title: Gene mapping and phylogenetic analysis of the complete genome from 30 single-stranded RNA male-specific coliphages (family Leviviridae).
abstract: Male-specific single-stranded RNA (FRNA) coliphages belong to the family Leviviridae. They are classified into two genera (Levivirus and Allolevivirus), which can be subdivided into four genogroups (genogroups I and II in Levivirus and genogroups III and IV in Allolevivirus). Relatively few strains have been completely characterized, and hence, a detailed knowledge of this virus family is lacking. In this study, we sequenced and characterized the complete genomes of 19 FRNA strains (10 Levivirus strains and 9 Allolevivirus strains) and compared them to the 11 complete genome sequences available in GenBank. Nucleotide similarities among strains of Levivirus genogroups I and II were 75% to 99% and 83 to 94%, respectively, whereas similarities among strains of Allolevivirus genogroups III and IV ranged from 70 to 96% and 75 to 95%, respectively. Although genogroup I strain fr and genogroup III strains MX1 and M11 share only 70 to 78% sequence identity with strains in their respective genogroups, phylogenetic analyses of the complete genome and the individual genes suggest that strain fr should be grouped in Levivirus genogroup I and that the MX1 and M11 strains belong in Allolevivirus genogroup III. Strains within each genus share >50% sequence identity, whereas between the two genera, strains have <40% nucleotide sequence identity. Overall, amino acid composition, nucleotide similarities, and replicase catalytic domain location contributed to phylogenetic assignments. A conserved eight-nucleotide signature at the 3' end of the genome distinguishes leviviruses (5' ACCACCCA 3') from alloleviviruses (5' TCCTCCCA 3').
authors.affiliation: U.S. Environmental Protection Agency, Gulf Ecology Division, 1 Sabine Island Drive, Gulf Breeze, FL 32561, USA. friedman.stephanie@epa.gov
authors.forename: Stephanie D
authors.initials: SD
authors.lastname: Friedman
authors.forename: Fred J
authors.initials: FJ
authors.lastname: Genthner
authors.forename: Jennifer
authors.initials: J
authors.lastname: Gentry
authors.forename: Mark D
authors.initials: MD
authors.lastname: Sobsey
authors.forename: Jan
authors.initials: J
authors.lastname: Vinjé
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D004279:DNA, Viral / Q000032:analysis*; D016679:Genome, Viral / Q000235:genetics*; D017907:Leviviridae / Q000145:classification / Q000235:genetics; D008297:Male; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D004279:DNA, Viral