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

Makarova KS, Wolf YI, Koonin EV - Life (Basel) (2015)

Bottom Line: Assessment of the current archaeal genome annotation in public databases indicates that consistent use of arCOGs can significantly improve the annotation quality.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.

View Article: PubMed Central - PubMed

Affiliation: National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA. makarova@ncbi.nlm.nih.gov.

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.

No MeSH data available.


Alternative phylogenies for the Themococci Thick lines show the relationships between Thermococci and their closest relatives, Methanococci, Methanobacteria, and Methanopyrus. Alternative topologies of Thermococci in the Euryarchaeota tree are indicated with Roman numerals (I and II). The topology II is shown as multifurcation because the specific order of branching of these lineages has not been addressed or analyzed in this work.
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life-05-00818-f002: Alternative phylogenies for the Themococci Thick lines show the relationships between Thermococci and their closest relatives, Methanococci, Methanobacteria, and Methanopyrus. Alternative topologies of Thermococci in the Euryarchaeota tree are indicated with Roman numerals (I and II). The topology II is shown as multifurcation because the specific order of branching of these lineages has not been addressed or analyzed in this work.

Mentions: Prompted by these observations, we sought evidence in support of either the basal position of the Thermococci in the Euryarchaea tree (topology I) or their clustering with class I methanogens (topology II) (Figure 2). First, we reconstructed 1366 phylogenetic trees for arCOGs that have at least four well-represented clades (see Methods for details; the trees are available on [87]); 951 of these trees contained the Thermococci clade. For each of these 951 trees, the affinity of the Thermococci to other clades was quantified (see Methods for details). Ranked by the average affinity, the most common neighbors of the Thermococci were Methanococci (0.49), followed by Korarchaeota (0.48) and Nanoarchaeota (0.44) (see Supplementary Table S2).


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

Makarova KS, Wolf YI, Koonin EV - Life (Basel) (2015)

Alternative phylogenies for the Themococci Thick lines show the relationships between Thermococci and their closest relatives, Methanococci, Methanobacteria, and Methanopyrus. Alternative topologies of Thermococci in the Euryarchaeota tree are indicated with Roman numerals (I and II). The topology II is shown as multifurcation because the specific order of branching of these lineages has not been addressed or analyzed in this work.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390880&req=5

life-05-00818-f002: Alternative phylogenies for the Themococci Thick lines show the relationships between Thermococci and their closest relatives, Methanococci, Methanobacteria, and Methanopyrus. Alternative topologies of Thermococci in the Euryarchaeota tree are indicated with Roman numerals (I and II). The topology II is shown as multifurcation because the specific order of branching of these lineages has not been addressed or analyzed in this work.
Mentions: Prompted by these observations, we sought evidence in support of either the basal position of the Thermococci in the Euryarchaea tree (topology I) or their clustering with class I methanogens (topology II) (Figure 2). First, we reconstructed 1366 phylogenetic trees for arCOGs that have at least four well-represented clades (see Methods for details; the trees are available on [87]); 951 of these trees contained the Thermococci clade. For each of these 951 trees, the affinity of the Thermococci to other clades was quantified (see Methods for details). Ranked by the average affinity, the most common neighbors of the Thermococci were Methanococci (0.49), followed by Korarchaeota (0.48) and Nanoarchaeota (0.44) (see Supplementary Table S2).

Bottom Line: Assessment of the current archaeal genome annotation in public databases indicates that consistent use of arCOGs can significantly improve the annotation quality.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.

View Article: PubMed Central - PubMed

Affiliation: National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA. makarova@ncbi.nlm.nih.gov.

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.

No MeSH data available.