erwan, Hahn, Marlene, Lobdell, Matthew, Hipp, Andrew L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6010771/
https://www.ncbi.nlm.nih.gov/pubmed/29938097
http://dx.doi.org/10.1002/ece3.4122
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author Fitzek, Elisabeth
Delcamp, Adline
Guichoux, Erwan
Hahn, Marlene
Lobdell, Matthew
Hipp, Andrew L.
author_facet Fitzek, Elisabeth
Delcamp, Adline
Guichoux, Erwan
Hahn, Marlene
Lobdell, Matthew
Hipp, Andrew L.
author_sort Fitzek, Elisabeth
collection PubMed
description DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restrictionsite‐associated DNA sequencing (RAD‐seq) to develop an economical single nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with postclustering bioinformatic tools to generate a list of 291 potential SNPs, 80 of which were included in a barcoding toolkit that is easily implemented using MassARRAY mass spectrometry technology. As a proof‐of‐concept, we used the genotyping toolkit to infer potential hybridization between North American white oaks transplanted outside of their native range (Q. michauxii, Q. montana, Q muehlenbergii/Q. prinoides, and Q. stellata) into a horticultural collection surrounded by natural forests of locally native trees (Q. alba and Q. macrocarpa) in the living collection at The Morton Arboretum (Lisle, IL, USA). Phylogenetic and clustering analyses suggested low rates of hybridization between cultivated and native species, with the exception of one Q. michauxii mother tree, the acorns of which exhibited high admixture from either Q. alba or Q. stellata and Q. macrocarpa, and a hybrid between Q. stellata that appears to have backcrossed almost exclusively to Q. alba. Together, RAD‐seq and MassARRAY technologies allow for efficient development and implementation of a multispecies barcode for one of the more challenging forest tree genera.
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spelling pubmed-60107712018-06-22 A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting Fitzek, Elisabeth Delcamp, Adline Guichoux, Erwan Hahn, Marlene Lobdell, Matthew Hipp, Andrew L. Ecol Evol Original Research DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restrictionsite‐associated DNA sequencing (RAD‐seq) to develop an economical single nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with postclustering bioinformatic tools to generate a list of 291 potential SNPs, 80 of which were included in a barcoding toolkit that is easily implemented using MassARRAY mass spectrometry technology. As a proof‐of‐concept, we used the genotyping toolkit to infer potential hybridization between North American white oaks transplanted outside of their native range (Q. michauxii, Q. montana, Q muehlenbergii/Q. prinoides, and Q. stellata) into a horticultural collection surrounded by natural forests of locally native trees (Q. alba and Q. macrocarpa) in the living collection at The Morton Arboretum (Lisle, IL, USA). Phylogenetic and clustering analyses suggested low rates of hybridization between cultivated and native species, with the exception of one Q. michauxii mother tree, the acorns of which exhibited high admixture from either Q. alba or Q. stellata and Q. macrocarpa, and a hybrid between Q. stellata that appears to have backcrossed almost exclusively to Q. alba. Together, RAD‐seq and MassARRAY technologies allow for efficient development and implementation of a multispecies barcode for one of the more challenging forest tree genera. John Wiley and Sons Inc. 2018-05-08 /pmc/articles/PMC6010771/ /pubmed/29938097 http://dx.doi.org/10.1002/ece3.4122 Text en © 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Research
Fitzek, Elisabeth
Delcamp, Adline
Guichoux, Erwan
Hahn, Marlene
Lobdell, Matthew
Hipp, Andrew L.
A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting
title A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting
title_full A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting
title_fullStr A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting
title_full_unstemmed A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting
title_short A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting
title_sort nuclear dna barcode for eastern north american oaks and application to a study of hybridization in an arboretum setting
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6010771/
https://www.ncbi.nlm.nih.gov/pubmed/29938097
http://dx.doi.org/10.1002/ece3.4122
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