ArticleLife (Basel, Switzerland)2015
Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales.
Article in Life (Basel, Switzerland), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 176 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
176 citing papers in PubMed, 1 synthesis or guideline pooled it, 281 citations in OpenAlex.
- Pooled it
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- Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages.Nature communications · 2026Article
- Comprehensive analyses of archaeal viral genomes reveal genomic characteristics, divergence, and host interactions.Microbiome · 2026Article
- CsmR controls both, motility and cell shape, in Haloferax volcanii.PLoS genetics · 2026Article
- Successive waves of transcriptional repression and de-repression license cell cycle progression in an archaeon.Nucleic acids research · 2026Article
- New lineages provide insights into the convergent evolution of extreme salt adaptation within symbiotic Archaea.Molecular biology and evolution · 2026Article
- Comparative pangenome analysis of methanogenic archaea from diverse ecosystems reveals potential targets for methane mitigation in rumen microbiome.Journal of animal science and technology · 2026Article
- The naked mole-rat microbiome is associated with healthy aging and social structure.Cell reports · 2026Article
- Horizontal gene transfer and gene loss drove the divergent evolution of host dependency in Micrarchaeota.National science review · 2026Article
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- Close spatial and metabolic association between heterotrophic and ammonia-oxidizing marine Nitrososphaerota.ISME communications · 2026Article
- A previously undescribed archaeal virus suppresses host immunity.EMBO reports · 2025Article
- Microbially-mediated halogenation and dehalogenation cycling of organohalides in the ocean.Nature communications · 2025Article
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- Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail.Science advances · 2025Article
- Uncovering the prevalence, key biogenesis enzymes, and biological significance of archaeal lipoproteins.Nature communications · 2025Article
- Phylogenomic Analyses Reveal that Panguiarchaeum Is a Clade of Genome-Reduced Asgard Archaea Within the Njordarchaeia.Molecular biology and evolution · 2025Article
- Article
116 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
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 untie 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.