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...

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Autores principales:	Martijn Staats, Argelia Cuenca, James E Richardson, Ria Vrielink-van Ginkel, Gitte Petersen, Ole Seberg, Freek T Bakker
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8f4a7893a7b94c889d394fd5fc210206
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spelling	oai:doaj.org-article:8f4a7893a7b94c889d394fd5fc2102062021-11-18T07:32:59ZDNA damage in plant herbarium tissue.1932-620310.1371/journal.pone.0028448https://doaj.org/article/8f4a7893a7b94c889d394fd5fc2102062011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22163018/?tool=EBIhttps://doaj.org/toc/1932-6203Dried 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.Martijn StaatsArgelia CuencaJames E RichardsonRia Vrielink-van GinkelGitte PetersenOle SebergFreek T BakkerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 12, p e28448 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Martijn Staats Argelia Cuenca James E Richardson Ria Vrielink-van Ginkel Gitte Petersen Ole Seberg Freek T Bakker DNA damage in plant herbarium tissue.
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	article
author	Martijn Staats Argelia Cuenca James E Richardson Ria Vrielink-van Ginkel Gitte Petersen Ole Seberg Freek T Bakker
author_facet	Martijn Staats Argelia Cuenca James E Richardson Ria Vrielink-van Ginkel Gitte Petersen Ole Seberg Freek T Bakker
author_sort	Martijn Staats
title	DNA damage in plant herbarium tissue.
title_short	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_sort	dna damage in plant herbarium tissue.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/8f4a7893a7b94c889d394fd5fc210206
work_keys_str_mv	AT martijnstaats dnadamageinplantherbariumtissue AT argeliacuenca dnadamageinplantherbariumtissue AT jameserichardson dnadamageinplantherbariumtissue AT riavrielinkvanginkel dnadamageinplantherbariumtissue AT gittepetersen dnadamageinplantherbariumtissue AT oleseberg dnadamageinplantherbariumtissue AT freektbakker dnadamageinplantherbariumtissue
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DNA damage in plant herbarium tissue.

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