GenomoBase: A comprehensive resource for the family Genomoviridae

Abstract The family Genomoviridae comprises circular single-stranded DNA viruses reported from fungi, plants, animals and environmental samples. Although metagenomics has accelerated their discovery, genomic sequences, annotations and metadata remain dispersed across repositories. Here we present GenomoBase (https://www.genomobase.org), a curated resource that integrates genomic, ecological and bibliographic data for all 237 ICTV-recognized genomovirus species. GenomoBase incorporates Serratus-filtered SRA screening outputs, enabling prioritization of metagenomes for targeted re-analysis. As a proof of concept, a targeted bait-and-assemble workflow of one prioritized SRA run recovered two complete genomes, both below the 78% species demarcation threshold for genomoviruses. GenomoBase streamlines comparative analyses and metagenome-guided genome recovery. Competing Interest Statement The authors have declared no competing interest. Footnotes This version of the manuscript has been revised to update the following: We updated the manuscript to strengthen the evidence that GenomoBase is not only a curated catalog of ICTV-recognized Genomoviridae species, but also a practical discovery and prioritization resource for genomovirus research. In addition to refining the database description (data sources, curation steps, annotation/metadata fields, and the web interface), we added a new proof-of-utility case study using the Explore Metagenomes module. Specifically, we present an end-to-end example in which a Serratus-prioritized SRA run is selected through GenomoBase, followed by targeted assembly and validation of a complete circular genomovirus genome from the metagenome. We then benchmark the recovered genome against reference genomes using pairwise identity-based comparisons (including species-level context) and confirm related sequences using database searches. This new analysis illustrates how GenomoBase can guide users from metagenomic screening outputs to the recovery and taxonomic placement of complete genomes, thereby enabling efficient identification of candidate datasets for downstream virological, ecological, and evolutionary studies. Figures, tables, and the Results/Discussion were updated accordingly to reflect the added analyses and to clarify the workflow and interpretation of the proof-of-utility example.