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Genome characterization and complete sequence of a new badnavirus from Pandanus amaryllifolius

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Abstract

A new badnavirus was sequenced from fragrant pandan grass (Pandanus amaryllifolius) displaying mosaic and chlorosis on the leaves. The complete genome sequence was determined by high-throughput sequencing. The new badnavirus was tentatively named "pandanus mosaic associated virus" (PMaV). Similar to those of other members of the genus Badnavirus, the genome of PMaV consists of a circular DNA molecule of 7,481 bp with three open reading frames (ORF) potentially coding for three proteins. ORF3 encodes a polyprotein with conserved protein domains including zinc finger, trimeric dUTPase, aspartic protease, reverse transcriptase (RT), and RNase H domains. Pairwise comparisons of the highly conserved RT + RNase H region revealed the highest nucleotide (nt) sequence identity (70.71%) to taro bacilliform CH virus-Et17 (MG017324). In addition to PMaV, viral sequences corresponding to orchid fleck dichorhavirus (OFV) were detected in the same plant sample. The complete sequence of the OFV coding region shared >98% nt sequence identity with other isolates of OFV available in the GenBank database. Disease symptoms could not be attributed exclusively to PMaV or OFV, as both viruses were present in the pandan grass exhibiting mosaic and chlorosis.

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Acknowledgements

We thank Joel Crippen and Joshua Spall at Mounts Botanical Garden (West Palm Beach, FL) for their help in sampling fragrant pandan grass (Pandanus amaryllifolius). Robert A. Alvarez-Quinto is supported by the Republic of Ecuador through the Ecuadorean Science and Technology Secretariat (SENESCYT).

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The authors have not disclosed any funding.

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Authors and Affiliations

  1. Department of Botany and Plant Pathology, 4575 Research Way Lab, Corvallis, OR, 97333, USA

    Robert A. Alvarez-Quinto

  2. USDA-ARS National Germplasm Resources Laboratory, USDA-ARS, Beltsville, MD, USA

    Samuel Grinstead

  3. CIRAD, UMR PHIM, 34398, Montpellier, France

    Philippe Rott

  4. PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France

    Philippe Rott

  5. USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR, 97330, USA

    Dimitre Mollov

Authors
  1. Robert A. Alvarez-Quinto
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  2. Samuel Grinstead
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  3. Philippe Rott
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  4. Dimitre Mollov
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Contributions

All authors have read and agreed to the published version of the manuscript. Conceptualization: Dimitre Mollov, Philippe Rott. Methodology: Robert Alvarez, Samuel C. Grinstead, Dimitre Mollov. Formal analysis and investigation: Robert Alvarez, Samuel C. Grinstead. Writing – original draft preparation: Robert Alvarez, Dimitre Mollov. Writing – review and editing: Robert Alvarez, Samuel C. Grinstead, Philippe Rott, Dimitre Mollov. Funding acquisition: Dimitre Mollov. Resources: Dimitre Mollov, Philippe Rott. Supervision: Dimitre Mollov

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Correspondence to Dimitre Mollov.

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

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Alvarez-Quinto, R.A., Grinstead, S., Rott, P. et al. Genome characterization and complete sequence of a new badnavirus from Pandanus amaryllifolius. Arch Virol 167, 1717–1720 (2022). https://doi.org/10.1007/s00705-022-05480-0

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  • DOI: https://doi.org/10.1007/s00705-022-05480-0

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