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The complete genome sequence, organization and affinities of carrot red leaf virus

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Summary.

A sequence of 5723 nucleotides (GenBank accession number: AY695933) is reported for the RNA genome of an isolate of Carrot red leaf virus (CtRLV). The sequence is predicted to contain six large open reading frames and non coding sequences of 28 nucleotides at the 5′ end, 110 nucleotides at the 3′ end, and 215 nucleotides between the two main blocks of coding sequences. The 5′ coding region encodes two polypeptides with calculated molecular masses (Mr) of 28.6 kDa (P0) and 68.2 kDa (P1) that overlap in different reading frames. Circumstantially, the third ORF in the 5′ block is putatively translated by frameshift read-through to yield a polypeptide (P1 + P2) with a calculated Mr of 116.9 kDa. Frameshifting is predicted at a “shifty” sequence (GGGAAAC; nt 1523–1529) also found in most members of the genus Polerovirus. The C-terminal region of the 116.9 kDa polypeptide includes the consensus sequence for the viral RNA-directed RNA polymerase. The 3′ block of coding sequence defines three putative polypeptides of: 23.0 kDa (P3), 21.3 kDa (P4, in a different reading frame) and 77.2 kDa (P3 + P5, by read-through of P3) respectively. From the genome structure of CtRLV, it is suggested that this virus belongs to the genus Polerovirus, rather than either the genus Luteovirus or the genus Enamovirus.

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References

  • Barker H, Smith HG (1999) The Luteoviridae. CABI, Wallingford

  • BA Chalhoub L Kelly C Robaglia HD Lapierre (1994) ArticleTitleSequence variability in the genome-3′-terminal region of BYDV for 10 geographically distinct Pav-like isolates of barley yellow dwarf virus – analysis of the Orf6 variation. Arch Virol 139 403–416 Occurrence Handle10.1007/BF01310801 Occurrence Handle7832645

    Article  PubMed  Google Scholar 

  • D’Arcy CJ, Domier LL (2000) Luteoviridae. In: Van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens E, Estes M, Lemon S, Maniloff J, Mayo MA, McGeoch D, Pringle CR, Wickner RB (ed) Virus taxonomy, VIIth Report of the International Committee on Taxonomy of Viruses. Academic Press, New York, pp 775–784

  • LL Domier NK McCoppin RC Larsen CJ D’Arcy (2002) ArticleTitleNucleotide sequence shows that bean leafroll virus has a luteovirus-like genome organization. J Gen Virol 83 1791–1798 Occurrence Handle12075101

    PubMed  Google Scholar 

  • J Felsenstein (1989) ArticleTitlePHYLIP – phylogeny inference package (Version 3.2). Cladistics 5 164–166

    Google Scholar 

  • Francki RIB, Fauquet CM, Knudson DL, Brown F (1991) Classification and nomenclature of viruses. Fifth Report of the International Committee on Taxonomy of Viruses. Arch Virol Suppl 2

  • A Garcia J Vanduin CWA Pleij (1993) ArticleTitleDifferential response to frameshift signals in eukaryotic and prokaryotic translational systems. Nucleic Acids Res 21 401–406 Occurrence Handle7680118

    PubMed  Google Scholar 

  • MJ Gibbs JI Cooper (1995) ArticleTitleA recombinational event in the history of luteoviruses probably induced by base-pairing between genomes of distinct viruses. Virology 296 1129–1132 Occurrence Handle10.1006/viro.1995.1037

    Article  Google Scholar 

  • MJ Gibbs JI Cooper PM Waterhouse (1996) ArticleTitleThe genome organization and affinities of an Australian isolate of carrot mottle umbravirus. Virology 224 310–313 Occurrence Handle10.1006/viro.1996.0533 Occurrence Handle8862426

    Article  PubMed  Google Scholar 

  • DP Giedroc CA Theimer PL Nixon (2000) ArticleTitleStructure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. J Mol Biol 298 167–185 Occurrence Handle10764589

    PubMed  Google Scholar 

  • R Goldbach O Le Gall J Wellink (1991) ArticleTitleAlpha-like viruses in plants. Sem Virol 2 19–25

    Google Scholar 

  • EV Koonin VV Dolja (1993) ArticleTitleEvolution and taxonomy of positive-strand RNA viruses-implications of comparative-analysis of amino-acid sequences. Crit Rev Biochem Mol Bio 28 375–430 Occurrence Handle8269709

    PubMed  Google Scholar 

  • AB Kujawa G Drugeon D Hulanicka AL Haenni (1993) ArticleTitleStructural requirements for efficient translational frameshifting in the synthesis of the putative viral RNA-dependent RNA polymerase of potato leaf roll virus. Nucleic Acids Res 21 2165–2171 Occurrence Handle8502558

    PubMed  Google Scholar 

  • S Kumar K Tamura IB Jakobsen M Nei (2001) ArticleTitleMEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17 1244–1245 Occurrence Handle10.1093/bioinformatics/17.12.1244 Occurrence Handle11751241

    Article  PubMed  Google Scholar 

  • RR Martin PK Keese MJ Young PM Waterhouse WL Gerlach (1990) ArticleTitleEvolution and molecular biology of luteoviruses. Annu Rev Phytopathol 28 341–363 Occurrence Handle10.1146/annurev.py.28.090190.002013

    Article  Google Scholar 

  • DH Mathews MD Disney JL Childs SJ Schroeder M Zuker DH Turner (2004) ArticleTitleIncorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA 101 7287–7292 Occurrence Handle10.1073/pnas.0401799101 Occurrence Handle15123812

    Article  PubMed  Google Scholar 

  • MA Mayo V Ziegler-Graff (1996) ArticleTitleMolecular biology of luteoviruses. Adv Virus Res 46 413–460 Occurrence Handle8824705

    PubMed  Google Scholar 

  • WA Miller PM Waterhouse WL Gerlach (1988) ArticleTitleSequence and organisation of barley yellow dwarf virus genomic RNA. Nucleic Acids Res 16 6097–6111 Occurrence Handle3399386

    PubMed  Google Scholar 

  • WA Miller SP Dineshkumar CP Paul (1995) ArticleTitleLuteovirus gene expression. CRC Crit Rev Plant Sci 14 179–211

    Google Scholar 

  • F Moonan J Molina TE Mirkov (2000) ArticleTitleSugarcane yellow leaf virus: an emerging virus that has evolved by recombination between luteoviral and poleroviral ancestors. Virology 269 156–171 Occurrence Handle10.1006/viro.1999.0162 Occurrence Handle10725208

    Article  PubMed  Google Scholar 

  • Murant AF, Robinson DJ, Taliansky ME, de Zoeten GA, Falk BW, Gibbs MJ, Pieterson G, Waterhouse PM (2000) Umbravirus. In: Van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens E, Estes M, Lemon S, Maniloff J, Mayo MA, McGeoch D, Pringle CR, Wickner RB (ed) Virus taxonomy, VIIth Report of the International Committee on Taxonomy of Viruses. Academic Press, New York, San Diago, pp 785–790

  • Naylor M, Godfray HCJ, Pallet DW, Tristem M, Reeves JP, Cooper JI (2002) Mutualistic interactions amongst viruses. In: Hails RS, Beringer JE, Godfray HCJ (ed) Genes in the environment. Cambridge University Press, Cambridge, pp 205–225

  • RDM Page (1996) ArticleTitleTreeView: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12 357–358 Occurrence Handle8902363

    PubMed  Google Scholar 

  • JP Rathjen LE Karageorgos N Habili PM Waterhouse RH Symons (1994) ArticleTitleSoybean dwarf luteovirus contains the 3rd variant genome type in the luteovirus group. Virology 198 671–679 Occurrence Handle10.1006/viro.1994.1079 Occurrence Handle8291248

    Article  PubMed  Google Scholar 

  • DJ Robinson EV Ryabov SK Raj IM Roberts ME Taliansky (1999) ArticleTitleSatellite RNA is essential for encapsidation of groundnut rosette umbravirus RNA by groundnut rosette assistor luteovirus coat protein. Virology 254 105–114 Occurrence Handle10.1006/viro.1998.9527 Occurrence Handle9927578

    Article  PubMed  Google Scholar 

  • J Rozas JC Sanchez-DelBarrio X Messeguer R Rozas (2003) ArticleTitleDnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 2496–2497 Occurrence Handle10.1093/bioinformatics/btg359 Occurrence Handle14668244

    Article  PubMed  Google Scholar 

  • KP Scott MJ Farmer DJ Robinson L Torrance AF Murant (1996) ArticleTitleComparison of the coat protein of ground nut rosette assistor virus with those of other luteoviruses. Ann Appl Biol 128 77–83

    Google Scholar 

  • GR Smith Z Borg BEL Lockhart KS Braithwaite MJ Gibbs (2000) ArticleTitleSugarcane yellow leaf virus: a novel member of the Luteoviridae that probably arose by inter-species recombination. J Gen Virol 81 1865–1869 Occurrence Handle10859394

    PubMed  Google Scholar 

  • JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins (1997) ArticleTitleThe ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 4876–4882 Occurrence Handle10.1093/nar/25.24.4876 Occurrence Handle9396791

    Article  PubMed  Google Scholar 

  • I Veidt H Lot M Leiser D Scheidecker H Guilley K Richards G Jonard (1988) ArticleTitleNucleotide sequence of beet western yellows virus RNA. Nucleic Acids Res 16 9917–9932 Occurrence Handle3194229

    PubMed  Google Scholar 

  • P Vercruysse M Gibbs L Tirry M Höfte (2000) ArticleTitleRT-PCR using redundant primers to detect the three viruses associated with carrot motley dwarf disease. J Virol Methods 88 153–161 Occurrence Handle10.1016/S0166-0934(00)00196-8 Occurrence Handle10960703

    Article  PubMed  Google Scholar 

  • PM Waterhouse AF Murant (1981) ArticleTitlePurification of carrot red leaf virus and evidence from four serological tests for its relationship to luteovirus. Ann Appl Biol 97 191–204

    Google Scholar 

  • PM Waterhouse AF Murant (1983) ArticleTitleFurther evidence on the nature of the dependence of carrot mottle virus on carrot red leaf virus for transmission by aphids. Ann Appl Biol 103 455–464

    Google Scholar 

  • Waterhouse PM, Gildow FE, Johnstone GR (1988) Luteovirus group. AAB Descriptions of plant viruses No. 339

  • M Watson EP Serjeant EA Lennon (1964) ArticleTitleCarrot motley dwarf and parsnip mottle viruses. Ann Appl Biol 54 153–166

    Google Scholar 

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Authors and Affiliations

  1. NERC/Centre for Ecology and Hydrology-Oxford (formerly Institute of Virology and Environmental Microbiology), Oxford, U.K.

    L. F. Huang, M. Naylor, D. W. Pallett, J. Reeves, J. I. Cooper & H. Wang

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  1. L. F. Huang
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  2. M. Naylor
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  3. D. W. Pallett
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  4. J. Reeves
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  5. J. I. Cooper
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  6. H. Wang
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Huang, L., Naylor, M., Pallett, D. et al. The complete genome sequence, organization and affinities of carrot red leaf virus. Arch Virol 150, 1845–1855 (2005). https://doi.org/10.1007/s00705-005-0537-6

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