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Sequence analysis of the entire RNA genome of a sweet potato chlorotic fleck virus isolate reveals that it belongs to a distinct carlavirus species

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Summary

Since the paucity of information on sweet potato chlorotic fleck virus (SPCFV) had precluded its classification, we have determined the complete nucleotide sequence of the single-stranded RNA genome of a Ugandan isolate of SPCFV. The genome is 9104 nucleotides long (excluding the poly(A) tail) and potentially includes six open reading frames (ORFs). Based on genomic organisation and sequence similarity, SPCFV appears to be a member of the genus Carlavirus (family Flexiviridae). However, SPCFV is distantly related to typical carlaviruses, as most of its putative gene products share amino acid sequence identities of <40% with those of typical carlaviruses. Its closest relative is melon yellowing-associated virus, a proposed carlavirus from Brazil, with which it shares ORF5 and ORF6 amino acid sequence identities of 61 and 46%, respectively.

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References

  • Adams MJ, Accotto GP, Agranovsky AA, Bar-Joseph M, Boscia D, Brunt AA, Candresse T, Coutts RHA, Dolja VV, Falk BW, Foster GD, Gonsalves D, Jelkmann W, Karasev A, Martelli GP, Mawassi M, Milne RG, Minafra A, Namba S, Rowhani A, Vetten HJ, Vishnichenko VK, Wisler GC, Yoshikawa N, Zavriev SK (2005) Family Flexiviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy: classification and nomenclature of viruses; Eighth Report of the International Committee on Taxonomy of Viruses. Academic Press, San Diego, pp 1089–1124

  • MJ Adams JF Antoniw M Bar-Joseph AA Brunt T Candresse GD Foster GP Martelli RG Milne SK Zavriev CM Fauquet (2004) ArticleTitleThe new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation Arch Virol 149 1045–1060 Occurrence Handle15098118 Occurrence Handle1:CAS:528:DC%2BD2cXjt1Sgtr4%3D

    PubMed  CAS  Google Scholar 

  • SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman (1997) ArticleTitleGapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 3389–3402 Occurrence Handle9254694 Occurrence Handle10.1093/nar/25.17.3389 Occurrence Handle1:CAS:528:DyaK2sXlvFyhu7w%3D

    Article  PubMed  CAS  Google Scholar 

  • CIP (1991) International Potato Centre Annual Report 1992. CIP, Lima, Peru

  • MA Frohman MK Dush GR Martin (1988) ArticleTitleRapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer Proc Natl Acad Sci USA 85 8998–9002 Occurrence Handle2461560 Occurrence Handle10.1073/pnas.85.23.8998 Occurrence Handle1:CAS:528:DyaL1MXntVCmtQ%3D%3D

    Article  PubMed  CAS  Google Scholar 

  • P Froussard (1992) ArticleTitleA random PCR method (rPCR) to construct whole cDNA library from low amounts of RNA Nucleic Acids Res 20 2900 Occurrence Handle1614887 Occurrence Handle10.1093/nar/20.11.2900 Occurrence Handle1:CAS:528:DyaK38XkvVCgsLg%3D

    Article  PubMed  CAS  Google Scholar 

  • S Fuentes LF Salazar (1992) ArticleTitleIdentification of a new sweetpotato virus Fitopatologia 27 50

    Google Scholar 

  • MT Haylor AA Brunt RH Coutts (1990) ArticleTitleConservation of the 3′ terminal nucleotide sequence in five carlaviruses Nucleic Acids Res 18 6127 Occurrence Handle2235495 Occurrence Handle10.1093/nar/18.20.6127 Occurrence Handle1:CAS:528:DyaK3MXhtlym

    Article  PubMed  CAS  Google Scholar 

  • TC Hodgman (1988) ArticleTitleA new superfamily of replicase protein Nature 333 22–23 Occurrence Handle3362205 Occurrence Handle10.1038/333022b0 Occurrence Handle1:CAS:528:DyaL1cXktF2ntrk%3D

    Article  PubMed  CAS  Google Scholar 

  • EV Koonin VV Dolja (1993) ArticleTitleEvolution and taxonomy of positive-strand RNA viruses: implication of comparative analysis of amino acid sequences Crit Rev Biochem Mol Biol 28 375–430 Occurrence Handle8269709 Occurrence Handle1:CAS:528:DyaK3sXms1KjsL0%3D

    PubMed  CAS  Google Scholar 

  • HA Lutke KC Chow FS Mickel KA Moss HF Kern GA Scheele (1987) ArticleTitleSelection of AUG initiation codons differs in plants and animals EMBO J 6 43–48

    Google Scholar 

  • A Marchler-Bauer AR Panchenko BA Shoemaker PA Thiessen LY Geer SH Bryant (2002) ArticleTitleCDD: a database of conserved domain alignments with links to domain three-dimensional structure Nucleic Acids Res 30 281–283 Occurrence Handle11752315 Occurrence Handle10.1093/nar/30.1.281 Occurrence Handle1:CAS:528:DC%2BD38Xht12rsrs%3D

    Article  PubMed  CAS  Google Scholar 

  • SY Morozov AG Solovyev (2003) ArticleTitleTriple gene block: modular design of a multifunctional machine for plant virus movement J Gen Virol 84 1351–1366 Occurrence Handle12771402 Occurrence Handle10.1099/vir.0.18922-0 Occurrence Handle1:CAS:528:DC%2BD3sXks1Gmtrs%3D

    Article  PubMed  CAS  Google Scholar 

  • SB Mukasa PR Rubaihayo JPT Valkonen (2003) ArticleTitleIncidence of viruses and virus-like diseases of sweet potato in Uganda Plant Dis 87 329–335

    Google Scholar 

  • T Nagata DMT Alves AK Inoue-Nagata T-Y Tian EW Kitajima JE Cardoso AC de Ávila (2005) ArticleTitleA novel melon flexivirus transmitted by whitefly Arch Virol 150 379–387 Occurrence Handle15526146 Occurrence Handle10.1007/s00705-004-0400-1 Occurrence Handle1:CAS:528:DC%2BD2MXksVKgsw%3D%3D

    Article  PubMed  CAS  Google Scholar 

  • NMN Rozanov EV Koonin AE Gorbalenya (1992) ArticleTitleConservation of the putative methytransferase domain: a hallmark of the sindbis-like supergroup of positive-strand RNA viruses J Gen Virol 73 2129–2134 Occurrence Handle1645151 Occurrence Handle1:CAS:528:DyaK38XlsVKrtbw%3D Occurrence Handle10.1099/0022-1317-73-8-2129

    Article  PubMed  CAS  Google Scholar 

  • Salazar LF, Fuentes S (2001) Current knowledge on major virus diseases of sweet potato. International Workshop on Sweetpotato Cultivar Decline Study, September 8–9, 2000. Kyushu National Agricultural Experiment Station, Miyakonojo, Miyazaki, Japan, pp 14–19

  • HJ Vetten SK Green D-E Lesemann (1992) ArticleTitleCharacterization of peanut stripe virus isolates from soybean in Taiwan J Phytopathol 135 107–124 Occurrence Handle1:CAS:528:DyaK38XlsVOjtLk%3D

    CAS  Google Scholar 

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Authors and Affiliations

  1. Biologische Bundesanstalt für Land- und Forstwirtschaft, Institut für Pflanzenvirologie, Mikrobiologie und biologische Sicherheit, Braunschweig, Germany

    V. Aritua, E. Barg & H. J. Vetten

  2. National Agricultural Biotechnology Center, Kawanda Agricultural Research Institute, Kampala, Uganda

    V. Aritua

  3. Department of Crop Science, Makerere University, Kampala, Uganda

    E. Adipala

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  1. V. Aritua
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  2. E. Barg
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  3. E. Adipala
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  4. H. J. Vetten
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Aritua, V., Barg, E., Adipala, E. et al. Sequence analysis of the entire RNA genome of a sweet potato chlorotic fleck virus isolate reveals that it belongs to a distinct carlavirus species. Arch Virol 152, 813–818 (2007). https://doi.org/10.1007/s00705-006-0891-z

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  • DOI: https://doi.org/10.1007/s00705-006-0891-z

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