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

  1. Judith Risse
  2. Marian Thomson
  3. Garry Blakely
  4. Georgios Koutsovoulos
  5. Mark Blaxter
  6. Mick Watson

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Abstract

Background

Second 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.

Results

We 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.

Conclusions

The 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.

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  1. GigaScience

    Now published in GigaScience doi: 10.1186/s13742-015-0101-6

    Judith Risse 1Edinburgh Genomics, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, EH9 3FLFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMarian Thomson 1Edinburgh Genomics, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, EH9 3FLFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGarry Blakely 2Institute of Cell Biology, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, EH9 3BFFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGeorgios Koutsovoulos 3Institute of Evolutionary Biology, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, EH9 3FLFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMark Blaxter 1Edinburgh Genomics, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, EH9 3FL3Institute of Evolutionary Biology, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, EH9 3FLFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMick Watson 1Edinburgh Genomics, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, EH9 3FL4The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RGFind this author on Google ScholarFind this author on PubMedSearch for this author on this site

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1186/s13742-015-0101-6 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.100346 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.100344

  2. Version published to 10.1101/024323v1 on bioRxiv