The use of Oxford Nanopore native barcoding for complete genome assembly

Sion C. Bayliss, Vicky L. Hunt, Maho Yokoyama, Harry A. Thorpe, Edward J. Feil

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Background: The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short-read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short-read data. The strain we used, MHO_001, represents the important community-acquired methicillin resistant Staphylococcus aureus lineage USA300.
Findings: Using a hybrid assembly of existing short read and barcoded long read sequences from multiplexed data, we completed a genome of the S. aureus USA300 strain MHO_001. The long-read data represented only ∼5-10% of an average MinION(TM) run (∼7x genomic coverage), but, using standard tools, this was sufficient to complete the circular chromosome of S. aureus strain MHO_001 (2.86 Mb) and two complete plasmids (27 Kb and 3 Kb). Minor differences were noted when compared to USA300 reference genome, USA300_FPR3757, including the translocation, loss and gain of mobile genetic elements.
Conclusion: Here we demonstrate that MinION(TM) reads, multiplexed using native barcoding, can be used in combination with short-read data, to fully complete a bacterial genome. The ability to complete multiple genomes, for which short-read data is already available, from a single MinION(TM) run is set to impact on our understanding of accessory genome content, plasmid diversity and genome rearrangements.
Original languageEnglish
Article numbergix001
Pages (from-to)1-6
JournalGigaScience
Volume6
Issue number3
Early online date24 Feb 2017
DOIs
Publication statusPublished - 1 Mar 2017

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Nanopores
Genes
Genome
Technology
Bacterial Genomes
Staphylococcus aureus
Plasmids
Interspersed Repetitive Sequences
Methicillin-Resistant Staphylococcus aureus
Turnaround time
Libraries
Accessories
Chromosomes
DNA
Demonstrations
Availability

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The use of Oxford Nanopore native barcoding for complete genome assembly. / Bayliss, Sion C.; Hunt, Vicky L.; Yokoyama, Maho; Thorpe, Harry A.; Feil, Edward J.

In: GigaScience, Vol. 6, No. 3, gix001, 01.03.2017, p. 1-6.

Research output: Contribution to journalArticle

Bayliss, Sion C. ; Hunt, Vicky L. ; Yokoyama, Maho ; Thorpe, Harry A. ; Feil, Edward J. / The use of Oxford Nanopore native barcoding for complete genome assembly. In: GigaScience. 2017 ; Vol. 6, No. 3. pp. 1-6.
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