title: The Pangenome of the Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV).
abstract: The alphabaculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is the world's most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations of Anticarsia gemmatalis (Velvetbean caterpillar) in soybean crops. During this period, genetic studies identified several variable loci in the AgMNPV; however, most of them were not characterized at the sequence level. In this study we report a full genome comparison among 17 wild-type isolates of AgMNPV. We found the pangenome of this virus to contain at least 167 hypothetical genes, 151 of which are shared by all genomes. The gene bro-a that might be involved in host specificity and carrying transporter is absent in some genomes, and new hypothetical genes were observed. Among these genes there is a unique rnf12-like gene, probably implicated in ubiquitination. Events of gene fission and fusion are common, as four genes have been observed as single or split open reading frames. Gains and losses of genomic fragments (from 20 to 900 bp) are observed within tandem repeats, such as in eight direct repeats and four homologous regions. Most AgMNPV genes present low nucleotide diversity, and variable genes are mainly located in a locus known to evolve through homologous recombination. The evolution of AgMNPV is mainly driven by small indels, substitutions, gain and loss of nucleotide stretches or entire coding sequences. These variations may cause relevant phenotypic alterations, which probably affect the infectivity of AgMNPV. This work provides novel information on genomic evolution of the AgMNPV in particular and of baculoviruses in general.
authors.affiliation: Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil.
authors.forename: Anderson Fernandes de
authors.initials: AF
authors.lastname: Brito
authors.affiliation: Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil.
authors.forename: Carla Torres
authors.initials: CT
authors.lastname: Braconi
authors.affiliation: Department of Virology, University Medical Center, Göttingen, Germany.
authors.forename: Manfred
authors.initials: M
authors.lastname: Weidmann
authors.affiliation: Department of Virology, University Medical Center, Göttingen, Germany.
authors.forename: Meik
authors.initials: M
authors.lastname: Dilcher
authors.affiliation: Department of Parasitology, Institute of Biomedical Sciences-ICB II, University of São Paulo-USP, São Paulo, SP, Brazil.
authors.forename: João Marcelo Pereira
authors.initials: JM
authors.lastname: Alves
authors.affiliation: Department of Parasitology, Institute of Biomedical Sciences-ICB II, University of São Paulo-USP, São Paulo, SP, Brazil.
authors.forename: Arthur
authors.initials: A
authors.lastname: Gruber
authors.affiliation: Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil pzanotto@usp.br.
authors.forename: Paolo Marinho de Andrade
authors.initials: PM
authors.lastname: Zanotto
mesh_terms: D000818:Animals; D016367:Baculoviridae / Q000235:genetics*; D001483:Base Sequence; D016679:Genome, Viral; D042822:Genomic Instability; D007915:Lepidoptera / Q000821:virology*; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic; D014452:Ubiquitins / Q000235:genetics; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014452:Ubiquitins; D014764:Viral Proteins
keywords: baculovirus; deep sequencing; evolution; genetic diversity; horizontal gene transfer; wild isolates