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DNA Damage in Plant Herbarium Tissue
Dried plant herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of amplif...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230621/ https://www.ncbi.nlm.nih.gov/pubmed/22163018 http://dx.doi.org/10.1371/journal.pone.0028448 |
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author | Staats, Martijn Cuenca, Argelia Richardson, James E. Vrielink-van Ginkel, Ria Petersen, Gitte Seberg, Ole Bakker, Freek T. |
author_facet | Staats, Martijn Cuenca, Argelia Richardson, James E. Vrielink-van Ginkel, Ria Petersen, Gitte Seberg, Ole Bakker, Freek T. |
author_sort | Staats, Martijn |
collection | PubMed |
description | Dried plant herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative assessment of DNA post-mortem damage is essential to determine the accuracy of molecular data from herbarium specimens. In this study we present an assessment of DNA damage as miscoding lesions in herbarium specimens using 454-sequencing of amplicons derived from plastid, mitochondrial, and nuclear DNA. In addition, we assess DNA degradation as a result of strand breaks and other types of polymerase non-bypassable damage by quantitative real-time PCR. Comparing four pairs of fresh and herbarium specimens of the same individuals we quantitatively assess post-mortem DNA damage, directly after specimen preparation, as well as after long-term herbarium storage. After specimen preparation we estimate the proportion of gene copy numbers of plastid, mitochondrial, and nuclear DNA to be 2.4–3.8% of fresh control DNA and 1.0–1.3% after long-term herbarium storage, indicating that nearly all DNA damage occurs on specimen preparation. In addition, there is no evidence of preferential degradation of organelle versus nuclear genomes. Increased levels of C→T/G→A transitions were observed in old herbarium plastid DNA, representing 21.8% of observed miscoding lesions. We interpret this type of post-mortem DNA damage-derived modification to have arisen from the hydrolytic deamination of cytosine during long-term herbarium storage. Our results suggest that reliable sequence data can be obtained from herbarium specimens. |
format | Online Article Text |
id | pubmed-3230621 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-32306212011-12-09 DNA Damage in Plant Herbarium Tissue Staats, Martijn Cuenca, Argelia Richardson, James E. Vrielink-van Ginkel, Ria Petersen, Gitte Seberg, Ole Bakker, Freek T. PLoS One Research Article Dried plant herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative assessment of DNA post-mortem damage is essential to determine the accuracy of molecular data from herbarium specimens. In this study we present an assessment of DNA damage as miscoding lesions in herbarium specimens using 454-sequencing of amplicons derived from plastid, mitochondrial, and nuclear DNA. In addition, we assess DNA degradation as a result of strand breaks and other types of polymerase non-bypassable damage by quantitative real-time PCR. Comparing four pairs of fresh and herbarium specimens of the same individuals we quantitatively assess post-mortem DNA damage, directly after specimen preparation, as well as after long-term herbarium storage. After specimen preparation we estimate the proportion of gene copy numbers of plastid, mitochondrial, and nuclear DNA to be 2.4–3.8% of fresh control DNA and 1.0–1.3% after long-term herbarium storage, indicating that nearly all DNA damage occurs on specimen preparation. In addition, there is no evidence of preferential degradation of organelle versus nuclear genomes. Increased levels of C→T/G→A transitions were observed in old herbarium plastid DNA, representing 21.8% of observed miscoding lesions. We interpret this type of post-mortem DNA damage-derived modification to have arisen from the hydrolytic deamination of cytosine during long-term herbarium storage. Our results suggest that reliable sequence data can be obtained from herbarium specimens. Public Library of Science 2011-12-05 /pmc/articles/PMC3230621/ /pubmed/22163018 http://dx.doi.org/10.1371/journal.pone.0028448 Text en Staats et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Staats, Martijn Cuenca, Argelia Richardson, James E. Vrielink-van Ginkel, Ria Petersen, Gitte Seberg, Ole Bakker, Freek T. DNA Damage in Plant Herbarium Tissue |
title | DNA Damage in Plant Herbarium Tissue |
title_full | DNA Damage in Plant Herbarium Tissue |
title_fullStr | DNA Damage in Plant Herbarium Tissue |
title_full_unstemmed | DNA Damage in Plant Herbarium Tissue |
title_short | DNA Damage in Plant Herbarium Tissue |
title_sort | dna damage in plant herbarium tissue |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230621/ https://www.ncbi.nlm.nih.gov/pubmed/22163018 http://dx.doi.org/10.1371/journal.pone.0028448 |
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