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

By Ana Laura Grazziotin, Eugene V. Koonin, David M. Kristensen. Nucleic Acids Res., 2016

351 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/d3966e884f5b7f5ea7fceffa67dae2795c73bbd7

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In Ecology

1. Karthik Anantharaman
2. Ariane Toussaint
3. Kristopher Kieft
4. C. Hill
5. A. Shkoporov
6. Zhichao Zhou

In Molecular Biology

1. R. Ross
2. Karthik Anantharaman
3. Ariane Toussaint
4. Kristopher Kieft
5. Clovis Galiez
6. C. Hill
7. A. Shkoporov
8. Zhichao Zhou

In Plant Science

1. Karthik Anantharaman
2. Kristopher Kieft
3. C. Hill
4. A. Shkoporov
5. Zhichao Zhou

Citations in the corpus

• Bacteriophages of the Human Gut: The "Known Unknown" of the Microbiome. (2019, methodology): “(D) SDS-PAGE gel electrophoresis displaying predominant polypeptide fractions in CsCl-gradient-purified human fecal VLP fraction (reproduced from Guerin et al., 2018).”
• PHROG: families of prokaryotic virus proteins clustered using remote homology (2021, methodology): “Viruses included in the pVOGs database (6) and complete virus genomes from GenBank were also downloaded.”
• The human gut virome is highly diverse, stable and individual-specific (2019, methodology): “1b1 package) was used to search 692 amino acid sequences of predicted protein products against an HMM database prokaryotic 693 viral orthologous groups (pVOGs) (Grazziotin et al., 2017).”
• VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences (2020, methodology): “V-score differs from the previously used “ virus quotient ” metric [69, 70] in that it does not take into account the annotation ’ s relatedness to bacteria or archaea.”
• mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements (2021, background): “0 (11), COMPASS (21), NCBI Plasmid RefSeq (22), GutPhage Database (18), pVOG (17), ISfinder (19), ACLAME (23), and immedb (20).”