title: DNA damage in plant herbarium tissue.
abstract: 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.
authors.affiliation: Biosystematics Group, Wageningen University, Wageningen, The Netherlands.
authors.forename: Martijn
authors.initials: M
authors.lastname: Staats
authors.forename: Argelia
authors.initials: A
authors.lastname: Cuenca
authors.forename: James E
authors.initials: JE
authors.lastname: Richardson
authors.forename: Ria
authors.initials: R
authors.lastname: Vrielink-van Ginkel
authors.forename: Gitte
authors.initials: G
authors.lastname: Petersen
authors.forename: Ole
authors.initials: O
authors.lastname: Seberg
authors.forename: Freek T
authors.initials: FT
authors.lastname: Bakker
mesh_terms: D002467:Cell Nucleus / Q000378:metabolism; D004249:DNA Damage; D053938:DNA Fragmentation; D004272:DNA, Mitochondrial / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics*; D020224:Expressed Sequence Tags; D020441:Ginkgo biloba / Q000235:genetics; D031296:Laburnum / Q000235:genetics; D008928:Mitochondria / Q000235:genetics; D008957:Models, Genetic; D015233:Models, Statistical; D009711:Nucleotides / Q000235:genetics; D010944:Plants / Q000235:genetics; D018087:Plastids / Q000378:metabolism; D016133:Polymerase Chain Reaction / Q000379:methods; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D017422:Sequence Analysis, DNA; D013997:Time Factors
chemical_list: D004272:DNA, Mitochondrial; D018744:DNA, Plant; D009711:Nucleotides