title: Complete nucleotide sequence and genome structure of a Japanese isolate of hibiscus latent Fort Pierce virus, a unique tobamovirus that contains an internal poly(A) region in its 3' end.
abstract: In this study, we detected a Japanese isolate of hibiscus latent Fort Pierce virus (HLFPV-J), a member of the genus Tobamovirus, in a hibiscus plant in Japan and determined the complete sequence and organization of its genome. HLFPV-J has four open reading frames (ORFs), each of which shares more than 98 % nucleotide sequence identity with those of other HLFPV isolates. Moreover, HLFPV-J contains a unique internal poly(A) region of variable length, ranging from 44 to 78 nucleotides, in its 3'-untranslated region (UTR), as is the case with hibiscus latent Singapore virus (HLSV), another hibiscus-infecting tobamovirus. The length of the HLFPV-J genome was 6431 nucleotides, including the shortest internal poly(A) region. The sequence identities of ORFs 1, 2, 3 and 4 of HLFPV-J to other tobamoviruses were 46.6-68.7, 49.9-70.8, 31.0-70.8 and 39.4-70.1 %, respectively, at the nucleotide level and 39.8-75.0, 43.6-77.8, 19.2-70.4 and 31.2-74.2 %, respectively, at the amino acid level. The 5'- and 3'-UTRs of HLFPV-J showed 24.3-58.6 and 13.0-79.8 % identity, respectively, to other tobamoviruses. In particular, when compared to other tobamoviruses, each ORF and UTR of HLFPV-J showed the highest sequence identity to those of HLSV. Phylogenetic analysis showed that HLFPV-J, other HLFPV isolates and HLSV constitute a malvaceous-plant-infecting tobamovirus cluster. These results indicate that the genomic structure of HLFPV-J has unique features similar to those of HLSV. To our knowledge, this is the first report of the complete genome sequence of HLFPV.
authors.affiliation: Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Yoshida
authors.forename: Yugo
authors.initials: Y
authors.lastname: Kitazawa
authors.forename: Ken
authors.initials: K
authors.lastname: Komatsu
authors.forename: Yutaro
authors.initials: Y
authors.lastname: Neriya
authors.forename: Kazuya
authors.initials: K
authors.lastname: Ishikawa
authors.forename: Naoko
authors.initials: N
authors.lastname: Fujita
authors.forename: Masayoshi
authors.initials: M
authors.lastname: Hashimoto
authors.forename: Kensaku
authors.initials: K
authors.lastname: Maejima
authors.forename: Yasuyuki
authors.initials: Y
authors.lastname: Yamaji
authors.forename: Shigetou
authors.initials: S
authors.lastname: Namba
mesh_terms: D020413:3' Untranslated Regions; D001483:Base Sequence; D016679:Genome, Viral; D031584:Hibiscus / Q000821:virology*; D007564:Japan; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D011061:Poly A / Q000737:chemistry / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics*; D017898:Tobamovirus / Q000737:chemistry / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*
chemical_list: D020413:3' Untranslated Regions; D012367:RNA, Viral; D011061:Poly A