title: Extensive gene remodeling in the viral world: new evidence for nongradual evolution in the mobilome network.
abstract: Complex nongradual evolutionary processes such as gene remodeling are difficult to model, to visualize, and to investigate systematically. Despite these challenges, the creation of composite (or mosaic) genes by combination of genetic segments from unrelated gene families was established as an important adaptive phenomena in eukaryotic genomes. In contrast, almost no general studies have been conducted to quantify composite genes in viruses. Although viral genome mosaicism has been well-described, the extent of gene mosaicism and its rules of emergence remain largely unexplored. Applying methods from graph theory to inclusive similarity networks, and using data from more than 3,000 complete viral genomes, we provide the first demonstration that composite genes in viruses are 1) functionally biased, 2) involved in key aspects of the arm race between cells and viruses, and 3) can be classified into two distinct types of composite genes in all viral classes. Beyond the quantification of the widespread recombination of genes among different viruses of the same class, we also report a striking sharing of genetic information between viruses of different classes and with different nucleic acid types. This latter discovery provides novel evidence for the existence of a large and complex mobilome network, which appears partly bound by the sharing of genetic information and by the formation of composite genes between mobile entities with different genetic material. Considering that there are around 10E31 viruses on the planet, gene remodeling appears as a hugely significant way of generating and moving novel sequences between different kinds of organisms on Earth.
authors.affiliation: UMR CNRS 7138 Evolution Paris Seine, IBPS, Université Pierre et Marie Curie, Paris, France.
authors.forename: Pierre-Alain
authors.initials: PA
authors.lastname: Jachiet
authors.affiliation: URMITE UMR CNRS 6236 IRD 198, Facultés de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Colson
authors.affiliation: UMR CNRS 7138 Evolution Paris Seine, IBPS, Université Pierre et Marie Curie, Paris, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Lopez
authors.affiliation: UMR CNRS 7138 Evolution Paris Seine, IBPS, Université Pierre et Marie Curie, Paris, France eric.bapteste@snv.jussieu.fr.
authors.forename: Eric
authors.initials: E
authors.lastname: Bapteste
mesh_terms: D019143:Evolution, Molecular; D053263:Gene Regulatory Networks; D016679:Genome, Viral; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D014780:Viruses / Q000145:classification / Q000235:genetics*
keywords: comparative genomics; composite genes; evolution; network; virus
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