GenomoBase: A comprehensive resource for the family Genomoviridae

Area of Science:

• Virology
• Bioinformatics
• Genomics

Background:

• Genomoviridae are circular single-stranded DNA viruses found across diverse hosts and environments.
• Metagenomics has increased genomovirus discovery, but data are fragmented across public repositories.
• A centralized, curated resource is needed to consolidate genomovirus genomic, ecological, and bibliographic information.

Purpose of the Study:

• To introduce GenomoBase, a comprehensive, curated database for all known genomovirus species.
• To facilitate the integration and exploration of genomic, ecological, and bibliographic data for genomoviruses.
• To enable enhanced discovery and analysis of genomoviruses within public metagenomic datasets.

Main Methods:

• GenomoBase was constructed by integrating data for 237 ICTV-recognized genomovirus species.
• The resource incorporates Serratus-filtered Sequence Read Archive (SRA) screening outputs.
• A bait-and-assemble workflow was used to re-analyze prioritized metagenomic data.

Main Results:

• GenomoBase provides a unified platform for genomovirus data, including genomic sequences, annotations, and metadata.
• Integration of Serratus-filtered SRA data allows for efficient prioritization of metagenomes for re-analysis.
• A proof-of-concept analysis successfully reconstructed two novel candidate circular genomovirus genomes from metagenomic reads.
• The newly identified genomovirus candidates fall below the 78% species demarcation threshold.

Conclusions:

• GenomoBase serves as a valuable, curated resource for genomovirus research.
• The database supports comparative genomics and taxonomically informed exploration of public metagenomes.
• GenomoBase facilitates the discovery of new genomoviruses and enhances our understanding of their diversity and evolution.