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Zucchini shoestring virus: a distinct potyvirus in the papaya ringspot virus cluster

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Abstract

Zucchini shoestring virus (ZSSV) has been proposed to be a putative potyvirus in the papaya ringspot virus (PRSV) cluster, based on the sequence similarity of its coat protein to those of related potyviruses. ZSSV has been associated with the outbreak of a damaging disease of baby marrow (Cucurbita pepo L.) that had been observed throughout the province of KwaZulu-Natal, in the Republic of South Africa (RSA). We report the genome sequence of ZSSV, determined by next-generation sequencing of total RNA extracted from an infected baby marrow (Cucurbita pepo L.). The ZSSV genome is 10,295 nucleotides long excluding the poly(A) tail and displays a typical potyvirus organization. Algerian watermelon mosaic virus (AWMV; EU410442.1) was identified as the closest relative of ZSSV, sharing the highest nucleotide sequence identity of 65.68%. The nucleotide and amino acid sequence identity values for each protein support the differentiation of ZSSV as a member of a distinct species in the genus Potyvirus. This taxonomic position was also confirmed using the Pairwise Sequence Comparison online tool from the National Center for Biotechnology Information. Phylogenetic analysis of the polyprotein coding sequence of ZSSV grouped ZSSV together with AWMV and Moroccan watermelon mosaic virus, but in different clusters. ZSSV is the second cucurbit-infecting virus in the PRSV cluster present in RSA.

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References

  1. Adams MJ, Antoniw JF, Beaudoin F (2005) Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Mol Plant Pathol 6:471–487

    Article  CAS  PubMed  Google Scholar 

  2. Adams MJ, Zerbini FM, French R, Rabenstein F, Stenger DC, Valkonen JPT (2012) Family Potyviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy: classification and nomenclature of viruses: Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier, San Diego, pp 1069–1089

    Google Scholar 

  3. Bao Y, Chetvernin V, Tatusova T (2014) Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification. Arch Virol 159:3293–3304

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Chung BYW, Miller WA, Atkins JF, Firth AE (2008) An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci USA 105:5897–5902

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Gibbs MJ, Armstrong JS, Gibbs AJ (2000) Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16(7):573–582. doi:10.1093/bioinformatics/16.7.573

    Article  CAS  PubMed  Google Scholar 

  7. Ibaba JD, Laing MD, Gubba A (2015) First Report of a Novel Potyvirus from the Papaya ringspot virus Cluster Infecting Zucchini (Cucurbita pepo) in KwaZulu-Natal, Republic of South Africa. Plant Dis 99:1289

    Article  Google Scholar 

  8. Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol 1(1):vev003. doi:10.1093/ve/vev003

    Article  Google Scholar 

  9. Martin DP, Posada D, Crandall KA, Williamson C (2005) A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 21(1):98–102. doi:10.1089/aid.2005.21.98

    Article  CAS  PubMed  Google Scholar 

  10. Martin D, Rybicki E (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics 16(6):562–563

    Article  CAS  PubMed  Google Scholar 

  11. Padidam M, Sawyer S, Fauquet CM (1999) Possible emergence of new geminiviruses by frequent recombination. Virology 265(2):218–225. doi:10.1006/viro.1999.0056

    Article  CAS  PubMed  Google Scholar 

  12. Romay G, Lecoq H, Desbiez C (2014) Zucchini tigré mosaic virus is a distinct potyvirus in the Papaya ringspot virus cluster: molecular and biological insights. Arch Virol 159:277–289

    Article  CAS  PubMed  Google Scholar 

  13. Smith J (1992) Analyzing the mosaic structure of genes. J Mol Evol 34(2):126–129. doi:10.1007/BF00182389

    CAS  PubMed  Google Scholar 

  14. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Wen RH, Hajimorad MR (2010) Mutational analysis of the putative pipo of Soybean mosaic virus suggests disruption of PIPO protein impedes movement. Virology 400:1–7

    Article  CAS  PubMed  Google Scholar 

  16. Yakoubi S, Desbiez C, Fakhfakh H, Wipf-Scheibel C, Marrakchi M, Lecoq H (2008) Biological characterization and complete nucleotide sequence of a Tunisian isolate of Moroccan watermelon mosaic virus. Arch Virol 153:117–125

    Article  CAS  PubMed  Google Scholar 

  17. Yakoubi S, Lecoq H, Desbiez C (2008) Algerian watermelon mosaic virus (AWMV): a new potyvirus species in the PRSV cluster. Virus Genes 37(1):103–109

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

We thank Mr. Jonathan Featherston and Ms. Thulile Faith Nhlapo, from the ARC-BTP, for the technical assistance with NGS.

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Authors and Affiliations

  1. Department of Plant Pathology, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa

    J. D. Ibaba, M. D. Laing & A. Gubba

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  1. J. D. Ibaba
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  2. M. D. Laing
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  3. A. Gubba
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Correspondence to A. Gubba.

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Ibaba, J.D., Laing, M.D. & Gubba, A. Zucchini shoestring virus: a distinct potyvirus in the papaya ringspot virus cluster. Arch Virol 161, 2321–2323 (2016). https://doi.org/10.1007/s00705-016-2899-3

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  • DOI: https://doi.org/10.1007/s00705-016-2899-3

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