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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
Article
  • 28 Downloads

Abstract

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.

Keywords

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

Notes

Acknowledgments

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

10658_2019_1886_MOESM1_ESM.docx (449 kb)
ESM 1 (DOCX 448 kb)

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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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