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.
Highlights
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
Fusobacterium nucleatum has recently been connected with colorectal cancer (CRC) [3, 4], with studies showing that this bacterium induces a proinflammatory microenvironment and chemoresistance against drugs used to treat CRC [5,6,7]
The motivation for complete sequencing and assembly of Fusobacterium genomes came from our discovery that bioinformatic analysis identified a high percentage of large genes (~3,000 to 12,000 bp) in the F. nucleatum subsp. nucleatum ATCC 23726 genome that appeared to correspond to proteins missing critical domains at either the N or C terminus (e.g., Ͼ2,000-amino acid deletions)
Summary
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. To provide ease of use and data accessibility to the community, we have used this study to launch the FusoPortal repository (http://fusoportal.org), which provides the first eight completely sequenced, assembled, and annotated Fusobacterium genomes using MinION and Illumina technology. While databases such as KEGG, NCBI, and UniProt are crucial for researchers to find open reading frames, our goal was to create a central database in which researchers interested in Fusobacterium biology could obtain high-quality data in an easy-to-navigate platform. We highlight how users can interact with the FusoPortal website and additional bioinformatic analysis that was made possible by improved genome sequencing and assembly
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