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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Production and Genetic Improvement Research Unit » Research » Publications at this Location » Publication #392081

Research Project: Genetic Improvement of Blackberry, Red and Black Raspberry, Blueberry, and Strawberry

Location: Horticultural Crops Production and Genetic Improvement Research Unit

Title: Genome characterization and complete sequence of a new badnavirus from pandanus amaryllifolius

item ALVAREZ-QUINTO, ROBERT - Oregon State University
item Grinstead, Sam
item ROTT, PHILIPPE - Cirad, France
item Mollov, Dimitre

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/11/2022
Publication Date: 5/24/2022
Citation: Alvarez-Quinto, R., Grinstead, S.C., Rott, P., Mollov, D.S. 2022. Genome characterization and complete sequence of a new badnavirus from pandanus amaryllifolius. Archives of Virology.

Interpretive Summary: Pandan is a monocot plant widely cultivated in Southeast Asia and used for flavoring and as a natural green colorant for several foods. Additionally pandan is used in landscape settings as ornamental plant in tropical environments. In this research we investigated plants from South Florida that showed virus like symptoms. Our results revealed infection with orchid fleck virus (OFV). OFV is associated with citrus diseases. This is a first report of OFV infecting pandan and is an important information for the citrus industry in Florida. Additionally the same plant was infected with a new badnavirus. We determined the complete genomic sequence of this new virus. These findings will facilitate development of diagnostic protocols and will help devise control strategies for managing this new viral disease.

Technical Abstract: A new badnavirus was sequenced from Pandanus amaryllifolius displaying mosaic and chlorosis on the leaves. The complete genome sequence was generated by high-throughput sequencing. The new badnavirus was tentatively named pandanus mosaic associated virus (PaMV). The genome of PaMV consists of a circular DNA molecule of 7,481 bp with three open reading frames (ORF) potentially coding for three proteins similarly to viruses of the genus Badnavirus. ORF3 encodes a polyprotein with conserved protein domains including zinc finger, trimeric dUTPase, aspartic protease, reverse transcriptase (RT), and RNase H. Pairwise comparisons of the highly conserved region ‘RT + RNase H’ revealed the highest nucleotide (nt) identity (70.71%) with taro bacilliform CH virus-Et17 (MG017324). In addition to PaMV, viral sequences corresponding to orchid fleck dichorhavirus (OFV) were detected in the same plant sample. The complete sequence of the OFV coding region shared >96% nt identity with other isolates of OFV available at GenBank. Because two distinct virus species were present in the diseased P. amaryllifolius, observed symptoms cannot be attributed exclusively to PaMV or OFV.