ArticleDatabase : the journal of biological databases and curation2020
An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic networks of symbiotic organisms.
Article in Database : the journal of biological databases and curation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed.
- Evolutionary signals in metabolic networks of insect endosymbionts revealed through comparative topological modeling.BMC genomics · 2026Article
- iSymBase: an integrative functional-genomic platform for ecological exploration of insect symbionts.ISME communications · 2026Article
- Metadag: a web tool to generate and analyse metabolic networks.BMC bioinformatics · 2025Article
- The Minimal Translation Machinery: What We Can Learn From Naturally and Experimentally Reduced Genomes.Frontiers in microbiology · 2022Article
- COG database update: focus on microbial diversity, model organisms, and widespread pathogens.Nucleic acids research · 2021Article
- The Metabolic Building Blocks of a Minimal Cell.Biology · 2020Article
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6 authors.
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Abstract
The Symbiotic Genomes Database (SymGenDB; http://symbiogenomesdb.uv.es/) is a public resource of manually curated associations between organisms involved in symbiotic relationships, maintaining a catalog of completely sequenced/finished bacterial genomes exclusively. It originally consisted of three modules where users could search for the bacteria involved in a specific symbiotic relationship, their genomes and their genes (including their orthologs). In this update, we present an additional module that includes a representation of the metabolic network of each organism included in the database, as Directed Acyclic Graphs (MetaDAGs). This module provides unique opportunities to explore the metabolism of each individual organism and/or to evaluate the shared and joint metabolic capabilities of the organisms of the same genera included in our listing, allowing users to construct predictive analyses of metabolic associations and complementation between systems. We also report a ~25% increase in manually curated content in the database, i.e. bacterial genomes and their associations, with a final count of 2328 bacterial genomes associated to 498 hosts. We describe new querying possibilities for all the modules, as well as new display features for the MetaDAGs module, providing a relevant range of content and utility. This update continues to improve SymGenDB and can help elucidate the mechanisms by which organisms depend on each other.
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