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.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Adams MJ, Antoniw JF, Kreuze J (2009) Virgaviridae: a new family of rod-shaped plant viruses. Arch Virol 154:1967–1972
Adkins S, Kamenova I, Achor D, Lewandowski DJ (2003) Biological and molecular characterization of a novel tobamovirus with a unique host range. Plant Dis 87:1190–1196
Adkins S, Kamenova I, Chiemsombat P, Baker CA, Lewandowski DJ (2006) Tobamoviruses from hibiscus in Florida and beyond. Acta Hortic 722:65–70
Allen JE, Kamenova I, Adkins S, Hanson SF (2005) First report of Hibiscus latent Fort Pierce virus in New Mexico. Plant Health Prog. doi:10.1094/PHP-2005-0105-01-HN
Almeyda-Becerra CV, Lockhart BE (2007) Association of a tobamovirus with a mosaic disease of flowering maple. Phytopathology 97:S3
Beauchemin C, Laliberte JF (2007) The poly(A) binding protein is internalized in virus-induced vesicles or redistributed to the nucleolus during turnip mosaic virus infection. J Virol 81:10905–10913
Doi Y, Toriyama S, Yora K, Asuyama H (1969) Direct negative staining method for detection of virus particles in fresh preparations from infected plant tissues. Ann Phytopathol Soc Jpn 35:180–187 (in Japanese with English summary)
Hwang J, Oh CS, Kang BC (2013) Translation elongation factor 1B (eEF1B) is an essential host factor for Tobacco mosaic virus infection in plants. Virology 439:105–114
Kashiwazaki S, Yamashita S, Doi Y (1982) Two hibiscus-infecting viruses: hibiscus yellow mosaic virus and hibiscus chlorotic ringspot virus. Ann Phytopathol Soc Jpn 48:395 (in Japanese)
Kim NR, Hong JS, Song YS, Chung BN, Park JW, Ryu KH (2012) The complete genome sequence of a member of a new species of tobamovirus (rattail cactus necrosis-associated virus) isolated from Aporcactus flagelliformis. Arch virol 157:185–187
Matsui Y, Adkins S, Natsuaki KT (2005) Hibiscus latent Fort Pierce virus (HLFPV) from Hibiscus rosa-sinesis in Japan and Indonesia. Jpn J Phytopathol 71:232–233 (in Japanese)
Okano Y, Maejima K, Shiraishi T, Hashimoto M, Senshu H, Ozeki J, Takahashi S, Komatsu K, Yamaji Y, Namba S (2010) Genetic heterogeneity found in the replicase gene of poinsettia mosaic virus isolates. Arch Virol 155:1367–1370
Osman TAM, Hemenway CL, Buck KW (2000) Role of the tRNA-like structure in tobacco mosaic virus minus-strand RNA synthesis by the viral RNA-dependent RNA polymerase in vitro. J Virol 74:11671–11680
Robaglia C, Caranta C (2006) Translation initiation factors: a weak link in plant RNA virus infection. Trends Plant Sci 11:40–45
Srinivasan KG, Min BE, Ryu KH, Adkins S, Wong SM (2005) Determination of complete nucleotide sequence of Hibiscus latent Singapore virus: evidence for the presence of an internal poly(A) tract. Arch Virol 150:153–166
Srinivasan KG, Narendrakumar R, Wong SM (2002) Hibiscus virus S is a new subgroup II tobamovirus: evidence from its unique coat protein and movement protein sequences. Arch Virol 147:1585–1598
Takamatsu N, Watanabe Y, Iwasaki T, Shiba T, Meshi T, Okada Y (1991) Deletion analysis of the 5′ untranslated leader sequence of tobacco mosaic virus RNA. J Virol 65:1619–1622
Takamatsu N, Watanabe Y, Meshi T, Okada Y (1990) Mutational analysis of the pseudoknot region in the 3′ noncoding region of tobacco mosaic virus RNA. J Virol 64:3686–3693
Watanabe T, Honda A, Iwata A, Ueda S, Hibi T, Ishihama A (1999) Isolation from tobacco mosaic virus-infected tobacco of a solubilized template-specific RNA-dependent RNA polymerase containing a 126 K/183 K protein heterodimer. J Virol 73:2633–2640
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415
Acknowledgments
This work was supported by Grants-in-Aids for Scientific Research from the Japan Society for the Promotion of Science.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Yoshida, T., Kitazawa, Y., Komatsu, K. et al. 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. Arch Virol 159, 3161–3165 (2014). https://doi.org/10.1007/s00705-014-2175-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-014-2175-3