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Life 2015, 5(1), 818-840; doi:10.3390/life5010818

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

National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA
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Academic Editors: Hans-Peter Klenk, Michael W. W. Adams and Roger A. Garrett
Received: 12 January 2015 / Revised: 25 February 2015 / Accepted: 28 February 2015 / Published: 10 March 2015
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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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. View Full-Text
Keywords: arCOGs; genome annotation; phylogenomics; Thermococci; methanogens arCOGs; genome annotation; phylogenomics; Thermococci; methanogens
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Makarova, K.S.; Wolf, Y.I.; Koonin, E.V. Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales. Life 2015, 5, 818-840.

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