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dc.contributor.authorNichols, Ruth V.
dc.contributor.authorVollmers, Christopher
dc.contributor.authorNewsom, Lee A.
dc.contributor.authorWang, Yue
dc.contributor.authorHeintzman, Peter D.
dc.contributor.authorLeighton, McKenna
dc.contributor.authorGreen, Richard E.
dc.contributor.authorShapiro, Beth
dc.date.accessioned2019-01-17T12:38:53Z
dc.date.available2019-01-17T12:38:53Z
dc.date.issued2018-05-24
dc.description.abstractDNA metabarcoding is an increasingly popular method to characterize and quantify biodiversity in environmental samples. Metabarcoding approaches simultaneously amplify a short, variable genomic region, or “barcode,” from a broad taxonomic group via the polymerase chain reaction (PCR), using universal primers that anneal to flanking conserved regions. Results of these experiments are reported as occurrence data, which provide a list of taxa amplified from the sample, or relative abundance data, which measure the relative contribution of each taxon to the overall composition of amplified product. The accuracy of both occurrence and relative abundance estimates can be affected by a variety of biological and technical biases. For example, taxa with larger biomass may be better represented in environmental samples than those with smaller biomass. Here, we explore how polymerase choice, a potential source of technical bias, might influence results in metabarcoding experiments. We compared potential biases of six commercially available polymerases using a combination of mixtures of amplifiable synthetic sequences and real sedimentary DNA extracts. We find that polymerase choice can affect both occurrence and relative abundance estimates and that the main source of this bias appears to be polymerase preference for sequences with specific GC contents. We further recommend an experimental approach for metabarcoding based on results of our synthetic experiments.en_US
dc.description.sponsorshipThe Gordon and Betty Moore Foundation The National Science Foundation The University of California Office of the Presidenten_US
dc.descriptionThis is the peer reviewed version of the following article: Nichols, R.V., Vollmers, C., Newsom, L.A., Wang, Y., Heintzman, P.D., Leighton, M., ... Shapiro, B. (2018). Minimizing polymerase biases in metabarcoding. <i>Molecular Ecology Resources, 18</i>(5), 927-939, which has been published in final form at <a href=https://doi.org/10.1111/1755-0998.12895> https://doi.org/10.1111/1755-0998.12895</a>. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.en_US
dc.identifier.citationNichols, R.V., Vollmers, C., Newsom, L.A., Wang, Y., Heintzman, P.D., Leighton, M., ... Shapiro, B. (2018). Minimizing polymerase biases in metabarcoding. <i>Molecular Ecology Resources, 18</i>(5), 927-939. https://doi.org/10.1111/1755-0998.12895en_US
dc.identifier.cristinIDFRIDAID 1588431
dc.identifier.doi10.1111/1755-0998.12895
dc.identifier.issn1755-098X
dc.identifier.issn1755-0998
dc.identifier.urihttps://hdl.handle.net/10037/14475
dc.language.isoengen_US
dc.publisherWileyen_US
dc.relation.journalMolecular Ecology Resources
dc.rights.accessRightsopenAccessen_US
dc.subjectVDP::Matematikk og naturvitenskap: 400::Zoologiske og botaniske fag: 480::Vegetasjonshistorie: 495en_US
dc.subjectVDP::Mathematics and natural scienses: 400::Zoology and botany: 480::Vegetation history: 495en_US
dc.subjectVDP::Matematikk og naturvitenskap: 400::Zoologiske og botaniske fag: 480::Økologi: 488en_US
dc.subjectVDP::Mathematics and natural scienses: 400::Zoology and botany: 480::Ecology: 488en_US
dc.subjectbiasen_US
dc.subjecteDNAen_US
dc.subjectenvironmental DNAen_US
dc.subjectmetabarcodingen_US
dc.subjectsoilen_US
dc.subjecttrnL P6 loopen_US
dc.titleMinimizing polymerase biases in metabarcodingen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


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