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

Life
K S MakarovaEugene V Koonin

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 b...Continue Reading

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Aug 31, 2016·Nature Microbiology·Brett J BakerThijs J G Ettema
Aug 11, 2015·Frontiers in Microbiology·Patrick Forterre
May 21, 2016·Frontiers in Microbiology·Kira S MakarovaSonja-Verena Albers
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Feb 3, 2019·Biochemical Society Transactions·Kira S MakarovaEugene V Koonin
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Methods Mentioned

BETA
dissection

Software Mentioned

TMHMM
MAFFT
FastTree
BLAST
RPS
PSI
ARMANs
HHpred
MUSCLE
arCOG

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