A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

BackgroundSecond and third generation sequencing technologies have revolutionised bacterial genomics. Short-read Illumina reads result in cheap but fragmented assemblies, whereas longer reads are more expensive but result in more complete genomes. The Oxford Nanopore MinION device is a revolutionary mobile sequencer that can produce thousands of long, single molecule reads.ResultsWe sequenced Bacteroides fragilis strain BE1 using both the Illumina MiSeq and Oxford Nanopore MinION platforms. We were able to assemble a single chromosome of 5.18 Mb, with no gaps, using publicly available software and commodity computing hardware. We identified gene rearrangements and the state of invertible promoters in the strain.ConclusionsThe single chromosome assembly of Bacteroides fragilis strain BE1 was achieved using only modest amounts of data, publicly available software and commodity computing hardware. This combination of technologies offers the possibility of ultra-cheap, high quality, finished bacterial genomes.

[1]  Benedict Paten,et al.  Improved data analysis for the MinION nanopore sequencer , 2015, Nature Methods.

[2]  M. Watson,et al.  Illuminating the future of DNA sequencing , 2014, Genome Biology.

[3]  A. Eley,et al.  Lipopolysaccharides of Bacteroides fragilis, Chlamydia trachomatis and Pseudomonas aeruginosa signal via toll-like receptor 2. , 2004, Journal of medical microbiology.

[4]  Walter Pirovano,et al.  SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information , 2014, BMC Bioinformatics.

[5]  T. Dallman,et al.  Performance comparison of benchtop high-throughput sequencing platforms , 2012, Nature Biotechnology.

[6]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[7]  Judith Risse,et al.  A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data , 2015, bioRxiv.

[8]  M. Schatz,et al.  Hybrid error correction and de novo assembly of single-molecule sequencing reads , 2012, Nature Biotechnology.

[9]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[10]  V. Babenko,et al.  Complete Genome Sequence of an Enterotoxigenic Bacteroides fragilis Clinical Isolate , 2015, Genome Announcements.

[11]  Charles E. Lawrence,et al.  Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION , 2015, bioRxiv.

[12]  C. Nord,et al.  Human immune response to an iron-repressible outer membrane protein of Bacteroides fragilis , 1991, Infection and immunity.

[13]  Aaron A. Klammer,et al.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.

[14]  Heng Li.  Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[15]  W. Pirovano,et al.  Toward almost closed genomes with GapFiller , 2012, Genome Biology.

[16]  D. Maclaren,et al.  Early events after intra-abdominal infection with Bacteroides fragilis and Escherichia coli. , 1991, Journal of medical microbiology.

[17]  Lisa C. Crossman,et al.  Extensive DNA Inversions in the B. fragilis Genome Control Variable Gene Expression , 2005, Science.

[18]  Mick Watson,et al.  poRe: an R package for the visualization and analysis of nanopore sequencing data , 2015, Bioinform..

[19]  N. Loman,et al.  A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.

[20]  Mick Watson,et al.  Successful test launch for nanopore sequencing , 2015, Nature Methods.

[21]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[22]  S. Patrick,et al.  Detection of Intrastrain Antigenic Variation of Bacteroides fragilis Surface Polysaccharides by Monoclonal Antibody Labelling , 1999, Infection and Immunity.

[23]  M. Hattori,et al.  Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[25]  Timothy P. L. Smith,et al.  Reducing assembly complexity of microbial genomes with single-molecule sequencing , 2013, Genome Biology.

[26]  M. Forsman,et al.  Scaffolding of a bacterial genome using MinION nanopore sequencing , 2015, Scientific Reports.

[27]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[28]  Paul Horton,et al.  Parameters for accurate genome alignment , 2010, BMC Bioinformatics.