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- Title
The use of Oxford Nanopore native barcoding for complete genome assembly.
- Authors
Bayliss, Sion C.; Hunt, Vicky L.; Maho Yokoyama; Thorpe, Harry A.; Feil, Edward J.
- 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% to 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 our understanding of accessory genome content, plasmid diversity, and genome rearrangements.
- Subjects
NANOPORES; NUCLEOTIDE sequencing
- Publication
GigaScience, 2017, Vol 6, Issue 3, p1
- ISSN
2047-217X
- Publication type
Article
- DOI
10.1093/gigascience/gix001