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Genome characterization of parsley severe stunt-associated virus in Iran

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Abstract

Parsley severe stunt-associated virus (PSSaV) is a recently identified nanovirus first reported in Germany. During a survey for identification of nanoviruses infecting apiaceous plants in south-eastern Iran, PSSaV was identified and characterized using a combination of rolling circle amplification (RCA) and high-throughput sequencing. Parsley plant samples were collected from vegetable production farms in Kerman province. From two symptomatic samples (39Ba and 40Ba), seven PSSaV components (DNA-C, -S, -M, -R, -N, -U1 and -U2) with two phylogenetically distinct variants of DNA-R (R1 and R2) were identified. In common with the German isolate of PSSaV, no DNA-U4 component was identified. In addition, associated alphasatellite molecules were identified in samples 39Ba [n = 6] and 40Ba [n = 5]. Sequence analyses showed that concatenated component sequences of the two Iranian PSSaVs share 97.2% nucleotide identity with each other and 82% to the German isolate. The coat proteins (CPs) of the PSSaV Iranian sequences share 97.2% amino acid identity and ~ 84% identity with that of the German isolate. Sequence and phylogenetic analyses of a total of 11 recovered alphasatellites from the two samples can be classified into the genera Fabenesatellite [n = 2], Milvetsatellite [n = 1], Mivedwarsatellite [n = 2], Subclovsatellite [n = 2], Sophoyesatellite [n = 4] in the family Alphasatellitidae. Identification of PSSaV and other nanoviruses in wild and cultivated plants in Iran reveals that nanoviruses could be causing yield reduction in crops plants in this country.

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Acknowledgements

This research work was supported by Research and Technology Institute of Plant Production (RTIPP), Shahid Bahonar University of Kerman, Iran (Grant No. P/900/106).

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Authors and Affiliations

  1. Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran

    Vahid Hasanvand, Jahangir Heydanejad & Hossain Massumi

  2. Research and Technology Institute of Plant Production (RTIPP), Shahid Bahonar University of Kerman, 7616914111, Kerman, Iran

    Jahangir Heydanejad

  3. Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany

    Tatjana Kleinow & Holger Jeske

  4. The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287-5001, USA

    Rafaela S. Fontenele, Simona Kraberger & Arvind Varsani

  5. Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa

    Arvind Varsani

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  1. Vahid Hasanvand
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Contributions

VH, HJ and JH designed the study; TK, HJ, HM and JH prepared and provided laboratory support; VH and HJ amplified and sequenced viral genome components; VH, HJ, JH, RSF, SK and AV analysed the sequence data; JH and AV drafted the manuscript, and all authors read and approved the final version.

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Correspondence to Jahangir Heydanejad.

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11262_2021_1835_MOESM1_ESM.xlsx

Supplementary Data 1. Pairwise identity matrices of the genome, individual components and those of the associated alphasatellites. Sequence of the DNA-U4 component of approved and proposed nanovirus species was removed to compare with the concatenated sequences of PSSaV. (XLSX 142 kb)

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Hasanvand, V., Heydanejad, J., Massumi, H. et al. Genome characterization of parsley severe stunt-associated virus in Iran. Virus Genes 57, 293–301 (2021). https://doi.org/10.1007/s11262-021-01835-y

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