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Discovery and molecular characterization of a new cryptovirus dsRNA genome from Japanese persimmon through conventional cloning and high-throughput sequencing

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Abstract

Through the application of next generation sequencing, in synergy with conventional cloning of DOP-PCR fragments, two double-stranded RNA (dsRNA) molecules of about 1.5 kbp in size were isolated from leaf tissue of a Japanese persimmon (accession SSPI) from Apulia (southern Italy) showing veinlets necrosis. High-throughput sequencing allowed whole genome sequence assembly, yielding a 1,577 and a 1,491 bp contigs identified as dsRNA-1 and dsRNA-2 of a previously undescribed virus, provisionally named as Persimmon cryptic virus (PeCV). In silico analysis showed that both dsRNA fragments were monocistronic and comprised the RNA-dependent RNA polymerase (RdRp) and the capsid protein (CP) genes, respectively. Phylogenetic reconstruction revealed a close relationship of these dsRNAs with those of cryptoviruses described in woody and herbaceous hosts, recently gathered in genus Deltapartitivirus. Virus-specific primers for RT-PCR, designed in the CP cistron, detected viral RNAs also in symptomless persimmon trees sampled from the same geographical area of SSPI, thus proving that PeCV infection may be fairly common and presumably latent.

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Acknowledgments

The authors are grateful to Prof. G. P. Martelli and Prof. V. N. Savino (Università degli Studi Aldo Moro, Bari, Italy) for help with manuscript editing and for invaluable contribution in planning the experimental activities during the Ph.D. studies of M.M., respectively.

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Authors and Affiliations

  1. Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), UOS Bari, Via Amendola 122/D, 70126, Bari, Italy

    M. Morelli, M. Chiumenti, A. De Stradis, P. La Notte & A. Minafra

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  1. M. Morelli
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  2. M. Chiumenti
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  3. A. De Stradis
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  4. P. La Notte
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Correspondence to M. Morelli.

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Morelli, M., Chiumenti, M., De Stradis, A. et al. Discovery and molecular characterization of a new cryptovirus dsRNA genome from Japanese persimmon through conventional cloning and high-throughput sequencing. Virus Genes 50, 160–164 (2015). https://doi.org/10.1007/s11262-014-1127-z

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