Cross-species gene-sharing network for 125 bacterial and archaeal pangenomes

Cross-species gene-sharing network reconstructed from the pangenomes of 125 bacterial and archaeal species (based on Manzano-Morales et al., Genome Biology 2023, DOI: 10.1186/s13059-023-03089-3).

Methods: The Genome Taxonomy Database (GTDB r95) was parsed to identify species with at least 15 available high-quality genomes, selecting at most one species per genus and discarding all medium and low-quality genomes. For computational reasons, species with more than 100 high-quality genomes were subsampled to keep a representative set of 100 genomes. Gene families were defined by mapping predicted open reading frames to the eggNOG database at the root level. The network was built by connecting each species-level pangenome to all the gene families that are present in it.

File content: Each row represents one link in the gene-sharing network (the first row contains headers). Tab-delimited columns: (1) Genome ID of GTDB r95 species representative; (2) gene family eggNOG ID; (3) 'true' if the gene family belongs to the core genome in that species, 'false' if it belongs to the accessory genome. The gene-sharing network is defined by columns (1) and (2). The third column can be used to filter core or accessory genes.