title: Ultra Deep Sequencing of a Baculovirus Population Reveals Widespread Genomic Variations.
abstract: Viruses rely on widespread genetic variation and large population size for adaptation. Large DNA virus populations are thought to harbor little variation though natural populations may be polymorphic. To measure the genetic variation present in a dsDNA virus population, we deep sequenced a natural strain of the baculovirus Autographa californica multiple nucleopolyhedrovirus. With 124,221X average genome coverage of our 133,926 bp long consensus, we could detect low frequency mutations (0.025%). K-means clustering was used to classify the mutations in four categories according to their frequency in the population. We found 60 high frequency non-synonymous mutations under balancing selection distributed in all functional classes. These mutants could alter viral adaptation dynamics, either through competitive or synergistic processes. Lastly, we developed a technique for the delimitation of large deletions in next generation sequencing data. We found that large deletions occur along the entire viral genome, with hotspots located in homologous repeat regions (hrs). Present in 25.4% of the genomes, these deletion mutants presumably require functional complementation to complete their infection cycle. They might thus have a large impact on the fitness of the baculovirus population. Altogether, we found a wide breadth of genomic variation in the baculovirus population, suggesting it has high adaptive potential.
authors.affiliation: Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université François Rabelais de Tours, Faculté des Sciences et Techniques, Avenue Monge-Parc Grandmont, 37200 Tours, France. aurelien.chateigner@univ-tours.fr.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Chateigner
authors.affiliation: Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université François Rabelais de Tours, Faculté des Sciences et Techniques, Avenue Monge-Parc Grandmont, 37200 Tours, France. annie.bezier@univ-tours.fr.
authors.forename: Annie
authors.initials: A
authors.lastname: Bézier
authors.affiliation: Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université François Rabelais de Tours, Faculté des Sciences et Techniques, Avenue Monge-Parc Grandmont, 37200 Tours, France. carole.labrousse@univ-tours.fr.
authors.forename: Carole
authors.initials: C
authors.lastname: Labrousse
authors.affiliation: Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université François Rabelais de Tours, Faculté des Sciences et Techniques, Avenue Monge-Parc Grandmont, 37200 Tours, France. davy.jiolle@pasteur.fr.
authors.forename: Davy
authors.initials: D
authors.lastname: Jiolle
authors.affiliation: Institut de Génomique, CEA, Génoscope, 2 rue Gaston Crémieux, 91057 Evry, France. vbarbe@genoscope.cns.fr.
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
authors.affiliation: Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université François Rabelais de Tours, Faculté des Sciences et Techniques, Avenue Monge-Parc Grandmont, 37200 Tours, France. elisabeth.herniou@univ-tours.fr.
authors.forename: Elisabeth A
authors.initials: EA
authors.lastname: Herniou
mesh_terms: D000818:Animals; D001483:Base Sequence; D014644:Genetic Variation; D016679:Genome, Viral; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D009036:Moths / Q000821:virology; D009154:Mutation; D017924:Nucleopolyhedroviruses / Q000235:genetics* / Q000302:isolation & purification; D020641:Polymorphism, Single Nucleotide; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins
keywords: AcMNPV; genome population variation; high-throughput sequencing; quasispecies theory