VICTOR: genome-based phylogeny and classification of prokaryotic viruses
TLDR
A novel in silico framework for phylogeny and classification of prokaryotic viruses is presented, in line with the principles of phylogenetic systematics, and using a large reference dataset of officially classified viruses.Abstract:
Motivation Bacterial and archaeal viruses are crucial for global biogeochemical cycles and might well be game-changing therapeutic agents in the fight against multi-resistant pathogens. Nevertheless, it is still unclear how to best use genome sequence data for a fast, universal and accurate taxonomic classification of such viruses. Results We here present a novel in silico framework for phylogeny and classification of prokaryotic viruses, in line with the principles of phylogenetic systematics, and using a large reference dataset of officially classified viruses. The resulting trees revealed a high agreement with the classification. Except for low resolution at the family level, the majority of taxa was well supported as monophyletic. Clusters obtained with distance thresholds chosen for maximizing taxonomic agreement appeared phylogenetically reasonable, too. Analysis of an expanded dataset, containing >4000 genomes from public databases, revealed a large number of novel species, genera, subfamilies and families. Availability and implementation The selected methods are available as the easy-to-use web service 'VICTOR' at https://victor.dsmz.de. Contact jan.meier-kolthoff@dsmz.de. Supplementary information Supplementary data are available at Bioinformatics online.read more
Citations
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TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy
TL;DR: TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy and analysis connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information.
Journal ArticleDOI
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
Ho Bin Jang,Benjamin Bolduc,Olivier Zablocki,Jens H. Kuhn,Simon Roux,Evelien M. Adriaenssens,Evelien M. Adriaenssens,J. Rodney Brister,Andrew M. Kropinski,Andrew M. Kropinski,Mart Krupovic,Rob Lavigne,Dann Turner,Matthew B. Sullivan +13 more
TL;DR: This work presents vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions, and applies it to analyze 15,280 Global Ocean Virome genome fragments.
Journal ArticleDOI
Minimum information about an uncultivated virus genome (MIUVIG)
Simon Roux,Evelien M. Adriaenssens,Bas E. Dutilh,Eugene V. Koonin,Andrew M. Kropinski,Mart Krupovic,Jens H. Kuhn,Rob Lavigne,J. Rodney Brister,Arvind Varsani,Arvind Varsani,Clara Amid,Ramy K. Aziz,Seth R. Bordenstein,Peer Bork,Mya Breitbart,Guy Cochrane,Rebecca A. Daly,Christelle Desnues,Melissa B. Duhaime,Joanne B. Emerson,François Enault,Jed A. Fuhrman,Pascal Hingamp,Philip Hugenholtz,Bonnie L. Hurwitz,Natalia Ivanova,Jessica M. Labonté,Kyung Bum Lee,Rex R. Malmstrom,Manuel Martinez-Garcia,Ilene Karsch Mizrachi,Hiroyuki Ogata,David Paez-Espino,Marie-Agnès Petit,Catherine Putonti,Thomas Rattei,Alejandro Reyes,Francisco Rodriguez-Valera,Karyna Rosario,Lynn M. Schriml,Frederik Schulz,Grieg F. Steward,Matthew B. Sullivan,Shinichi Sunagawa,Curtis A. Suttle,Ben Temperton,Susannah G. Tringe,Rebecca Vega Thurber,Nicole S. Webster,Nicole S. Webster,Katrine Whiteson,Steven W. Wilhelm,K. Eric Wommack,Tanja Woyke,Kelly C. Wrighton,Pelin Yilmaz,Takashi Yoshida,Mark J. Young,Natalya Yutin,Lisa Zeigler Allen,Lisa Zeigler Allen,Nikos C. Kyrpides,Emiley A. Eloe-Fadrosh +63 more
TL;DR: The MIUViG (Minimum Information about an Uncultivated Virus Genome) as mentioned in this paper standard was developed within the Genomic Standards Consortium framework and includes virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction.
Journal ArticleDOI
Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee
Mart Krupovic,Bas E. Dutilh,Bas E. Dutilh,Bas E. Dutilh,Evelien M. Adriaenssens,Johannes Wittmann,Finn K. Vogensen,Mathew B. Sullivan,Janis Rumnieks,David Prangishvili,Rob Lavigne,Andrew M. Kropinski,Jochen Klumpp,Annika Gillis,François Enault,Robert Edwards,Siobain Duffy,Martha R C Clokie,Jakub Barylski,Hans-Wolfgang Ackermann,Jens H. Kuhn +20 more
TL;DR: Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species in the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019.
Journal ArticleDOI
VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses
TL;DR: VIRIDIC is developed, which implements the traditional algorithm used by the International Committee on Taxonomy of Viruses (ICTV), Bacterial and Archaeal Viruses Subcommittee, to calculate virus intergenomic similarities, and proved best at estimating the relatedness between more distantly-related phages.
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