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. 2017 Nov 1;33(21):3396-3404.
doi: 10.1093/bioinformatics/btx440.

VICTOR: genome-based phylogeny and classification of prokaryotic viruses

Jan P Meier-Kolthoff  1 , Markus Göker  1
Affiliations

VICTOR: genome-based phylogeny and classification of prokaryotic viruses

Jan P Meier-Kolthoff et al. Bioinformatics. .

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.

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Figures

Fig. 1.
Fig. 1.
Relative performance of GBDP settings and optimality criteria. The two principal components (PC1 and PC2) that explained most of the variation (given in percent) in the data are displayed. Dots represent the individual GBDP settings, whereas arrows represent the loadings of the relevant variables and thus the performance of each combination of GBDP parameters. Normal probability ellipsoids for 95% confidence limits are shown separately for amino acid and nucleotide sequences (Color version of this figure is available at Bioinformatics online.)
Fig. 2.
Fig. 2.
Phylogeny of prokaryotic viruses inferred from the amino-acid sequences contained in the reference dataset. Four dashed branches were downscaled by a factor of four to ease visualization of the tree. Genome size, genomic G + C content, ICTV genera and families as well as clusters derived from the ICTV genera and families are shown next to the tips within circles 1–6. For both the tree and the clusterings the optimal GBDP settings (Table 1) were used. Branch support ≥ 60% is shown as a colour gradient from red to green; terminal branches and branches with support < 60% are black. A linear visualization is provided in Supplement File S3 (Color version of this figure is available at Bioinformatics online.)
Fig. 3.
Fig. 3.
Taxon support at each taxonomic rank for ICTV taxa and clusters derived from these taxa. The underlying phylogenies and clusterings are based on the optimal GBDP settings provided in Table 1 for nucleotide and amino-acid sequences, the clusterings also on the according distance thresholds T. The dashed lines indicate areas of significant support (≥95%) or conflict ( ≤−95%); taxon support is displayed as negative in the case of non-monophyletic taxa (Color version of this figure is available at Bioinformatics online.)
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References

    1. Abedon S.T. et al. (2011) Phage treatment of human infections. Bacteriophage, 1, 66–85. - PMC - PubMed
    1. Ackermann H.W. (2007) 5500 Phages examined in the electron microscope. Arch. Virol., 152, 227–243. - PubMed
    1. Ackermann H.W. (2009) Phage classification and characterization In: Clokie M. R, Kropinski A M (eds.) Bacteriophages, Vol 501, chapter 13. Humana Press, New York City, pp 127–140. - PubMed
    1. Adams M.J. et al. (2017) 50 years of the International Committee on Taxonomy of Viruses: progress and prospects. Arch. Virol., 162, 1441–1446. - PubMed
    1. Ågren J. et al. (2012) Gegenees: Fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups. PLoS ONE, 7, - PMC - PubMed