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Genetic diversity and pathogenicity of potato spindle tuber viroid and chrysanthemum stunt viroid isolates in Russia

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Abstract

To investigate the current status of viroid infection in potato fields in Russia, potato spindle tuber viroid (PSTVd) and chrysanthemum stunt viroid (CSVd) were detected in potato (Solanum tuberosum) and S. nigrum plants growing in the Volga (V), North-Western (NW), and Far Eastern (FE) federal districts in Russia. While both PSTVd and CSVd were detected in potato samples from the V and FE regions, only CSVd was detected in potato samples from NW. CSVd was detected in S. nigrum from FE, and this was the first detection of CSVd in S. nigrum. Analysis of the complete genomes of 30 PSTVd and 10 CSVd variants revealed that 5 and 7 PSTVd variants from V and FE, respectively, and 2, 4, and 3 CSVd variants from V, NW, and FE, respectively, were new. Analysis of the infectivity of and symptoms caused by 15 Russian PSTVd isolates in tomato revealed that 14 PSTVd isolates caused intermediate or severe symptoms, and only FP14 caused mild symptoms. Our survey revealed that most of the Russian PSTVd isolates from V and FE caused intermediate symptoms in tomato, and the genome sequences were identical to that of PSTVd isolated from S. demissum. Phylogenetic analysis of nucleotide sequences of the Russian PSTVd variants showed their close relationship to previously studied PSTVd isolates, suggesting that most strains in Russia have not substantially changed genetically, but have widely spread in potato fields.

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Data availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

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Acknowledgments

We thank Dr. T. K. Kovalenko, head of the Department of Biological Methods of Plant Protection at the Federal State Budget Scientific Institution “Far Eastern Research Institute of Plant Protection,” for helping us sample potato tubers, and Y. Narita and Y. Matsumura for preparing the experimental materials. This study was supported, in part, by the Strategic International Collaborative Research Project promoted by the Ministry of Agriculture, Forestry and Fisheries, Tokyo, Japan (No. J008837) administered by the Ministry of Agriculture, Forestry and Fisheries in Japan, and in part by a grant from the Russian Science Foundation (No. 20-46-07001).

Funding

This study was supported, in part, by the Strategic International Collaborative Research Project promoted by the Ministry of Agriculture, Forestry and Fisheries, Tokyo, Japan (No. J008837) administered by the Ministry of Agriculture, Forestry and Fisheries in Japan, and in part by a grant from the Russian Science Foundation (No. 20–46-07001).

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Authors and Affiliations

  1. NARO, Institute of Vegetable and Floriculture Science, Tsukuba, Ibaraki, 305-8519, Japan

    Yosuke Matsushita

  2. NARO, Central Region Agricultural Research Center, Tsukuba, Ibaraki, 305-8666, Japan

    Hironobu Yanagisawa & Yasuo Ohto

  3. Federal State Budget Scientific Institution, All-Russian Institute of Plant Protection (FSBSI VIZR), Shosse Podbelskogo, Pushkin, Saint Petersburg, 196608, Russia

    Aleksandr Khiutti, Nina Mironenko & Olga Afanasenko

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  1. Yosuke Matsushita
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  2. Hironobu Yanagisawa
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  3. Aleksandr Khiutti
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  4. Nina Mironenko
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  5. Yasuo Ohto
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  6. Olga Afanasenko
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Contributions

All authors contributed to the study conception and design. Material preparation was performed by Yosuke Matsushita, Hironobu Yanagisawa, Aleksandr Khiutti, Nina Mironenko, Yasuo Ohto and Olga Afanasenko. Data collection and analysis were performed by Hironobu Yanagisawa, Yosuke Matsushita, Aleksandr Khiutti and Nina Mironenko. The first draft of the manuscript was written by Yosuke Matsushita and Hironobu Yanagisawa and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Yosuke Matsushita.

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Matsushita, Y., Yanagisawa, H., Khiutti, A. et al. Genetic diversity and pathogenicity of potato spindle tuber viroid and chrysanthemum stunt viroid isolates in Russia. Eur J Plant Pathol 161, 529–542 (2021). https://doi.org/10.1007/s10658-021-02339-z

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