Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

Abstract

Viruses are the most abundant and diverse biological entities on earth, and while most of this diversity remains completely unexplored, advances in genome sequencing have provided unprecedented glimpses into the virosphere. The Prokaryotic Virus Orthologous Groups (pVOGs, formerly called Phage Orthologous Groups, POGs) resource has aided in this task over the past decade by using automated methods to keep pace with the rapid increase in genomic data. The uses of pVOGs include functional annotation of viral proteins, identification of genes and viruses in uncharacterized DNA samples, phylogenetic analysis, large-scale comparative genomics projects, and more. The pVOGs database represents a comprehensive set of orthologous gene families shared across multiple complete genomes of viruses that infect bacterial or archaeal hosts (viruses of eukaryotes will be added at a future date). The pVOGs are constructed within the Clusters of Orthologous Groups (COGs) framework that is widely used for orthology identification in prokaryotes. Since the previous release of the POGs, the size has tripled to nearly 3000 genomes and 300 000 proteins, and the number of conserved orthologous groups doubled to 9518. User-friendly webpages are available, including multiple sequence alignments and HMM profiles for each VOG. These changes provide major improvements to the pVOGs database, at a time of rapid advances in virus genomics. The pVOGs database is hosted jointly at the University of Iowa at http://dmk-brain.ecn.uiowa.edu/pVOGs and the NCBI at ftp://ftp.ncbi.nlm.nih.gov/pub/kristensen/pVOGs/home.html.

Sequence analysis of malacoherpesvirus proteins: Pan-herpesvirus capsid module and replication enzymes with an ancient connection to “Megavirales”

“…We expect that re-sequencing of virus-like replicons associated with the amphioxus and annelid genomes will reveal more gene products shared with other herpesviruses. Based on these data and the evidence in the literature, the fraction of widely conserved genes (in the first approximation, having homologs beyond the family level) in herpesviruses may be at least 30% and perhaps closer to 50%, similarly to what has been suggested for bacteriophages with similarlysized DNA genomes (Kristensen et al, 2011;Grazziotin et al, 2017). Given the observations of the putative herpesviruses associated with diverse marine invertebrates, the family name Malacoherpesviridae may be worth replacing with a more inclusive one, perhaps "Ectoherpesviridae".…”

How to Name and Classify Your Phage: An Informal Guide

“…Comparison of protein groups, predicted proteomes, identification of signature genes: CoreGenes 3.5 [36,37], Roary (core and accessory genome analysis) [38], prokaryotic Virus Orthologous Groups resource (pVOGs) [39]. …”

ACI‐1 beta‐lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages

“…Separately, we predicted proteins with MetaGeneMark version 3.38 (Zhu et al, 2010) using default parameters for 50 kb either side of aci1. Subsequently, we annotated proteins taking the top ranked (in terms of E-value) annotated BLASTp hit from NR and by scanning each protein with HMMSCAN (HMMER, 2017) against a database of viral protein families represented as profile hidden markov models from the prokaryotic Viral Orthologous Groups (Grazziotin et al, 2017). We inspected all regions manually to resolve discrepant annotations and define the boundaries of the mobile elements.…”