Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Abstract

Viruses of bacteria and archaea are likely to be critical to all natural, engineered and human ecosystems, and yet their study is hampered by the lack of a universal or scalable taxonomic framework. Here, we introduce vConTACT 2.0, a network-based application to establish prokaryotic virus taxonomy that scales to thousands of uncultivated virus genomes, and integrates confidence scores for all taxonomic predictions. Performance tests using vConTACT 2.0 demonstrate near-identical correspondence to the current official viral taxonomy (>85% genus-rank assignments at 96% accuracy) through an integrated distance-based hierarchical clustering approach. Beyond "known viruses", we used vConTACT 2.0 to automatically assign 1,364 previously unclassified reference viruses to tentative taxa, and scaled it to. CC-BY 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

Integrative omics analysis ofPseudomonas aeruginosavirus PA5oct highlights the molecular complexity of jumbo phages

“…To build a gene-sharing network, we retrieved 231,166 protein sequences representing the genomes of 2,304 bacterial and archaeal viruses from NCBI RefSeq (version 85) and used the network analytics tool, vConTACT (version 2.0; https://bitbucket.org/MAVERICLab/vcontact2) (Jang et al, 2019), as an app at iVirus (Bolduc et al, 2017a). Briefly, including protein sequences from PA5oct, a total of 231,627 sequences were subjected to all-to-all BLASTp searches, with an E-value threshold of 10 -4 , and defined as the homologous protein clusters (PCs) in the same manner as previously described (Bolduc et al, 2017b).…”

“…Based on the number of shared PCs between the genomes, vConTACT v2.0 calculated the degree of similarity as the negative logarithmic score by multiplying hypergeometric similarity P-value by the total number of pairwise comparisons. Subsequently, pairs of closely related genomes with a similarity score of ≥ 1 were grouped into viral clusters (VCs), with default parameters of vConTACT v2.0 (Jang et al, 2019). The network was visualized with Cytoscape (version 3.5.1; http://cytoscape.org/), using an edge-weighted spring embedded model, which places the genomes or fragments sharing more PCs closer to each other.…”

“…The taxonomic affiliation was taken from the International Adriaenssens et al, 2017). Further, the proportion of shared PCs between two genomes was characterized, as previously described (Bolduc et al, 2017b andJang et al, 2019).…”

“…A subsequent analysis found 60 coherent groups of viral genomes (i.e., viral clusters, VCs) embedded in this subnetwork ( Figure 3B; Table S5), of which six jumbo phages including PA5oct and Escherichia phages 121Q/PBECO 4, Klebsiella virus RaK2, Klebsiella virus K64-1, and Cronobacter virus GAP32 showed stronger connections to each other but weaker connections outside the group due to their more common genes (i.e., homologous protein clusters, PCs) than the rest of the network ( Figure 3B). Notably, a further inspection of their relationships (phage K64-1 was excluded as it has an incomplete protein annotation profile in NCBI) uncovered its sub-structure where PA5oct shares less common PCs (~11-15%) to the remaining members ( Figure 3C), indicating its distant relationships as a outlier genome (Jang et al, 2019).…”

Polinton-like viruses and virophages are widespread in aquatic ecosystems

“…To understand the relationships between the large numbers of virophages and PLVs in our dataset, we used a network-based analysis of shared protein clusters using vConTACT v.2.0 21 . Such an approach is suitable when faced with numerous distantly related viruses which may undergo frequent genetic exchange.…”