Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales

By Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin. 2015

254 citations recorded by the source corpus.

With the continuously accelerating genome sequencing from diverse groups of archaea and bacteria, accurate identification of gene orthology and availability of readily expandable clusters of orthologous genes are essential for the functional annotation of new genomes. We report an update of the collection of archaeal Clusters of Orthologous Genes (arCOGs) to cover, on average, 91% of the protein-coding genes in 168 archaeal genomes. The new arCOGs were constructed using refined algorithms for orthology identification combined with extensive manual curation, including incorporation of the results of several completed and ongoing research projects in archaeal genomics. A new level of classification is introduced, superclusters that unit two or more arCOGs and more completely reflect gene family evolution than individual, disconnected arCOGs. Assessment of the current archaeal genome annotation in public databases indicates that consistent use of arCOGs can significantly improve the annotation quality. In addition to their utility for genome annotation, arCOGs also are a platform for phylogenomic analysis. We explore this aspect of arCOGs by performing a phylogenomic study of the Thermococci that are traditionally viewed as the basal branch of the Euryarchaeota. The results of phylogenomic analysis that involved both comparison of multiple phylogenetic trees and a search for putative derived shared characters by using phyletic patterns extracted from the arCOGs reveal a likely evolutionary relationship between the Thermococci, Methanococci, and Methanobacteria. The arCOGs are expected to be instrumental for a comprehensive phylogenomic study of the archaea.

Subfields: Ecology, Genetics, Molecular Biology

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Citations in the corpus

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018, methodology): “In addition, manually curated OGs available for the three domains of life were integrated into the corresponding levels in eggNOG, namely bacterial subset of COGs (23), archaeal arCOGs (24) and eukaryotic KOGs (25).”
Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation (2016, background): “All other COG-based resources currently use full-length proteins rather than domains (e.g. COGs (8,9), KOGs (39), arCOGs (40), NCVOGs (41), mimiCOGs (42), etc.), although those resources use manual curation to provide ‘domain-aware’ orthology predictions, avoiding grouping together of COGs due to…”
COG database update: focus on microbial diversity, model organisms, and widespread pathogens (2020, methodology): “In the past, the COG approach has been used to delineate clusters of orthologous genes for cyanobacteria (24,25), lactobacilli (26), spore-forming firmicutes (27,28) and archaea (7,29,30).”
SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways (2020, methodology): “The orthology databases used for database merging and homologous gene identification in this study included arCOG (Makarova et al., 2015), COG (Galperin et al., 2015), eggNOG (Huerta-Cepas et al., 2019) and KEGG (Kanehisa et al., 2016).”