eggNOG 6.0: enabling comparative genomics across 12 535 organisms

Abstract

The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database is a bioinformatics resource providing orthology data and comprehensive functional information for organisms from all domains of life. Here, we present a major update of the database and website (version 6.0), which increases the number of covered organisms to 12 535 reference species, expands functional annotations, and implements new functionality. In total, eggNOG 6.0 provides a hierarchy of over 17M orthologous groups (OGs) computed at 1601 taxonomic levels, spanning 10 756 bacterial, 457 archaeal and 1322 eukaryotic organisms. OGs have been thoroughly annotated using recent knowledge from functional databases, including KEGG, Gene Ontology, UniProtKB, BiGG, CAZy, CARD, PFAM and SMART. eggNOG also offers phylogenetic trees for all OGs, maximising utility and versatility for end users while allowing researchers to investigate the evolutionary history of speciation and duplication events as well as the phylogenetic distribution of functional terms within each OG. Furthermore, the eggNOG 6.0 website contains new functionality to mine orthology and functional data with ease, including the possibility of generating phylogenetic profiles for multiple OGs across species or identifying single-copy OGs at custom taxonomic levels. eggNOG 6.0 is available at http://eggnog6.embl.de.

Figure 1.

Summary card and extended information for the AP5SY OG. (A) OG general information, functional annotations summarised from various sources, and hierarchical information pointing to parent and child OGs. (B) Extended information about the OG using the new interactive visualisation tool for phylogenetic trees. Tree topology is annotated with duplication (red) and speciation (blue) events, branch length (grey), and bootstrap values (orange); common gene names are aligned with their corresponding branches, sequence domain structure is depicted schematically, while colored bands indicate the last common ancestor of each clade.

Figure 2.

Distribution and copy number of genes belonging to 10 orthologous groups (COGs) associated with virulence factors across 26 Enterobacteriaceae species. The figure was generated automatically using the new eggNOG phylogenetic profiling functionality.