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How to open the treasure chest? optimising DNA extraction from herbarium specimens

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dc.creatorSärkinen, Tiinaspa
dc.creatorStaats, Martijnspa
dc.creatorRichardson, James-Edwardspa
dc.creatorCowan, Robyn S.spa
dc.creatorBakker, Freek T.spa
dc.date.accessioned2020-08-19T14:44:02Z
dc.date.available2020-08-19T14:44:02Z
dc.date.created2012-08-28spa
dc.description.abstractHerbarium collections are potentially an enormous resource for DNA studies, but the use of herbarium specimens in molecular studies has thus far been slowed down by difficulty in obtaining amplifiable DNA. Here we compare a set of commercially available DNA extraction protocols and their performance in terms of DNA purity and yield, and PCR amplification success as measured by using three differentially sized markers, the rbcL barcoding marker (cpDNA), the LEAFY exon 3 (nrDNA), and the trnL(UAA) P6 loop (cpDNA). Results reveal large differences between extraction methods, where DNA purity rather than yield is shown to be strongly correlated with PCR success. Amplicon size shows similarly strong correlation with PCR success, with the shortest fragment showing the highest success rate (78%, P6 loop, 10–143 base pairs (bp)) and the largest fragment the lowest success (10%, rbcL, 670 bp). The effect of specimen preparation method on PCR success was also tested. Results show that drying method strongly affects PCR success, especially the availability of fragments longer than 250 bp, where longer fragments are more available for PCR amplification in air dried material compared to alcohol dried specimens. Results from our study indicate that projects relying on poor-quality starting material such as herbarium or scat samples should focus on extracting pure DNA and aim to amplify short target regions (<200–300 bp) in order to maximise outcomes. Development of shorter barcoding regions, or mini-barcodes within existing ones should be of high importance as only a few options are currently available; this is particularly important if we hope to incorporate the millions of herbarium samples available into barcoding initiatives and other molecular studies.eng
dc.format.mimetypeapplication/pdf
dc.identifier.doihttps://doi.org/10.1371/journal.pone.0043808
dc.identifier.issnEISSN: 1932-6203
dc.identifier.urihttps://repository.urosario.edu.co/handle/10336/27815
dc.language.isoengspa
dc.publisherPLOS Public Library of Sciencespa
dc.relation.citationIssueNo. 8
dc.relation.citationStartPageE43808
dc.relation.citationTitlePLoS One
dc.relation.citationVolumeVol. 7
dc.relation.ispartofPLoS One, EISSN: 1932-6203, Vol.7, No.8 (August 2012); pp. E43808spa
dc.relation.urihttps://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0043808&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.keywordPolymerase chain reactionspa
dc.subject.keywordDNA extractionspa
dc.subject.keywordAlcoholsspa
dc.subject.keywordDNA polymerasespa
dc.subject.keywordAncient DNAspa
dc.subject.keywordSpecimen preparation and treatmentspa
dc.subject.keywordDNA damagespa
dc.subject.keywordPlatinumspa
dc.titleHow to open the treasure chest? optimising DNA extraction from herbarium specimensspa
dc.title.TranslatedTitle¿Cómo abrir el cofre del tesoro? optimizar la extracción de ADN de las muestras de herbariospa
dc.typearticleeng
dc.type.hasVersioninfo:eu-repo/semantics/publishedVersion
dc.type.spaArtículospa
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