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

doi:10.1128/mSphere.00228-18

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

mSphere. 2018 Jul 5;3(4):e00228-18. doi: 10.1128/mSphere.00228-18.

Authors

Blake E Sanders^#¹, Ariana Umana^#¹, Justin A Lemkul¹, Daniel J Slade²

Affiliations

¹ Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA.
² Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA dslade@vt.edu.

^# Contributed equally.

Abstract

Here we present FusoPortal, an interactive repository of Fusobacterium genomes that were sequenced using a hybrid MinION long-read sequencing pipeline, followed by assembly and annotation using a diverse portfolio of predominantly open-source software. Significant efforts were made to provide genomic and bioinformatic data as downloadable files, including raw sequencing reads, genome maps, gene annotations, protein functional analysis and classifications, and a custom BLAST server for FusoPortal genomes. FusoPortal has been initiated with eight complete genomes, of which seven were previously only drafts that ranged from 24 to 67 contigs. We have showcased that the genomes in FusoPortal provide accurate open reading frame annotations and have corrected a number of large (>3-kb) genes that were previously misannotated due to contig boundaries. In summary, FusoPortal (http://fusoportal.org) is the first database of MinION-sequenced and completely assembled Fusobacterium genomes, and this central Fusobacterium genomic and bioinformatic resource will aid the scientific community in developing a deeper understanding of how this human pathogen contributes to an array of diseases, including periodontitis and colorectal cancer.IMPORTANCE In this report, we describe a hybrid MinION whole-genome sequencing pipeline and the genomic characteristics of the first eight Fusobacterium strains deposited in the FusoPortal database. This collection of highly accurate and complete genomes drastically improves upon previous multicontig assemblies by correcting and newly identifying a significant number of open reading frames. We believe that the availability of this resource will result in the discovery of proteins and molecular mechanisms used by an oral pathogen, with the potential to further our understanding of how Fusobacterium nucleatum contributes to a repertoire of diseases, including periodontitis, preterm birth, and colorectal cancer.

Keywords: Fusobacterium; Fusobacterium nucleatum; colon cancer; colorectal cancer; genomics; host-pathogen; pathogenesis.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Databases, Nucleic Acid*
Fusobacterium / genetics*
Genome, Bacterial*
Internet
Molecular Sequence Annotation / methods*
Sequence Analysis, DNA*