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riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions

View ORCID ProfileNicholas R. Waters, View ORCID ProfileFlorence Abram, View ORCID ProfileFiona Brennan, Ashleigh Holmes, View ORCID ProfileLeighton Pritchard
doi: https://doi.org/10.1101/159798
Nicholas R. Waters
1Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
2Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
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Florence Abram
1Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
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Fiona Brennan
1Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
3Soil and Environmental Microbiology, Environmental Research Centre, Teagasc, Johnstown Castle, Wexford, Ireland
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Ashleigh Holmes
4Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
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Leighton Pritchard
2Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
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  • For correspondence: leighton.pritchard@hutton.ac.uk
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Abstract

The vast majority of bacterial genome sequencing has been performed using Illumina short reads. Because of the inherent difficulty of resolving repeated regions with short reads alone, only ≈10% of sequencing projects have resulted in a closed genome. The most common repeated regions are those coding for ribosomal operons (rDNAs), which occur in a bacterial genome between 1 and 15 times, and are typically used as sequence markers to classify and identify bacteria. Here, we exploit conservation in the genomic context in which rDNAs occur across taxa to improve assembly of these regions relative to de novo sequencing by using the conserved nature of rDNAs across taxa and the uniqueness of their flanking regions within a genome. We describe a method to construct targeted pseudocontigs generated by iteratively assembling reads that map to a reference genome’s rDNAs. These pseudocontigs are then used to more accurately assemble the newly-sequenced chromosome. We show that this method, implemented as riboSeed, correctly bridges across adjacent contigs in bacterial genome assembly and, when used in conjunction with other genome polishing tools, can assist in closure of a genome.

  • Abbreviations:
    rDNA
    DNA region coding for ribosomal RNA operon
    rRNA
    ribosomal RNA
    SRA
    Sequence Read Archive
    ENA
    European Nucleotide Archive
    IG
    intergenic
    GAGE-B
    Genome Assembly Gold-standard Evaluation for Bacteria
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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    Posted February 09, 2018.
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    riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions
    Nicholas R. Waters, Florence Abram, Fiona Brennan, Ashleigh Holmes, Leighton Pritchard
    bioRxiv 159798; doi: https://doi.org/10.1101/159798
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    riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions
    Nicholas R. Waters, Florence Abram, Fiona Brennan, Ashleigh Holmes, Leighton Pritchard
    bioRxiv 159798; doi: https://doi.org/10.1101/159798

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