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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

  • 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.

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Author:Henrik KrehenwinkelORCiD, Aaron PomerantzORCiD, James B. Henderson, Susan R. Kennedy, Yun Ying Lim, Varun Swamy, Juan Diego Shoobridge, Natalie Graham, Nipam H. Patel, Rosemary G. Gillespie, Stefan ProstORCiD
Parent Title (English):GigaScience
Publisher:Oxford University Press
Place of publication:Oxford
Document Type:Article
Date of completion:2019/07/18
Date of publication:2019/03/02
Publishing institution:Universität Trier
Contributing corporation:The publication was funded by the Open Access Fund of Universität Trier and the German Research Foundation (DFG)
Release Date:2019/07/18
Tag:MinION; Oxford Nanopore Technologies; biodiversity; eukaryotes; long DNA barcodes; metabarcoding; ribosomal
GND Keyword:Biodiversität; DNS-Sequenz; Feldforschung; Sequenzanalyse / Chemie
Volume (for the year ...):8
Issue / no.:5
Number of pages:16
Institutes:Fachbereich 6 / Raum- und Umweltwissenschaften
Dewey Decimal Classification:9 Geschichte und Geografie / 90 Geschichte / 900 Geschichte und Geografie
Licence (German):License LogoCC BY: Creative-Commons-Lizenz 4.0 International

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