Origin of viruses revealed by the genomic study of protein domain structures

The discovery of giant viruses with complex proteomes, remnants of translation machinery and virus-specific parasites have raised important questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life. Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of viruses and cells that define viruses as a ‘fourth supergroup’ along with cellular superkingdoms Archaea, Bacteria, and Eukarya. Universal trees of life (uToLs) place viruses at their root and trees of domains indicate they have evolved via massive reductive evolutionary processes. Since viral domains are widespread among cellular proteomes we propose that viruses mediate gene transfer between cellular species and crucially enhance biodiversity. Results call for a change in the way viruses are perceived. They likely represent a distinct and most ancient form of life and a very crucial part of our planet’s biosphere. Additionally, we assign functions to molecular structures in nearly a thousand proteomes and highlight the conserved nature of cellular proteomes