Abstract
The three double-stranded (ds) RNAs were detected in Rosa multiflora plants showing rose spring dwarf (RSD) symptoms. Northern blot analysis revealed three dsRNAs in preparations of both dsRNA and total RNA from R. multiflora plants. The complete sequences of the dsRNAs (referred to as dsRNA 1, dsRNA 2 and dsRNA 3) were determined based on a combination of shotgun cloning of dsRNA cDNAs and reverse transcription-polymerase chain reaction (RT-PCR). The largest dsRNA (dsRNA 1) was 1,762 bp long with a single open reading frame (ORF) that encoded a putative polypeptide containing 479 amino acid residues with a molecular mass of 55.9 kDa. This polypeptide contains amino acid sequence motifs conserved in the RNA-dependent RNA polymerases (RdRp) of members of the family Partitiviridae. Both dsRNA 2 (1,475 bp) and dsRNA 3 (1,384 bp) contained single ORFs, encoding putative proteins of unknown function. The 5′ untranslated regions (UTR) of all three segments shared regions of high sequence homology. Phylogenetic analysis using the RdRp sequences of the various partitiviruses revealed that the new sequences would constitute the genome of a virus in family Partitiviridae. This virus would cluster with Fragaria chiloensis cryptic virus and Raphanus sativus cryptic virus 2. We suggest that the three dsRNA segments constitute the genome of a novel cryptic virus infecting roses; we propose the name Rosa multiflora cryptic virus (RMCV). Detection primers were developed and used for RT-PCR detection of RMCV in rose plants.
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References
Adams MJ, Swaby AG, Jones P (1988) Confirmation of the transmission of Barley yellow mosaic virus (BaYMV) by the fungus and Polymixa graminis. Ann Appl Biol 112:133–141
Ahn I P, Lee YH (2001) A viral double-stranded RNA up regulates the fungal virulence of Nectria radicicola. Mol Plant Microbe Interact 14:496–507
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Boccardo G, Candresse T (2005) Complete sequence of the RNA1 of an isolate of White clover cryptic virus 1, type species of the genus Alphacryptovirus. Arch Virol 150:399–402
Boccardo G, Lisa V, Luisoni E, Milne GR (1987) Cryptic plant viruses. Adv Virus Res 32:171–214
Bruening G (2002) Virus-dependent RNA agents. In: Maloy O, Murray T (eds) Encyclopedia of plant pathology, vol. 2. John Wiley & Sons, Inc, New York, pp 1170–1177
Bruenn JA (1993) A closely related group of RNA-dependent RNA polymerases from double-stranded RNA viruses. Nucleic Acids Res 21:2667–5669
Chen L, Chen JS, Zhang H, Chen SN (2006a) Complete nucleotide sequences of three dsRNA segments from Raphanus sativus-root cv. Yipinghong with leaf yellow edge symptoms. Arch Virol 151:2077–2083
Chen L, Chen JS, Liu L, Yu X, Yu S, Fu TZ, Liu WH (2006b) Complete nucleotide sequences and genome characterization of double-stranded RNA 1 and RNA 2 in the Raphanus sativus-root cv. Yipinghong. Arch Virol 151:849–859
Coutts RHA, Covelli L, Di Serio F, Citir A, Acikgoz S, Hernandez C, Ragozzino A, Flores R (2004) Cherry chlorotic rusty spot and Amasya cherry diseases are associated with a complex pattern of mycoviral-like double-stranded RNAs II. Characterization of a new species in the genus Partitivirus. J Gen Virol 85:3399–3403
Crawford LJ, Osman TA, Booy FP, Coutts RHA, Brasier CM, Buck KW (2006) Molecular characterization of a partitivirus from Ophiostoma himal-ulmi. Virus Genes 33:33–39
Dodds AJ, Morris JT, Jordan LR (1984) Plant viral double-stranded RNA. Ann Rev Phytopathol 22:151–168
Ghabrial SA (1998) Origin, adaptation and evolutionary pathways of fungal viruses. Virus Genes 16:119–131
Ghabrial SA (2001) Cryptoviruses. In: Maloy O, Murray T (eds) Encyclopedia of plant pathology, vol. 1. John Wiley & Sons, Inc, New York, pp 267–269
Ghabrial SA, Buck KW, Hillman BI, Milne RG (2005) Family Partitiviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses, San Diego, pp. 580–590
Gould AR, Francki RIB (1981) Immunochemical detection of dsRNA in healthy and virus-infected plants and specific detection of viral dsRNA by hybridization to labeled complementary DNA. J Virol Methods 2:277–286
Handley MK (1986) Identification and partial characterization of two cryptic viruses in rose by analysis of double-stranded RNA content. Ph.D. dissertation. Department of Plant Pathology, University of California, Davis, 89 pp
Jiang D, Ghabrial S (2004) Molecular characterization of Penicillium chrysogenum virus: reconsideration of the taxonomy of the genus Chrysovirus. J Gen Virol 85:2111–2121
Kim JW, Kim SY, Kim KM (2003) Genome organization and expression of the Penicillium stoloniferum virus S. Virus Genes 27:249–256
Kim JW, Choi EY, Kim YT (2006) Intergeneric relationship between the Aspergillus ochraceous virus F and the Penicillium stoloniferum virus S. Virus Res 120:212–215
Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244–1245
Nogawa M, Kageyama T, Nakatani A, Taguchi G, Shimosaka M, Okazaki M (1996) Cloning and characterization of mycovirus double-stranded RNA from the plant pathogenic fungus, Fusarium solani f. sp. Robiniae. Biosci Biotechnol Biochem 60:784–788
Oh CS, Hillman BI (1995) Genome organization of a partitivirus from the filamentous ascomycete Atkinsonella hypoxylon. J Gen Virol 76:1461–1470
Osaki H, Kudo A, Ohtsu Y (1998) Nucleotide sequence of seed- and pollen-transmitted double stranded RNA, which encodes a putative RNA-dependent RNA polymerase, detected from Japanese pear. Biosci Biotechnol Biochem 62:2101–2106
Osaki H, Nomura K, Iwanami T, Kanematsu S, Okabe I, Matsumoto N, Sasaki A, Ohtsu Y (2002) Detection of a double-stranded RNA virus from a strain of the violet root rot fungus Helicobasidium mompa Tanaka. Virus Genes 25:139–145
Rao AS, Brakke MK (1969) Relation of soil-borne Wheat mosaic virus and its fungal vector. Phytopathology 59:581–587
Rong R, Rao S, Scott SW, Carner GR, Tainter FH (2002) Complete sequence of the genome of two dsRNA viruses from Discula destructiva. Virus Res 90:217–224
Salem N, Golino DA, Falk BW, Rowhani A (2007) Identification and partial characterization of a new luteovirus associated with rose spring dwarf disease. Plant Dis (In press)
Sambrook J, Russell D (2001) Molecular Cloning: a laboratory Manual, 3rd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
Sasaki A, Miyanishi M, Ozaki K, Onoue M, Yoshida K (2005) Molecular characterization of a partitivirus from the plant pathogenic ascomycete Rosellinia necatrix. Arch Virol 150:1069–1083
Strauss EE, Lakshman DK, Tavantzis SM (2000) Molecular characterization of the genome of a partitivirus from the basidomycete Rhizoctonia solani. J Gen Virol 81:549–555
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTALX windows interface; flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882
Tzanetakis IE, Martin RR (2005) Fragaria chiloensis cryptic virus: a new strawberry virus found in Fragaria chilloensis plants from Chile. Plant Dis 89:1241
Tuomivirta TT, Hantula J (2003) Two unrelated double-stranded RNA molecule patterns in Gremmeniella abietina type A code for putative viruses of the families Totiviridae and Partitiviridae. Arch Virol 148:2293–2305
Tuomivirta TT, Hantula J (2005) Three unrelated viruses occure in single isolate of Gremmeniella abietina varabietina type A. Virus Res 110:31–39
Valverde RA, Nameth ST, Jordan RL (1990) Analysis of double-stranded RNA for plant virus diagnosis. Plant Dis 74:255–258
Veliceasa D, EnÜnlÜ N, Kós PB, Köster S, Beuther E, Morgun B, Deshmukh SD, Lukacs N (2006) Searching for a new putative cryptic virus in Pinus sylvestris L. Virus Genes 32:177–186
Xie SW, Antoniw FJ, White FR (1993) Nucleotide sequence of beet cryptic virus 3 dsRNA2 which encodes a putative RNA-dependent RNA polymerase. J Gen Virol 74:1467–1470
Acknowledgments
N. Salem is grateful to the Fulbright Commission for a postdoctoral fellowship. We would like to acknowledge Dr. Steven Daubert (Department of Plant Pathology, UC Davis) for invaluable comments and suggestion on the manuscript, Dr. Anne-Laure Moyne (Department of Plant Pathology, UC Davis), Susan T. Sim, Judy Lee and Mike Cunningham (Foundation Plant Services, UC Davis) for their technical support. This project was also partially supported by funding from the Garden Rose Council.
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Salem, N.M., Golino, D.A., Falk, B.W. et al. Complete nucleotide sequences and genome characterization of a novel double-stranded RNA virus infecting Rosa multiflora . Arch Virol 153, 455–462 (2008). https://doi.org/10.1007/s00705-007-0008-3
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DOI: https://doi.org/10.1007/s00705-007-0008-3