FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced <italic toggle="yes">Fusobacterium</italic> Genomes Improves Gene Identification and Characterization

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 provi...

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Autores principales:	Blake E. Sanders, Ariana Umana, Justin A. Lemkul, Daniel J. Slade
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	Fusobacterium Fusobacterium nucleatum pathogenesis colon cancer colorectal cancer genomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/5ecb3ccf103f4b71b4ea5ba2f095e59d
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spelling	oai:doaj.org-article:5ecb3ccf103f4b71b4ea5ba2f095e59d2021-11-15T15:25:50ZFusoPortal: an Interactive Repository of Hybrid MinION-Sequenced <italic toggle="yes">Fusobacterium</italic> Genomes Improves Gene Identification and Characterization10.1128/mSphere.00228-182379-5042https://doaj.org/article/5ecb3ccf103f4b71b4ea5ba2f095e59d2018-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00228-18https://doaj.org/toc/2379-5042ABSTRACT 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.Blake E. SandersAriana UmanaJustin A. LemkulDaniel J. SladeAmerican Society for MicrobiologyarticleFusobacteriumFusobacterium nucleatumpathogenesiscolon cancercolorectal cancergenomicsMicrobiologyQR1-502ENmSphere, Vol 3, Iss 4 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Fusobacterium Fusobacterium nucleatum pathogenesis colon cancer colorectal cancer genomics Microbiology QR1-502
spellingShingle	Fusobacterium Fusobacterium nucleatum pathogenesis colon cancer colorectal cancer genomics Microbiology QR1-502 Blake E. Sanders Ariana Umana Justin A. Lemkul Daniel J. Slade FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced <italic toggle="yes">Fusobacterium</italic> Genomes Improves Gene Identification and Characterization
description	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.
format	article
author	Blake E. Sanders Ariana Umana Justin A. Lemkul Daniel J. Slade
author_facet	Blake E. Sanders Ariana Umana Justin A. Lemkul Daniel J. Slade
author_sort	Blake E. Sanders
title	FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced <italic toggle="yes">Fusobacterium</italic> Genomes Improves Gene Identification and Characterization
title_short	FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced <italic toggle="yes">Fusobacterium</italic> Genomes Improves Gene Identification and Characterization
title_full	FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced <italic toggle="yes">Fusobacterium</italic> Genomes Improves Gene Identification and Characterization
title_fullStr	FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced <italic toggle="yes">Fusobacterium</italic> Genomes Improves Gene Identification and Characterization
title_full_unstemmed	FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced <italic toggle="yes">Fusobacterium</italic> Genomes Improves Gene Identification and Characterization
title_sort	fusoportal: an interactive repository of hybrid minion-sequenced <italic toggle="yes">fusobacterium</italic> genomes improves gene identification and characterization
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/5ecb3ccf103f4b71b4ea5ba2f095e59d
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FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced <italic toggle="yes">Fusobacterium</italic> Genomes Improves Gene Identification and Characterization

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