Identification of the novel potato virus Y recombinant variants.
- Authors: Antipov A.D1, Surganova J.A1, Taranov V.V1, Lebedeva M.V1
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Affiliations:
- All-Russia Research Institute of Agricultural Biotechnology
- Section: Methodology in ecological genetics
- Submitted: 09.05.2025
- Accepted: 14.05.2025
- Published: 30.06.2025
- URL: https://journals.eco-vector.com/ecolgenet/article/view/679294
- DOI: https://doi.org/10.17816/ecogen679294
- ID: 679294
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Abstract
Background
Potato virus Y (PVY) is one of the most distributed plant RNA-viruses. PVY affects a wide host range including crops and wild plants from different families. Potato virus Y exists as a strain complex which produce a numerous recombinant variants. Usual diagnostic methods based on ELISA and PCR are able to define strain group at the best case, however not particular recombinant variant. Actually, only high-throughput sequencing of plant transcriptomes allow to obtain viral full-genome sequence and reveal all recombinant variants. However, the apply of this approach is limited by the relatively high cost of single sample analysis, which doesn’t allow to explore large-scale samples.
The aim was to develop an approach for the bulk examination of PVY strain diversity.
Materials and methods
Total RNA was isolated from potato leaves. cDNA was synthesized using different reverse transcriptases. PVY genome amplification was performed using different DNA polymerases. Amplicons were used for the sequencing libraries preparation, which were sequenced on MinION platform. Reads after processing were mapped on reference. SNP-calling was performed for the revealing different PVY isolates.
Results
The possibility of different reverse transcriptases and DNA polymerases for PVY genome amplification for farther sequencing was evaluated. Among exterminated sample 10 PVY isolates were revealed. The isolates belong to 5 different recombinant variants, three of them belong to common variants, while two another haven’t been previously described. One of them, N-Wi(s) is similar to the N-Wi, however the recombination point in Hc-Pro gene is shifted to the 5’-end and matches the NO-short variant. Another, SYR-IIa is similar to the SYR-II, however the recombination point in NIb gene is shifted about 50 nucleotides to the 5’-end.
Conclusions
Probably the diversity of PVY recombinant variants is still underestimated since even in the small exterminated sample two novel variants were found. Developed protocol allows to explore PVY strain diversity and has two main advantages: low cost of single sample and each read holds a whole viral genome allowing unambigously identify a recombinant variant.
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About the authors
Alexandr D Antipov
All-Russia Research Institute of Agricultural Biotechnology
Email: antipovdm37@gmail.com
ORCID iD: 0000-0003-3522-1674
SPIN-code: 8244-7171
Russian Federation, 127550, Russia, Moscow, Timiryazevskaya st. 42
Julia A Surganova
All-Russia Research Institute of Agricultural Biotechnology
Email: yuliasyrganova@gmail.com
ORCID iD: 0009-0004-4148-9217
127550, Russia, Moscow, Timiryazevskaya st. 42
Vasiliy V Taranov
All-Russia Research Institute of Agricultural Biotechnology
Email: v.taranov1@gmail.com
ORCID iD: 0000-0002-0728-0346
SPIN-code: 5008-4691
Scopus Author ID: 15761481700
Russian Federation, 127550, Russia, Moscow, Timiryazevskaya st. 42
Marina V Lebedeva
All-Russia Research Institute of Agricultural Biotechnology
Author for correspondence.
Email: marilistik@mail.ru
ORCID iD: 0000-0001-5711-8331
SPIN-code: 1681-8890
127550, Russia, Moscow, Timiryazevskaya st. 42
References
- Quenouille J, Vassilakos N, Moury B. Potato virus Y: a major crop pathogen that has provided major insights into the evolution of viral pathogenicity. Molecular Plant Pathology. 2013; 14:439-452. doi: 10.1111/mpp.12024 EDN: PZSYLV
- Scholthof KB, Adkins S, Czosnek H, et al. Top 10 plant viruses in molecular plant pathology. Molecular plant pathology. 2011; 12(9):938–954. doi: 10.1111/j.1364-3703.2011.00752.x EDN: PGSYPV
- Kaliciak A, Syller J. New hosts of Potato virus Y (PVY) among common wild plants in Europe. European Journal of Plant Pathology. 2009; 124:707–713. doi: 10.1007/s10658-009-9452-0 EDN: LVZTHU
- Salehzadeh M, Afsharifar A, Farashah SD. First report of the incidence of potato virus Y in some ornamental plants in Iran. Iran Agricultural Research. 2023; 42(1):47-54. doi: 10.22099/iar.2023.48019.1550
- Nanayakkara U, Nie X, Giguere M-A, et al. Chenopodium album L. as a Host for Potato Virus Y (PVY) in New Brunswick, Canada. American Journal of Potato Research. 2012; 89:245-247. doi: 10.1007/s12230-012-9243-6
- Lancomme C, Glais L, Bellstedt DU, et al., editors. PVY: biodyversity, pathogenicity, epidemiology and management. Cham: Springer Cham; 2017. doi: 10.1007/978-3-319-58860-5
- Singh KS, Cordeiro EMG, Troczka BJ, et al. Global patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzus persicae. Communications biology. 2021; 4(847). doi: 10.1038/s42003-021-02373-x EDN: XMDZDR
- Sobko OA. On the vector properties of Henosepilachna vigintioctomaculata Motschulsky, 1858 (Coleoptera: Coccinellidae) in the transmission of potato viruses. Far Eastern Entomologist. 2024; 501:17-24. doi: 10.25221/fee.501.2 EDN: IUARMY
- Kreuze JF, Souza-Dias JAC, Jeevalatha A, et al. Viral diseases in potato. In: Campos H, Ortiz O, editors. The potato crop. New York: Springer; 2020. P:389–430. doi: 10.1007/978-3-030-28683-5_11 EDN: JLBTKQ
- Gray SM, Power AG. Anthropogenic influences on emergence of vector-borne plant viruses: the persistent problem of Potato virus Y. Current Opinion in Virology. 2018; 33:177-183. doi: 10.1016/j.coviro.2018.10.002 EDN: YVNZMZ
- Green KJ, Brown CJ, Gray SM, Karasev AV. Phylogenetic study of recombinant strains of Potato virus Y. Virology. 2017; (507):40-52. doi: 10.1016/j.virol.2017.03.018 EDN: YYKHQN
- Green KJ, Brown CJ, Karasev AV. Genetic diversity of potato virus Y (PVY): sequence analyses reveal ten novel PVY recombinant structures. Archives of Virology. 2018; (163):23-32. doi: 10.1007/s00705-017-3568-x EDN: YDDKWD
- Gao F, Chang F, Shen J, et al. Complete genome analysis of a novel recombinant isolate of potato virus Y from China. Archives of Virology. 2014; (159): 3439-3442. doi: 10.1007/s00705-014-2184-2 EDN: QCZBXL
- Samarskaya V, Kuznetsova M, Gryzunov N, et al. Identification of Two Novel Recombinant Types of Potato Virus Y from Solanum tuberosum Plants in Southern Region of Russia. Plant Disease. 2024; 0:ja. doi: 10.1094/PDIS-10-24-2151-SC EDN: UBZCFN
- Lorenzen JH, Piche LM, Gudmestad NC, et al. A Multiplex PCR Assay to Characterize Potato virus Y Isolates and Identify Strain Mixtures. Plant Disease. 2006; 90(7):935–940. doi: 10.1094/PD-90-0935
- Chikh Ali M, Maoka T, Natsuaki KT, Natsuaki T. The simultaneous differentiation of Potato virus Y strains including the newly described strain PVY NTN-NW by multiplex PCR assay. Journal of Virological Methods. 2010; 165(1):15-20. doi: 10.1016/j.jviromet.2009.12.010
- Avrahami-Moyal L, Tam Y, Sela N, et al. Characterization of potato virus Y populations in potato in Israel. Archives of virology. 2019; (164):1691–1695. doi: 10.1007/s00705-019-04250-9 EDN: VTTVRW
- Sierra A, Gallo Y, Estrada M, et al. Detection of four RNA viruses in commercial and informal potato seed tubers in Antioquia (Colombia). Archives of Phytopathology and Plant Protection. 2020; 54(5–6): 273–294. doi: 10.1080/03235408.2020.1829424
- Glasa M, Hancinsky R, Soltys K, et al. Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains. Plants. 2021; 10(4):753. doi: 10.3390/plants10040753 EDN: JCOIAT
- Della Bartola M, Byrne S, Mullins E. Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses. Viruses. 2020; 12(4):478. doi: 10.3390/v12040478 EDN: BTAXLQ
- De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018; 34(15):2666-2669. doi: 10.1093/bioinformatics/bty149
- De Coster W, Rademakers R. NanoPack2: population-scale evaluation of long-read sequencing data. Bioinformatics. 2023; 39(5):btad311. doi: 10.1093/bioinformatics/btad311 EDN: OTXXYJ
- Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018; 34(18):3094-3100. doi: 10.1093/bioinformatics/bty191
- Danecek P, Bonfield JK, Liddle J, et al. Twelve years of samtools and bcftools. GigaScience. 2021; 10(2):giab008. doi: 10.1093/gigascience/giab008 EDN: DCCLOC
- Yanagisawa H, Matsushita Y, Khiutti A, et al. Occurrence and distribution of viruses infecting potato in Russia. Letters in Applied Microbiology. 2021; 73:64-72. doi: 10.1111/lam.13476 EDN: QFBICC
- Biryukova VA, Varitsev YA, Uskov AI, et al. Identification of Potato Virus Y Strains Found in Central Region of Russia. Theoretical & Applied Problems of Agro-Indastry. 2019; 4:19-24. doi: 10.32935/2221-7312-2019-42-4-19-24 EDN: TYAXVQ
- Samarskaya V O, Ryabov E V, Gryzunov N, et al, The Temporal and Geographical Dynamics of Potato Virus Y Diversity in Russia. International Journal of Molecular Sciences. 2023; 24(19):14833. doi: 10.3390/ijms241914833 EDN: ECQAZU
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