Genomic sequence variability of an Italian Zucchini yellow mosaic virus isolate

  • Giovanni BubiciEmail author
  • Beatriz Navarro
  • Anna Vittoria Carluccio
  • Marina Ciuffo
  • Francesco Di Serio
  • Fabrizio CilloEmail author


Zucchini yellow mosaic virus (ZYMV) was first reported in Italy, but no Italian isolates have been sequenced so far. A ZYMV isolate, designated Z104, was isolated from a zucchini plant grown in the open field in Piedmont, Italy, and showing severe disease symptoms. We report the full-length genome sequence of Z104 as determined by Sanger sequencing and small (s)RNA deep sequencing. The latter technique was useful to confirm the isolate sequence, that was deposited in the NCBI database with the accession number MK956829 and to investigate the sequence variability of Z104 isolate. The genome of 9611 nucleotides (nt) consisted of an open reading frame of 9243 nt encoding a polyprotein of 3080 amino acids (349.88 kDa), flanked by the 5′- and 3′-untranslated regions, and an overlapping ORF of 74 amino acids, the P3N-PIPO. As in previously sequenced ZYMV isolates, Z104 polyprotein consists of 10 putative functional proteins. Several domains in the HC-Pro and P3 proteins related to the transmissibility by aphids and virus aggressiveness are conserved in Z104. Symptoms induced both in the field and laboratory by Z104 together with its molecular features indicate that it is an aggressive strain. Deep sequencing of sRNAs revealed a particularly high variability in the genome sequence at eight nucleotide positions, three of which resulted in missense mutations in the P3, 6K1, and NIb proteins. This may be indicative of the natural ZYMV genome variability within the host. The phylogenetic analysis of the whole genome or the sole coat protein of several ZYMV isolates did not provide evidence for a close relationship of Z104 with other isolates from European countries. To the best of our knowledge, this is the first-reported complete genome of a ZYMV isolate from Italy.


Next-generation sequencing Small RNA sequencing Virus genome sequencing Detection Zucchini yellow mosaic virus ZYMV 



This research was supported by a grant to the Public-Private Laboratory GenoHORT “Valorizzazione di produzioni ortive campane di eccellenza con strumenti di genomica avanzata” (GenHort, Cod. PON02_00395_3215002).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical responsibilities of authors

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

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ESM 1 (DOCX 448 kb)


  1. Adams, M., Zerbini, F., French, R., Rabenstein, F., Stenger, D., & Valkonen, J. (2012). Potyviridae. In A. King, M. Adams, E. Carstens, & E. Lefkowitz (Eds.), Virus taxonomy: Ninth report of the International Committee on Taxonomy of Viruses (pp. 1069–1089). London: Elsevier Academic Press.Google Scholar
  2. Afgan, E., Baker, D., Batut, B., van den Beek, M., Bouvier, D., Cech, M., Chilton, J., Clements, D., Coraor, N., Gruning, B. A., Guerler, A., Hillman-Jackson, J., Hiltemann, S., Jalili, V., Rasche, H., Soranzo, N., Goecks, J., Taylor, J., Nekrutenko, A., & Blankenberg, D. (2018). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Research, 46, W537–W544. Scholar
  3. Blanc, S., López-Moya, J.-J., Wang, R., García-Lampasona, S., Thornbury, D. W., & Pirone, T. P. (1997). A specific interaction between coat protein and helper component correlates with aphid transmission of a Potyvirus. Virology, 231, 141–147. Scholar
  4. Choi, S. K., Yoon, J. Y., Ryu, K. H., Choi, J. K., & Park, W. M. (2002). First report of Zucchini yellow mosaic virus on hollyhock (Althaea rosea). The Plant Pathology Journal, 18, 121–125. Scholar
  5. Chung, B. Y., Miller, W. A., Atkins, J. F., & Firth, A. E. (2008). An overlapping essential gene in the Potyviridae. Proceedings of the National Academy of Sciences of the United States of America, 105, 5897–5902. Scholar
  6. Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., & Ruden, D. M. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly, 6, 80–92. Scholar
  7. Coutts, B. A., Kehoe, M. A., Webster, C. G., Wylie, S. J., & Jones, R. A. C. (2011). Zucchini yellow mosaic virus: Biological properties, detection procedures and comparison of coat protein gene sequences. Archives of Virology, 156, 2119–2131. Scholar
  8. Desbiez, C., & Lecoq, H. (1997). Zucchini yellow mosaic virus. Plant Pathology, 46, 809–829. Scholar
  9. Desbiez, C., Gal-On, A., Girard, M., Wipf-Scheibel, C., & Lecoq, H. (2003). Increase in Zucchini yellow mosaic virus symptom severity in tolerant zucchini cultivars is related to a point mutation in P3 protein and is associated with a loss of relative fitness on susceptible plants. Phytopathology, 93, 1478–1484. Scholar
  10. Desbiez, C., Girard, M., & Lecoq, H. (2010). A novel natural mutation in HC-Pro responsible for mild symptomatology of Zucchini yellow mosaic virus (ZYMV, Potyvirus) in cucurbits. Archives of Virology, 155, 397–401. Scholar
  11. Dunham, J. P., Simmons, H. E., Holmes, E. C., & Stephenson, A. G. (2014). Analysis of viral (Zucchini yellow mosaic virus) genetic diversity during systemic movement through a Cucurbita pepo vine. Virus Research, 191, 172–179. Scholar
  12. Gal-On, A. (2000). A point mutation in the FRNK motif of the Potyvirus helper component-protease gene alters symptom expression in cucurbits and elicits protection against the severe homologous virus. Phytopathology, 90, 467–473. Scholar
  13. Gal-On, A. (2007). Zucchini yellow mosaic virus: Insect transmission and pathogenicity – the tails of two proteins. Molecular Plant Pathology, 8, 139–150. Scholar
  14. Gal-On, A., Antignus, Y., Rosner, A., & Raccah, B. (1992). A Zucchini yellow mosaic virus coat protein gene mutation restores aphid transmissibility but has no effect on multiplication. The Journal of General Virology, 73, 2183–2187. Scholar
  15. Garrison, E., & Marth, G. (2012). Haplotype-based variant detection from short-read sequencing. arXiv, 1207, 3907.Google Scholar
  16. Glasa, M., & Pittnerová, S. (2006). Complete genome sequence of a Slovak isolate of Zucchini yellow mosaic virus (ZYMV) provides further evidence of a close molecular relationship among central European ZYMV isolates. Journal of Phytopathology, 154, 436–440. Scholar
  17. Granier, F., Durandtardif, M., Cassedelbart, F., Lecoq, H., & Robaglia, C. (1993). Mutations in Zucchini yellow mosaic virus helper component protein associated with loss of aphid transmissibility. Journal of General Virology, 74, 2737–2742. Scholar
  18. Huet, H., Galon, A., Meir, E., Lecoq, H., & Raccah, B. (1994). Mutations in the helper component protease gene of Zucchini yellow mosaic-virus affect its ability to mediate aphid transmissibility. Journal of General Virology, 75, 1407–1414. Scholar
  19. Kang, B., Peng, B., Wu, H., Liu, L., Wu, W., & Gu, Q. (2018). Host-associated selection of a P3 mutant of Zucchini yellow mosaic virus affects viral infectivity in watermelon. Archives of Virology, 163, 1449–1454. Scholar
  20. Katis, N. I., Tsitsipis, J. A., Lykouressis, D. P., Papapanayotou, A., Margaritopoulos, J. T., Kokinis, G. M., Perdikis, D. C., & Manoussopoulos, I. N. (2006). Transmission of Zucchini yellow mosaic virus by colonizing and non-colonizing aphids in Greece and new aphid species vectors of the virus. Journal of Phytopathology, 154, 293–302. Scholar
  21. Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35, 1547–1549. Scholar
  22. Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357. Scholar
  23. Lecoq, H., & Desbiez, C. (2008). Watermelon mosaic virus and Zucchini yellow mosaic virus. In B. Mahy & M. Van Regenmortel (Eds.), Encyclopedia of virology (3rd ed., pp. 433–440). Oxford: Elsevier.CrossRefGoogle Scholar
  24. Lecoq, H., Lisa, V., & Dellavalle, G. (1983). Serological identity of Muskmelon yellow stunt and Zucchini yellow mosaic-viruses. Plant Disease, 67, 824–825. Scholar
  25. Lecoq, H., Lemaire, J. M., & Wipfscheibel, C. (1991). Control of Zucchini yellow mosaic-virus in squash by cross protection. Plant Disease, 75, 208–211. Scholar
  26. Lin, S. S., Wu, H. W., Jan, F. J., Hou, R. F., & Yeh, S. D. (2007). Modifications of the helper component-protease of Zucchini yellow mosaic virus for generation of attenuated mutants for cross protection against severe infection. Phytopathology, 97, 287–296. Scholar
  27. Lisa, V., & Lecoq, H. (1984). Zucchini yellow mosaic virus. CMI/AAB description of plant viruses (p. 4). Kew: Commonwealth Mycological Institute.Google Scholar
  28. Lisa, V., Boccardo, G., Dagostino, G., Dellavalle, G., & Daquilio, M. (1981). Characterization of a Potyvirus that causes zucchini yellow mosaic. Phytopathology, 71, 667–672. Scholar
  29. Llave, C., Martinez, B., Diaz-Ruiz, J. R., & Lopez-Abella, D. (2002). Amino acid substitutions within the Cys-rich domain of the Tobacco etch potyvirus HC-Pro result in loss of transmissibility by aphids. Archives of Virology, 147, 2365–2375. Scholar
  30. Maghamnia, H. R., Hajizadeh, M., & Azizi, A. (2018). Complete genome sequence of Zucchini yellow mosaic virus strain Kurdistan, Iran. 3 Biotech, 8, 147. Scholar
  31. Nováková, S., Svoboda, J., & Glasa, M. (2014). Analysis of the complete sequences of two biologically distinct Zucchini yellow mosaic virus isolates further evidences the involvement of a single amino acid in the virus pathogenicity. Acta Virologica, 58, 364–367. Scholar
  32. Peng, Y. H., Kadoury, D., Gal-On, A., Huet, H., Wang, Y., & Raccah, B. (1998). Mutations in the HC-Pro gene of Zucchini yellow mosaic potyvirus: Effects on aphid transmission and binding to purified virions. The Journal of General Virology, 79, 897–904. Scholar
  33. Pfeiffer, F., Gröber, C., Blank, M., Händler, K., Beyer, M., Schultze, J. L., & Mayer, G. (2018). Systematic evaluation of error rates and causes in short samples in next-generation sequencing. Scientific Reports, 8, 10950. Scholar
  34. Shiboleth, Y. M., Haronsky, E., Leibman, D., Arazi, T., Wassenegger, M., Whitham, S. A., Gaba, V., & Gal-On, A. (2007). The conserved FRNK box in HC-Pro, a plant viral suppressor of gene silencing, is required for small RNA binding and mediates symptom development. Journal of Virology, 81, 13135–13148. Scholar
  35. Simmons, H. E., Dunham, J. P., Stack, J. C., Dickins, B. J., Pagan, I., Holmes, E. C., & Stephenson, A. G. (2012). Deep sequencing reveals persistence of intra- and inter-host genetic diversity in natural and greenhouse populations of Zucchini yellow mosaic virus. The Journal of General Virology, 93, 1831–1840. Scholar
  36. Sorefan, K., Pais, H., Hall, A. E., Kozomara, A., Griffiths-Jones, S., Moulton, V., & Dalmay, T. (2012). Reducing ligation bias of small RNAs in libraries for next generation sequencing. Silence, 3, 4. Scholar
  37. Tamura, K., & Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial-DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512–526. Scholar
  38. Wang, W.-Q., Natsuaki, T., Kosaka, Y., & Okuda, S. (2006). Comparison of the nucleotide and amino acid sequences of parental and attenuated isolates of Zucchini yellow mosaic virus. Journal of General Plant Pathology, 72, 52–56. Scholar
  39. Wickham, H. (2009). ggplot2: Elegant graphics for data analysis. New York: Springer.CrossRefGoogle Scholar
  40. Zerbino, D. R., & Birney, E. (2008). Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18, 821–829. Scholar

Copyright information

© Koninklijke Nederlandse Planteziektenkundige Vereniging 2019

Authors and Affiliations

  1. 1.Istituto per la Protezione Sostenibile delle PianteConsiglio Nazionale delle RicercheBariItaly
  2. 2.Istituto per la Protezione Sostenibile delle PianteConsiglio Nazionale delle RicercheTorinoItaly

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