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Genetic variability of watermelon mosaic virus isolates infecting cucurbit crops in Italy

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Abstract

Watermelon mosaic virus (WMV; genus Potyvirus, family Potyviridae) is responsible for serious cucurbit yield losses worldwide. Different WMV genetic groups have been characterized so far. Among these, the “classical” (CL) group has been present in the Mediterranean basin for 40 years, whereas the “emergent” (EM) group includes isolates that are associated with more-severe symptoms observed since 2000. Information on the spatial and temporal evolution of WMV isolates in Italy is currently sparse. In this study, 39 WMV isolates samples collected in different regions over the last two decades were analysed at two different genomic regions that are known to be highly variable and contain recombination breakpoints. Most of the isolates collected between 2002 and 2009 were found to belong to the CL group, whereas the isolates from 2012 onwards were classified as EM, indicating that EM isolates have progressively displaced the CL population in Italy. Although genetic variability was observed within both CL and EM groups and recombinant isolates were detected, no positive selection or haplotype geographic structure were inferred. This suggest that the shift from CL to EM populations was likely due to multiple introductions of EM isolates in different regions of Italy rather than from genetic differentiation of local populations. The progressive increase in prevalence of the highly virulent EM populations is a serious concern because of their symptom severity, and the presence of multiple EM variants that include recombinants necessitates new efforts to develop durable control strategies.

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Acknowledgements

The authors are grateful to Prof. Fernando García-Arenal (Centro de Biotecnología y Genómica de Plantas UPM-INIA, Campus de Montegancedo, Universidad Politécnica de Madrid, Spain) for his kind suggestions on sequence analysis. This work was supported by the project “EMERAMB, Emergent Viruses and Virus Vectors in Mediterranean Basin Crops”, which is funded through the ARIMNet2 2015 Call. ARIMNet2 (2014—2017) is an ERA-NET coordinated by INRA (France); it has received funding from the European Union’s Seventh Framework Programme for Research, Technological Development and Demonstration under Grant Agreement No. 618127.

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Authors and Affiliations

  1. CREA Research Centre for Plant Protection and Certification, Via C.G. Bertero 22, Rome, Italy

    Sabrina Bertin, Ariana Manglli & Laura Tomassoli

  2. Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain

    Michael McLeish

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  1. Sabrina Bertin
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Correspondence to Sabrina Bertin.

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705_2020_4584_MOESM1_ESM.pdf

Fig. S1 Maximum-parsimony (MP) tree obtained using an 813-nt NIb/CP fragment of WMV isolates from Italy (in bold) and GenBank, for a total of 65 sequences. A sequence of the NIb/CP region of SMV was used as the outgroup. The bootstrap consensus tree inferred from 1000 replicates is represented, and the branches corresponding to partitions reproduced in less than 50% of the bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test is shown next to the branches. (PDF 66 kb)

705_2020_4584_MOESM2_ESM.pdf

Fig. S2 Maximum-parsimony (MP) tree obtained using a 1371-nt HC-Pro fragment of 39 WMV isolates from Italy. A sequence of the HC-Pro region of SMV was used as the outgroup. The bootstrap consensus tree inferred from 1000 replicates is represented, and the branches corresponding to partitions reproduced in less than 50% of the bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test is shown next to the branches. (PDF 48 kb)

705_2020_4584_MOESM3_ESM.pdf

Fig. S3 A randomised minimum spanning tree (RMST) combined with multidimensional scaling (MDS) analysis (a), showing the relationships among WMV haplotype groups (1 to 7) and their geographic affiliations, visualized using a maximum-parsimony network (b) (PDF 110 kb)

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Bertin, S., Manglli, A., McLeish, M. et al. Genetic variability of watermelon mosaic virus isolates infecting cucurbit crops in Italy. Arch Virol 165, 937–946 (2020). https://doi.org/10.1007/s00705-020-04584-9

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  • DOI: https://doi.org/10.1007/s00705-020-04584-9

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