Fusobacterium genomics using MinION and Illumina sequencing enables genome completion and correction

Abstract

Understanding 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 F. nucleatum subsp. nucleatum ATCC 25586 (seven total species, eight total 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 MinION (>80 kbp) platforms, coupled with genome assembly using the open-source software Unicycler. When compared to currently available draft assemblies (previously 24-67 contigs), these genomes are highly accurate and consist of only one complete chromosome. We present the complete genome sequence of F. nucleatum 23726, a genetically tractable and biomedically important strain, and in addition, reveal that the previous F. nucleatum 25586 genome assembly contains a 452 kb genomic inversion that has been corrected using our sequencing and assembly pipeline. To enable the scientific community, we concurrently use these genomes to launch FusoPortal, a repository of interactive and downloadable genomic data, genome maps, gene annotations, and protein functional analysis and classification. In summary, this study provides detailed methods for accurately sequencing, assembling, and annotating Fusobacterium genomes, which will enhance efforts to properly identify virulence proteins that may contribute to a repertoire of diseases including periodontitis, pre-term birth, and colorectal cancer.