The use of Oxford Nanopore native barcoding for complete genome assembly.
Gigascience
; 6(3): 1-6, 2017 03 01.
Article
in En
| MEDLINE
| ID: mdl-28327913
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 â¼5% to 10% of an average MinION(TM) run (â¼7x 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.Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Genome, Bacterial
/
DNA Barcoding, Taxonomic
/
High-Throughput Nucleotide Sequencing
/
Nanopores
Language:
En
Journal:
Gigascience
Year:
2017
Document type:
Article