Background The concept of a genomic core, defined as the set of genes ubiquitous in all
genomes of a monophyletic group, has become crucial in comparative and evolutionary …

Background Phylogenetic analysis of the Archaea has been mainly established by 16S
rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is …

Until recently, phylogenetic analyses of Archaea have mainly been based on ribosomal
RNA (rRNA) sequence comparisons, leading to the distinction of the two major archaeal …

Initial studies of the archaeal phylogeny relied mainly on the analysis of the RNA component
of the small subunit of the ribosome (SSU rRNA). The resulting phylogenies have provided …

Abstract Background Collections of Clusters of Orthologous Genes (COGs) provide
indispensable tools for comparative genomic analysis, evolutionary reconstruction and …

Little more than 30 years since the discovery of the Archaea, over one hundred archaeal
genome sequences are now publicly available, of which∼ 40% have been released in the …

Core gene phylogenies provide a window into early evolution, but different gene sets and
analytical methods have yielded substantially different views of the tree of life. Trees inferred …

Gene-by-gene and traditional biochemical approaches continue to reveal surprising
molecular features in the archaeal domain. In addition, the complete sequencing of several …

Genome remodeling and exchange of sequences are widespread in the prokaryotic world
and mosaic genomes challenge the classification of prokaryotes, which cannot be properly …

Among the 78 eukaryotic ribosomal proteins, eleven are specific to Eukarya, 33 are common
only to Archaea and Eukarya and 34 are homologous (at least in part) to those of both …