eggNOG v4.0: nested orthology inference across 3686 organisms

Abstract

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.

Distinct gene expression profile of Xanthomonas retroflexus engaged in synergistic multispecies biofilm formation

“…To get an overview of the changed functions in the four-species biofilm, the 141 responding genes were annotated to eggNOG functional groups and Figure 2b illustrates the distributions within the categories (Supplementary Table S3; Powell et al, 2014). Of the 12 genes annotated to 'Amino Acid Metabolism and Transport', two were specifically involved in branched-chain amino acid synthesis and two were involved in tryptophan synthesis.…”

Systematic Characterization and Prediction of Post-Translational Modification Cross-Talk *

“…Residue Co-Evolution-For each human protein as the reference, the multiple sequence alignment (MSA) across ϳ50 vertebrates were obtained from the "align" data set of the vertebrates nonsupervised orthologous groups in the eggNOG v4.0 database (31). When multiple paralogs from one species were available, only the one with the smallest editing distance to the human homolog was included in MSA.…”

Global biogeography of Prochlorococcus genome diversity in the surface ocean

“…We used the permutation multivariate analysis of variance test (function adonis; Oksanen et al, 2013) to test if regions explain abundance variation. Using sequence similarity to non-core genes (BLASTp), we identified the categories of Clusters of Orthologous Groups of proteins (COGs) from cyanobacterial eggNOG database (Powell et al, 2014). We measured the association between sampling regions and either COG categories using a point biserial correlation coefficient (r.g.)…”