title: The Apis mellifera Filamentous Virus Genome.
abstract: A complete reference genome of the Apis mellifera Filamentous virus (AmFV) was determined using Illumina Hiseq sequencing. The AmFV genome is a double stranded DNA molecule of approximately 498,500 nucleotides with a GC content of 50.8%. It encompasses 247 non-overlapping open reading frames (ORFs), equally distributed on both strands, which cover 65% of the genome. While most of the ORFs lacked threshold sequence alignments to reference protein databases, twenty-eight were found to display significant homologies with proteins present in other large double stranded DNA viruses. Remarkably, 13 ORFs had strong similarity with typical baculovirus domains such as PIFs (per os infectivity factor genes: pif-1, pif-2, pif-3 and p74) and BRO (Baculovirus Repeated Open Reading Frame). The putative AmFV DNA polymerase is of type B, but is only distantly related to those of the baculoviruses. The ORFs encoding proteins involved in nucleotide metabolism had the highest percent identity to viral proteins in GenBank. Other notable features include the presence of several collagen-like, chitin-binding, kinesin and pacifastin domains. Due to the large size of the AmFV genome and the inconsistent affiliation with other large double stranded DNA virus families infecting invertebrates, AmFV may belong to a new virus family.
authors.affiliation: Agroscope, Swiss Bee Research Centre, Schwarzenburgstrasse 161, CH-3003 Bern, Switzerland. laurent.gauthier@agroscope.admin.ch.
authors.forename: Laurent
authors.initials: L
authors.lastname: Gauthier
authors.affiliation: Bee Research Laboratory, Beltsville, MD 20705, USA. scott.cornman@gmail.com.
authors.forename: Scott
authors.initials: S
authors.lastname: Cornman
authors.affiliation: Agroscope, Swiss Bee Research Centre, Schwarzenburgstrasse 161, CH-3003 Bern, Switzerland. uli.hartmann@gmx.ch.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Hartmann
authors.affiliation: Agroscope, Swiss Bee Research Centre, Schwarzenburgstrasse 161, CH-3003 Bern, Switzerland. coussera@supagro.inra.fr.
authors.forename: François
authors.initials: F
authors.lastname: Cousserans
authors.affiliation: Bee Research Laboratory, Beltsville, MD 20705, USA. jay.evans@ars.usda.gov.
authors.forename: Jay D
authors.initials: JD
authors.lastname: Evans
authors.affiliation: Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden. joachim.de.miranda@slu.se.
authors.forename: Joachim R
authors.initials: JR
authors.lastname: de Miranda
authors.affiliation: Agroscope, Swiss Bee Research Centre, Schwarzenburgstrasse 161, CH-3003 Bern, Switzerland. peter.neumann@vetsuisse.unibe.ch.|Institute of Bee Health, Vetsuisse Faculty, University of Bern, CH-3001 Bern, Switzerland. peter.neumann@vetsuisse.unibe.ch.
authors.forename: Peter
authors.initials: P
authors.lastname: Neumann
mesh_terms: D000818:Animals; D001516:Bees / Q000821:virology*; D004267:DNA Viruses / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D016679:Genome, Viral; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D016415:Sequence Alignment; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D014764:Viral Proteins
keywords: Apis mellifera; filamentous virus; genome annotation