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Type of publication: Journal Article
Type of document: Full Paper

Year: 2019

Authors: Krehenwinkel, H; Pomerantz, A; Henderson, JB; Kennedy, SR; Lim, JY; Swamy, V; Shoobridge, JD; Graham, N; Patel, NH; Gillespie, RG; Prost, S

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

Source: Gigascience 8(5): 1-16.



Vetmed Research Units
Research Institute of Wildlife Ecology


Abstract:
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).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.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.© The Author(s) 2019. Published by Oxford University Press.

Keywords Pubmed: Animals
Biodiversity
Classification
DNA Barcoding, Taxonomicmethods
DNA, Ribosomalgenetics
Ecosystem
High-Throughput Nucleotide Sequencing
Nanopore Sequencing
Phylogeny
RNA, Ribosomal, 16Sgenetics
Sequence Analysis, DNAmethods

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