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Analysis of the Complete Tomato Aspermy Virus Genomes Suggests Reassortment in Russian Isolates from Chrysanthemum

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Abstract—Tomato aspermy virus (TAV, genus Cucumovirus from the family Bromoviridae) is one of the most common and harmful chrysanthemum viruses, causing severe flower distortion, size reduction, and color breaking. Metatranscriptome sequencing of chrysanthemum plants of the Ribonette and Golden Standard cultivars from the collection of the Nikita Botanical Garden (Yalta, Republic of Crimea) generated TAV‑related RNA reads. The complete genomes of two Russian isolates of the virus were assembled from the reads. This is the first report of full-length TAV genomes from Russia. Typically of cucumoviruses, the segmented TAV genome is represented by three single-stranded positive-sense linear RNA molecules of 3412 (RNA1), 3097 (RNA2) and 2219 (RNA3) nucleotides. Five open reading frames (ORF) have been identified that encode replicase (ORF1), RNA-dependent RNA polymerase (ORF2a), silencing suppressor protein (OFR2b), movement protein (OFR3a) and the coat protein (ORF3b). The identity of TAV genomes from the two chrysanthemum cultivars was 99.8% for all three viral RNAs; with other TAV isolates from GenBank it was 97.5–99.7% (RNA1), 93.8–99.8% (RNA2), and 89.3–99.3% (RNA3). Phylogenetic analysis showed that RNA1 and RNA3 of the Russian isolates were assigned to heterogeneous groups of TAV isolates found on various plant species in different regions of the world. At the same time, RNA2 clearly clustered with tomato isolates SKO20ST2 from Slovenia and PV-0220 from Bulgaria and, to a lesser extent, with the Iranian isolate Ker.Mah.P from petunia and the Chinese isolate Henan from chrysanthemum. The incongruence of phylogenetic trees reconstructed from different genome segments suggests pseudo-recombination (reassortment) in the Russian TAV isolates.

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ACKNOWLEDGMENTS

The authors thank Dr. N.V. Smykova and Dr. I.V. Mitrofanova for help in the survey of the chrysanthemum collection of the Nikita Botanical Garden—National Scientific Center of the Russian Academy of Sciences. High-throughput sequencing was performed using the equipment of the Genome Center of the Engelhardt Institute of Molecular Biology, Russian Academy of Sciences (http://www.eimb.ru/ ru1/ckp/ccu_ genome_c.php).

Funding

The work was supported by a grant from the Ministry of Science and Higher Education of the Russian Federation no. 075-15-2019-1670.

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Authors and Affiliations

  1. Faculty of Biology, Moscow State University, 119234, Moscow, Russia

    A. A. Sheveleva & S. N. Chirkov

  2. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia

    G. S. Krasnov, A. V. Kudryavtseva, A. V. Snezhkina & E. V. Bulavkina

  3. Kurchatov Genomic Center of the Nikita Botanical Garden–National Scientific Center, Russian Academy of Sciences, 298648, Yalta, Russia

    S. N. Chirkov

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  1. A. A. Sheveleva
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  2. G. S. Krasnov
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Correspondence to S. N. Chirkov.

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Sheveleva, A.A., Krasnov, G.S., Kudryavtseva, A.V. et al. Analysis of the Complete Tomato Aspermy Virus Genomes Suggests Reassortment in Russian Isolates from Chrysanthemum. Mol Biol 57, 816–824 (2023). https://doi.org/10.1134/S0026893323050151

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