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

dc.contributor.authorTodd, S. Michelleen
dc.contributor.authorSettlage, Robert E.en
dc.contributor.authorLahmers, Kevin K.en
dc.contributor.authorSlade, Daniel J.en
dc.date.accessioned2018-07-24T17:01:39Zen
dc.date.available2018-07-24T17:01:39Zen
dc.date.issued2018en
dc.description.abstractUnderstanding the virulence mechanisms of human pathogens from the genus Fusobacterium has been hindered by a lack of properly assembled and annotated genomes. Here we report the first complete genomes for seven Fusobacterium strains, as well as resequencing of the reference strain Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (total of seven species; total of eight genomes). A highly efficient and cost-effective sequencing pipeline was achieved using sample multiplexing for short-read Illumina (150 bp) and long-read Oxford Nanopore Min- ION (80 kbp) platforms, coupled with genome assembly using the open-source software Unicycler. Compared to currently available draft assemblies (previously 24 to 67 contigs), these genomes are highly accurate and consist of only one complete chromosome. We present the complete genome sequence of F. nucleatum subsp. nucleatum ATCC 23726, a genetically tractable and biomedically important strain and, in addition, reveal that the previous F. nucleatum subsp. nucleatum ATCC 25586 genome assembly contains a 452-kb genomic inversion that has been corrected using our sequencing and assembly pipeline. To enable genomic analyses by the scientific community, we concurrently used these genomes to launch FusoPortal, a repository of interactive and downloadable genomic data, genome maps, gene annotations, and protein functional analyses and classifications. In summary, this report provides detailed methods for accurately sequencing, assembling, and annotating Fusobacterium genomes, while focusing on using open-source software to foster the availability of reproducible and open data. This resource will enhance efforts to properly identify virulence proteins that may contribute to a repertoire of diseases that includes periodontitis, preterm birth, and colorectal cancer.en
dc.description.sponsorshipUSDA National Institute of Food and Agricultureen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1128/mSphere.00269-18en
dc.identifier.issue4en
dc.identifier.urihttp://hdl.handle.net/10919/84335en
dc.identifier.volume3en
dc.language.isoenen
dc.publisherAmerican Society for Microbiologyen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectcanceren
dc.subjectcolorectal canceren
dc.subjectFusobacteriumen
dc.subjectFusobacterium nucleatumen
dc.subjectIlluminaen
dc.subjectMinIONen
dc.titleFusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correctionen
dc.title.serialmSphereen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
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