IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses

By Simon Roux, David Páez-Espino, I-Min A. Chen, Krishna Palaniappan, Anna Ratner, Ken Chu, T. Reddy, Stephen Nayfach, Frederik Schulz, Lee Call and 5 more. Nucleic Acids Res., 2020

296 citations recorded by the source corpus.

Viruses are integral components of all ecosystems and microbiomes on Earth. Through pervasive infections of their cellular hosts, viruses can reshape microbial community structure and drive global nutrient cycling. Over the past decade, viral sequences identified from genomes and metagenomes have provided an unprecedented view of viral genome diversity in nature. Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. Here, we present the third version of IMG/VR, composed of 18 373 cultivated and 2 314 329 uncultivated viral genomes (UViGs), nearly tripling the total number of sequences compared to the previous version. These clustered into 935 362 viral Operational Taxonomic Units (vOTUs), including 188 930 with two or more members. UViGs in IMG/VR are now reported as single viral contigs, integrated proviruses or genome bins, and are annotated with a new standardized pipeline including genome quality estimation using CheckV, taxonomic classification reflecting the latest ICTV update, and expanded host taxonomy prediction. The new IMG/VR interface enables users to efficiently browse, search, and select UViGs based on genome features and/or sequence similarity. IMG/VR v3 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.

Subfields: Ecology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/64b1ec96779f59825029debab509c4f81b6409d1

Citations in the corpus

• iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria (2023, unknown): “SpacePHARER predictions were based on the predictmatch function from SpacePHARER v2.fc5e668 [12] applied to the input virus genomes with a sensitivity of 7.5 (“-s 7.5”) and a maximum number of results per query sequence of 10,000, using the IMG/VR v3 CRISPR database [8].”
• INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes (2021, unknown): “The integrated microbial genomes viral resource (IMG/VR) provides access to greater than 2 million viral genomes, including phages, via a graphical interface (53).”