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.
| Original language | English |
|---|---|
| Article number | gix001 |
| Journal | GigaScience |
| Volume | 6 |
| Issue number | 3 |
| DOIs | |
| Publication status | Published - 1 Mar 2017 |
Bibliographical note
Funding Information:The authors would like to acknowledge the contribution of Nick Loman and the rest of the organizing committee of the Pore-Camp 2015 nanopore training workshop, which was hosted in the Centre for Computational Biology at the University of Birmingham during December 2015. We would like to thank ONT for allowing the University of Bath access to the MinION(TM) Access Programme (MAP). The authorswould like to acknowledge BBSRC/NERC grant number BB/M026388/1 for providing funding for SB. SB and VH were also funded by a grant from the United Kingdom Clinical Research Collaboration Translational Infection Research initiative, and the Medical Research Council (Grant Number G1000803, held by Prof. Sharon Peacock) with contributions from the Biotechnology and Biological Sciences Research Council, the National Institute for Health Research on behalf of the Department of Health, and the Chief Scientist Office of the Scottish Government Health Directorate. The authors are grateful for travel funds provided by NERC (NE/N000501/1) for SB and Medical Research Council Cloud Infrastructure for Microbial Bioinformatics for VH to attend.
Publisher Copyright:
© The Author 2017.
Keywords
- Bacterial genomics
- Hybrid assembly
- Long read
- MinION
- Multiplexing
- Native barcoding
- Staphylococcus aureus
- Whole genome sequencing