title: Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya.
abstract: BACKGROUND
  The discovery of giant viruses with genome and physical size comparable to cellular organisms, remnants of protein translation machinery and virus-specific parasites (virophages) have raised intriguing questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life.
  
  
  RESULTS
  Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of cellular organisms and double-stranded DNA viruses with medium-to-very-large proteomes (giant viruses). Trees of proteomes define viruses as a 'fourth supergroup' along with superkingdoms Archaea, Bacteria, and Eukarya. Trees of domains indicate they have evolved via massive and primordial reductive evolutionary processes. The distribution of domain structures suggests giant viruses harbor a significant number of protein domains including those with no cellular representation. The genomic and structural diversity embedded in the viral proteomes is comparable to the cellular proteomes of organisms with parasitic lifestyles. Since viral domains are widespread among cellular species, we propose that viruses mediate gene transfer between cells and crucially enhance biodiversity.
  
  
  CONCLUSIONS
  Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet's biosphere.
authors.affiliation: Evolutionary Bioinformatics Laboratory, Department of Crop Science, University of Illinois, Urbana, IL 61801, USA.
authors.forename: Arshan
authors.initials: A
authors.lastname: Nasir
authors.forename: Kyung Mo
authors.initials: KM
authors.lastname: Kim
authors.forename: Gustavo
authors.initials: G
authors.lastname: Caetano-Anolles
mesh_terms: D001105:Archaea / Q000821:virology; D001419:Bacteria / Q000821:virology; D005075:Biological Evolution; D056890:Eukaryota / Q000821:virology; D022761:Gene Transfer, Horizontal; D056686:Mimiviridae; D008958:Models, Molecular; D010802:Phylogeny; D014176:Protein Biosynthesis; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000032:analysis; D014764:Viral Proteins / Q000032:analysis; D014780:Viruses / Q000145:classification* / Q000235:genetics*
chemical_list: D020543:Proteome; D014764:Viral Proteins