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Resource Report | Host-Microbe Biology

Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction

S. Michelle Todd, Robert E. Settlage, Kevin K. Lahmers, Daniel J. Slade
Sarah E. F. D'Orazio, Editor
S. Michelle Todd
aDepartment of Biomedical Sciences and Pathology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia, USA
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  • ORCID record for S. Michelle Todd
Robert E. Settlage
bAdvanced Research Computing, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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  • ORCID record for Robert E. Settlage
Kevin K. Lahmers
aDepartment of Biomedical Sciences and Pathology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia, USA
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  • ORCID record for Kevin K. Lahmers
Daniel J. Slade
cDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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  • ORCID record for Daniel J. Slade
Sarah E. F. D'Orazio
University of Kentucky
Roles: Editor
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DOI: 10.1128/mSphere.00269-18
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  • FIG 1 
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    FIG 1 

    Phred analysis of Illumina and MinION reads for the F. nucleatum subsp. nucleatum ATCC 25586 genome. (A) Q scores for Illumina reads. (B) Q scores (Phred quality) for MinION reads 20 to 80 kb in length. (C) Q scores for MinION reads up to 20 kb in length.

  • FIG 2 
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    FIG 2 

    Statistics and mapping of F. necrophorum funduliforme 1_1_36S MinION long reads. After complete genome assembly, MinION reads were mapped to the F. necrophorum funduliforme 1_1_36S genome using Geneious version 9.1.4 software.

  • FIG 3 
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    FIG 3 

    Genome assembly and annotation of eight Fusobacterium genomes from seven species. Short-read-only and complete genome assembly representations were created using Bandage (21).

  • FIG 4 
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    FIG 4 

    Analysis of Fusobacterium nucleatum ATCC 23726 genomes compared to previous builds. (A) Alignment of the complete F. nucleatum subsp. nucleatum ATCC 23726 genome with the 67-contig draft assembly (GenBank accession number ADVK01000000). (B) Confirmation of a 452-kb genomic inversion in the previous F. nucleatum subsp. nucleatum ATCC 25586 genome assembly (GenBank accession number GCA_000007325.1).

Tables

  • Figures
  • Supplemental Material
  • TABLE 1 

    Data deposited at NCBI for all sequenced Fusobacterium strains

    SpeciesStrainGenBank genome
    accession no.
    BioProject
    accession no.
    BioSample
    accession no.
    SRAa Illumina
    accession no.
    SRA MinION
    accession no.
    F. nucleatum23726GCA_003019785.1PRJNA433545SAMN08501025SRX3740879SRX3740878
    F. nucleatum25586GCA_003019295.1PRJNA433545SAMN08706662SRX3786193SRX3786192
    F. varium27725GCA_003019655.1PRJNA433545SAMN08501142SRX3740889SRX3740888
    F. ulcerans49185GCA_003019675.1PRJNA433545SAMN08501141SRX3740885SRX3740884
    F. mortiferum9817GCA_003019315.1PRJNA433545SAMN08501148SRX3740887SRX3740886
    F. gonidiaformans25563GCA_003019695.1PRJNA433545SAMN08501140SRX3740881SRX3740880
    F. periodonticum2_1_31GCA_003019755.1PRJNA433545SAMN08501101SRX3740877SRX3740876
    F. necrophorum1_1_36SGCA_003019715.1PRJNA433545SAMN08501105SRX3740883SRX3740882
    • ↵a SRA, sequence read archive at NCBI.

Supplemental Material

  • Figures
  • Tables
  • TABLE S1 

    Statistics for short-read Illumina sequencing. Download TABLE S1, PDF file, 0.1 MB.

    Copyright © 2018 Todd et al.

    This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

  • TABLE S2 

    Experimental details of MinION sequencing. Download TABLE S2, PDF file, 0.1 MB.

    Copyright © 2018 Todd et al.

    This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

  • TABLE S3 

    Results of MinION sequencing. Download TABLE S3, PDF file, 0.1 MB.

    Copyright © 2018 Todd et al.

    This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

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Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction
S. Michelle Todd, Robert E. Settlage, Kevin K. Lahmers, Daniel J. Slade
mSphere Jul 2018, 3 (4) e00269-18; DOI: 10.1128/mSphere.00269-18

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Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction
S. Michelle Todd, Robert E. Settlage, Kevin K. Lahmers, Daniel J. Slade
mSphere Jul 2018, 3 (4) e00269-18; DOI: 10.1128/mSphere.00269-18
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KEYWORDS

cancer
colorectal cancer
Fusobacterium
Fusobacterium nucleatum
Illumina
MinION

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