eggNOG v4.0: nested orthology inference across 3686 organisms

By Sean Powell, Kristoffer Forslund, Damian Szklarczyk, Kalliopi Trachana, Alexander C. J. Roth, Jaime Huerta-Cepas, Toni Gabaldón, Thomas Rattei, Christopher J. Creevey, Michael Kuhn and 3 more. Nucleic Acids Res., 2013

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With the increasing availability of various ‘omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available at http://eggnog.embl.de) that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive characterization and analysis pipeline to the resulting gene families. Compared with the previous version, we have more than tripled the underlying species set to cover 3686 organisms, keeping track with genome project completions while prioritizing the inclusion of high-quality genomes to minimize error propagation from incomplete proteome sets. Major technological advances include (i) a robust and scalable procedure for the identification and inclusion of high-quality genomes, (ii) provision of orthologous groups for 107 different taxonomic levels compared with 41 in eggNOGv3, (iii) identification and annotation of particularly closely related orthologous groups, facilitating analysis of related gene families, (iv) improvements of the clustering and functional annotation approach, (v) adoption of a revised tree building procedure based on the multiple alignments generated during the process and (vi) implementation of quality control procedures throughout the entire pipeline. As in previous versions, eggNOGv4 provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. Users can access the complete database of orthologous groups via a web interface, as well as through bulk download.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/81e0802d68a2567564ed4039240612276a56af41

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Citations in the corpus

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements (2014, methodology): “The need for orthology inference has led to the development of numerous methods (reviewed in 5) and databases, notably including EggNOG (6), Ensembl Compara (7), Inparanoid (8), MBGD (9), OrthoDB (10), OrthoMCL (11), Panther (12), PhylomeDB (13), Plaza (14) and OMA (15).”
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy (2015, background): “orthogroups; an orthogroup is the set of genes that are descended from a single gene in the last common ancestor of all the species being considered [2, 5–9].”
PLAZA 3.0: an access point for plant comparative genomics (2014, background): “Platforms focusing on gene families rely on grouping homologous (derived from a common ancestor) genes (9) and within a family detailed phylogenetic reconstructions are possible (10).”
Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell‐lines (2015, background): “Orthology relationships in PaxDb are precomputed, through the eggNOG mechanism [29], and can be browsed at various levels of phylogenetic depth (e.g. “mammals,” “animals,” or “eukaryotes”).”
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2015, background): “The database currently covers 2031 eukaryotic and prokaryotic organisms, as well as precomputed mappings for 1655 additional prokaryotes (12).”
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2020, background): “…annotations from different systems (GO terms (Ashburner et al., 2000) , KEGG modules (Kanehisa et al., 2014) , KO identifiers, Pfam accessions (Finn et al., 2014) , EC numbers (Bairoch, 2000) , and eggNOG accessions (Powell et al., 2014) ) associated with the UniProtKB entry.”
Genenames.org: the HGNC resources in 2015 (2014, methodology): “HCOP currently collates orthology assertions from eggNOG (34), Ensembl Compara (2), HGNC, HomoloGene (31), InParanoid (35), OMA (36), OrthoDB (37), OrthoMCL (38), PANTHER (39), PhylomeDB (40), Treefam (41) and ZFIN (18) into a single tool, enabling comparison of these data to identify a consensus or”
Expanded microbial genome coverage and improved protein family annotation in the COG database (2014, methodology): “A major extension of the COGs is implemented in the EggNOG database, with an increased number of genomes included and new clusters of orthologs (denoted NOGs, after Non-supervised Orthologous Groups); however, EggNOG is completely automatic, without manual supervision of the cluster membership or an”