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Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

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dc.contributor.author Krehenwinkel, H.
dc.contributor.author Pomerantz, A.
dc.contributor.author Henderson, J.B.
dc.contributor.author Kennedy, S.R.
dc.contributor.author Lim, J.Y.
dc.contributor.author Swamy, V.
dc.contributor.author Shoobridge, J.D.
dc.contributor.author Graham, N.
dc.contributor.author Patel, N.H.
dc.contributor.author Gillespie, R.G.
dc.contributor.author Prost, S.
dc.date.accessioned 2019-07-04T17:00:19Z
dc.date.available 2019-07-04T17:00:19Z
dc.date.issued 2019
dc.identifier.uri https://hdl.handle.net/20.500.12866/6864
dc.description.abstract BACKGROUND: In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies). FINDINGS: Using a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed Nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates. CONCLUSIONS: Sequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost-effective, portable, and universal approach for eukaryote DNA barcoding. Although bulk community analyses using long-amplicon approaches may introduce biases, the long rDNA amplicons approach signifies a powerful tool for enabling the accurate recovery of taxonomic and phylogenetic diversity across biological communities. en_US
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartofseries Gigascience
dc.rights info:eu-repo/semantics/restrictedAccess
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject biodiversity en_US
dc.subject eukaryotes en_US
dc.subject long DNA barcodes en_US
dc.subject metabarcoding en_US
dc.subject MinION en_US
dc.subject Oxford Nanopore Technologies en_US
dc.subject ribosomal en_US
dc.title Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale en_US
dc.type info:eu-repo/semantics/article
dc.identifier.doi https://doi.org/10.1093/gigascience/giz006
dc.subject.ocde https://purl.org/pe-repo/ocde/ford#1.02.01
dc.subject.ocde https://purl.org/pe-repo/ocde/ford#1.02.03
dc.relation.issn 2047-217X


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