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Resource Report | Host-Microbe Biology

FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced Fusobacterium Genomes Improves Gene Identification and Characterization

Blake E. Sanders, Ariana Umana, Justin A. Lemkul, Daniel J. Slade
Sarah E. F. D'Orazio, Editor
Blake E. Sanders
aDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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  • ORCID record for Blake E. Sanders
Ariana Umana
aDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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  • ORCID record for Ariana Umana
Justin A. Lemkul
aDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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Daniel J. Slade
aDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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Sarah E. F. D'Orazio
University of Kentucky
Roles: Editor
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DOI: 10.1128/mSphere.00228-18
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  • FIG 1 
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    FIG 1 

    Schematic of all genomic, bioinformatic, and scripting workflows used to create FusoPortal.

  • FIG 2 
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    FIG 2 

    Correction of open reading frames in Fusobacterium genomes. (A) A comparison of the genome size to the number of protein-encoding genes per genome in both the NCBI and FusoPortal genomes. (B) A comparison of all proteins for average gene size in the NCBI and FusoPortal genomes. (C) Analysis of all proteins 1,000 residues in size and above in annotated FusoPortal proteomes and of how many residues were added (or, in rare cases, removed) compared to the previous annotations present in the NCBI database. n = number of proteins 1,000 residues in size or greater in each genome.

  • FIG 3 
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    FIG 3 

    Phylogenetic analysis of complete Fusobacterium genomes. (A) Tree created using complete proteomes in the microPan package in R. Bootstrap values are indicated in red. Locations of where strains were isolated in the human body are highlighted. (B) Micropan analysis of pan-genome gene families with models predicting the percentages of core genes, shell genes (present in most genomes), and cloud genes (found in few genomes). (C) Analysis of the number of unique gene clusters found among the eight complete FusoPortal genomes.

  • FIG 4 
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    FIG 4 

    Navigating the FusoPortal Web interface for genome analysis. (A) Links are provided for downloading all genomic data (raw and analyzed), with Bandage plots to show the completeness of each genome build. (B) Whole-genome maps were produced with links to custom webpages for each gene that provide access to all genomic and bioinformatic analysis. (C) Each gene contains a full InterPro analysis page with links to multiple functional prediction databases (e.g., PFAM, TIGR, Gene3D, CDD, GO). No IPR, no InterPro accession number.

  • FIG 5 
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    FIG 5 

    A custom BLAST database to search FusoPortal genomes built with SequenceServer. (A) Data entry panel that autodetects protein or DNA sequences. (B) The available genomes that users can choose to search. (C) BLAST results for identified genes. (D) Links to downloadable files.

Tables

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  • TABLE 1 

    Statistics and NCBI accession numbers for FusoPortal genomes

    SpeciesStrainNCBI GenBank
    sequence
    accession no.
    No. of NCBI
    contigsa
    Size
    (Mb)
    No. of
    protein
    genes
    FusoPortal GenBank
    sequence
    accession no.
    No. of
    FusoPortal
    contigs
    Size
    (Mb)
    No. of
    protein
    genes
    F. nucleatum23726GCF_000178895.1672.231,983GCA_003019785.112.302,111
    F. nucleatum25586GCA_000007325.112.171,968GCA_003019295.112.182,019
    F. varium27725GCA_000159915.2393.303,008GCA_003019655.113.353,054b
    F. ulcerans49185GCA_000158315.2493.493,191GCA_003019675.113.543,230
    F. mortiferum9817GCA_000158195.2442.672,538GCA_003019315.112.722,631
    F. gonidiaformans25563GCA_000158835.2241.701,618GCA_003019695.111.681,617
    F. periodonticum2_1_31GCA_000158215.3612.552,375GCA_003019755.112.542,388
    F. necrophorum1_1_36SGCA_000242215.1402.313,197GCA_003019715.112.2921,215
    • ↵a Contig, continuous stretch of genomic DNA with breaks.

    • ↵b Data include 70 genes from a 42-kb plasmid (GCA_003019655.1).

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FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced Fusobacterium Genomes Improves Gene Identification and Characterization
Blake E. Sanders, Ariana Umana, Justin A. Lemkul, Daniel J. Slade
mSphere Jul 2018, 3 (4) e00228-18; DOI: 10.1128/mSphere.00228-18

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FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced Fusobacterium Genomes Improves Gene Identification and Characterization
Blake E. Sanders, Ariana Umana, Justin A. Lemkul, Daniel J. Slade
mSphere Jul 2018, 3 (4) e00228-18; DOI: 10.1128/mSphere.00228-18
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KEYWORDS

Fusobacterium
Fusobacterium nucleatum
pathogenesis
colon cancer
colorectal cancer
genomics
host-pathogen

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