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DNA damage in plant herbarium tissue

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dc.creatorStaats, Martijnspa
dc.creatorCuenca, Argeliaspa
dc.creatorRichardson, James-Edwardspa
dc.creatorVrielink-van Ginkel, Riaspa
dc.creatorPetersen, Gittespa
dc.creatorSeberg, Olespa
dc.creatorBakker, Freek T.spa
dc.date.accessioned2020-08-19T14:42:37Z
dc.date.available2020-08-19T14:42:37Z
dc.date.created2011-12-05spa
dc.description.abstractDried 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.eng
dc.format.mimetypeapplication/pdf
dc.identifier.doihttps://doi.org/10.1371/journal.pone.0028448
dc.identifier.issnEISSN: 1932-6203
dc.identifier.urihttps://repository.urosario.edu.co/handle/10336/27537
dc.language.isoengspa
dc.publisherPLOS Public Library of Sciencespa
dc.relation.citationIssueNo. 12
dc.relation.citationStartPagee28448
dc.relation.citationTitlePLoS One
dc.relation.citationVolumeVol. 6
dc.relation.ispartofPLoS One, EISSN: 1932-6203, Vol.6, No.12 (December 2011); pp. e28448spa
dc.relation.urihttps://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0028448&type=printablespa
dc.rights.accesRightsinfo:eu-repo/semantics/openAccess
dc.rights.accesoAbierto (Texto Completo)spa
dc.sourcePLoS Onespa
dc.source.instnameinstname:Universidad del Rosario
dc.source.reponamereponame:Repositorio Institucional EdocUR
dc.subject.keywordDNA damagespa
dc.subject.keywordPlastids Mitochondriaspa
dc.subject.keywordPolymerase chain reactionspa
dc.subject.keywordNucleotidesspa
dc.subject.keywordDNAspa
dc.subject.keywordDNA extractionspa
dc.subject.keywordSpecimen preparation and treatmentspa
dc.titleDNA damage in plant herbarium tissuespa
dc.title.TranslatedTitleDaño del ADN en el tejido del herbario vegetalspa
dc.typearticleeng
dc.type.hasVersioninfo:eu-repo/semantics/publishedVersion
dc.type.spaArtículospa
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