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Akbaş B, Morca AF, Coşkan S, Santosa AI, Çulal-Kılıç H, Çelik A. First complete sequences and genetic variation of plum pox virus T strain in Prunus dulcis and Prunus cerasus. 3 Biotech 2023; 13:332. [PMID: 37681114 PMCID: PMC10480364 DOI: 10.1007/s13205-023-03746-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 08/16/2023] [Indexed: 09/09/2023] Open
Abstract
The complete genome of plum pox virus strain T isolates from five different Prunus spp., including almond (P. dulcis) and sour cherry (P. ceracus) isolates, was fully sequenced using the primer pairs designed in this study. The five isolates were aligned with other 50 PPV-T isolates whose complete genome sequences were available in GenBank and then subjected to phylogenetic and diversity analyses. Recombination analysis showed no significant signal detected in the five newly sequenced isolates while confirming four recombinant isolates reported in a previous study. Nucleotide and amino acid phylogenetic trees clustered the tested isolates into three major groups: Balkan 1, 2, and 3. Strain T isolates shared high nucleotide and amino acid identities among them. Diversity analysis applied different parameters to found that the sequences of P3 and 6K1 genes were more conserved over other genes. In accordance, the highly variable P1 and CP genes were found to experience weaker purifying pressures, ω = 0.127 and 0.219, respectively, than other genes. The three neutrality tests gave negative values to all genes, suggesting that strain T populations have expanding or bottleneck selections. Genetic make-up of the only known sour cherry isolate is highly identical to isolates from other Prunus spp. Therefore, this study has updated our knowledge of T strain diversity in new hosts and provided a clear picture of genetic variation and host relationships. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03746-1.
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Affiliation(s)
- Birol Akbaş
- Directorate of Plant Protection Central Research Institute, Gayret Mah. Fatih Sultan Mehmet Bulv., 06172 Yenimahalle, Ankara Turkey
| | - Ali Ferhan Morca
- Directorate of Plant Protection Central Research Institute, Gayret Mah. Fatih Sultan Mehmet Bulv., 06172 Yenimahalle, Ankara Turkey
| | - Sevgi Coşkan
- Directorate of Plant Protection Central Research Institute, Gayret Mah. Fatih Sultan Mehmet Bulv., 06172 Yenimahalle, Ankara Turkey
| | - Adyatma Irawan Santosa
- Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Jl. Flora No. 1, Sleman, 55281 Yogyakarta, Indonesia
| | - Handan Çulal-Kılıç
- Department of Plant Protection, Faculty of Agriculture, Isparta University of Applied Sciences, 32000 Isparta, Turkey
| | - Ali Çelik
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant İzzet Baysal University, 14030 Bolu, Turkey
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Chirkov S, Sheveleva A, Gasanova T, Kwon D, Sharko F, Osipov G. New Cherry-Adapted Plum Pox Virus Phylogroups Discovered in Russia. PLANT DISEASE 2022; 106:2591-2600. [PMID: 35442710 DOI: 10.1094/pdis-01-22-0006-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plum pox virus (PPV) is the most pathogenic virus of stone fruit crops worldwide. Unusual PPV isolates were discovered on sour cherry (Prunus cerasus L.) and steppe cherry (P. fruticosa Pall.) in the Republic of Tatarstan and the Middle Ural region, Russia. They induced typical sharka symptoms and tested positive for PPV by ELISA and RT-PCR, but were not detected by PCR using known strain-specific primers. Their complete genomes were determined using high-throughput sequencing. Phylogenetic analysis allocated new isolates to four clearly distinguished lineages (SC, TAT, Y, Tat-26) within a cluster of PPV cherry-adapted strains. The phylogroups SC and TAT had 84.5 to 86.9% average nucleotide identity to each other and strain CR, with which they comprised a common subcluster. Isolates from the Middle Ural region (group Y) were closer to strain C, sharing 96.9% identity. The fourth lineage is represented by the isolate Tat-26, which was a recombinant of strain CR and C isolates as major and minor parents, respectively. These results show that the genetic diversity of PPV is higher than thought and may contribute to a better understanding of the origin and evolution of cherry-adapted strains of the virus. P. fruticosa was reported as a new natural PPV host for the first time.
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Affiliation(s)
- Sergei Chirkov
- Department of Virology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Anna Sheveleva
- Department of Virology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Tatiana Gasanova
- Department of Virology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Dmitry Kwon
- Genomic Sequencing Facility, National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Fedor Sharko
- Laboratory of Bioinformatics and Big Data, National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Gennady Osipov
- Department of Agricultural Biotechnology, Tatar Research Institute of Agriculture, Kazan 420059, Russia
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3
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Collum TD, Stone AL, Sherman DJ, Damsteegt VD, Schneider WL, Rogers EE. Viral Reservoir Capacity of Wild Prunus Alternative Hosts of Plum Pox Virus Through Multiple Cycles of Transmission and Dormancy. PLANT DISEASE 2022; 106:101-106. [PMID: 34293916 DOI: 10.1094/pdis-04-21-0802-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plum pox virus (PPV) is a significant pathogen of Prunus worldwide and is known for having a broad experimental host range. Many of these hosts represent epidemiological risks as potential wild viral reservoirs. A comparative study of the PPV reservoir capacity of three commonly found native North American species, western choke cherry (Prunus virginiana var. demissa), black cherry (Prunus serotina), and American plum (Prunus americana) was conducted. Pennsylvania isolates of PPV-D were transmitted from the original host peach (Prunus persica cv. GF305) to all three species. Viral accumulation and transmission rates to alternative hosts and peach were monitored over the course of five vegetative growth and cold induced dormancy (CID) cycles. The three alternative host species demonstrated differences in their ability to maintain PPV-D and the likelihood of transmission to additional alternative hosts or back transmission to peach. Western choke cherry had low (5.8%) initial infection levels, PPV-D was not transmissible to additional western choke cherry, and transmission of PPV-D from western choke cherry to peach was only possible before the first CID cycle. Black cherry had intermediate initial infection levels (26.6%) but did not maintain high infection levels after repeated CID cycles. Conversely, American plum had a high level (50%) of initial infection that was not significantly different from initial infection in peach (72.2%) and maintained moderate levels (15 to 25%) of infection and PPV-D transmission to both American plum and peach through all five cycles of CID. Our results indicate that American plum has the greatest potential to act as a reservoir host for Pennsylvania isolates of PPV-D.
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Affiliation(s)
- Tamara D Collum
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture, Agricultural Research Service, Frederick, MD 21702
| | - Andrew L Stone
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture, Agricultural Research Service, Frederick, MD 21702
| | - Diana J Sherman
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture, Agricultural Research Service, Frederick, MD 21702
| | - Vernon D Damsteegt
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture, Agricultural Research Service, Frederick, MD 21702
| | - William L Schneider
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture, Agricultural Research Service, Frederick, MD 21702
| | - Elizabeth E Rogers
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture, Agricultural Research Service, Frederick, MD 21702
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Plum Pox Virus Strain C Isolates Can Reduce Sour Cherry Productivity. PLANTS 2021; 10:plants10112327. [PMID: 34834688 PMCID: PMC8621038 DOI: 10.3390/plants10112327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 01/16/2023]
Abstract
The impact of plum pox virus (PPV) on sour cherry (Prunus cerasus L.) productivity has been studied by comparing the yield of PPV-infected and PPV-free fruit-bearing trees. A total of 152 16- to 17-year-old trees of nine cultivars and hybrids were surveyed in the production orchards (cultivar collection and hybrid testing plots) in the Republic of Tatarstan, Russia. Sixty trees tested positive for PPV using ELISA and RT-PCR. Among them, 58 PPV isolates belonged to the strain C and the other 2 isolates to the strain CV. For the cultivars Sevastyanovskaya, Shakirovskaya, hybrids 88-2 and 80-8, the average (2012 to 2019) productivity of infected trees was 38% to 45% lower than for PPV-free trees of the same cultivar or hybrid. No ilarviruses (prunus necrotic ringspot virus, prune dwarf virus, apple mosaic virus, American plum line pattern virus) were detected in PPV-infected trees, suggesting that reduced cherry productivity was attributed to the PPV infection. Thus, it was shown for the first time that PPV can reduce the productivity of at least some sour cherry cultivars and hybrids, and strain C isolates are responsible for crop losses.
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Maejima K, Hashimoto M, Hagiwara‐Komoda Y, Miyazaki A, Nishikawa M, Tokuda R, Kumita K, Maruyama N, Namba S, Yamaji Y. Intra-strain biological and epidemiological characterization of plum pox virus. MOLECULAR PLANT PATHOLOGY 2020; 21:475-488. [PMID: 31978272 PMCID: PMC7060144 DOI: 10.1111/mpp.12908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 05/21/2023]
Abstract
Plum pox virus (PPV) is one of the most important plant viruses causing serious economic losses. Thus far, strain typing based on the definition of 10 monophyletic strains with partially differentiable biological properties has been the sole approach used for epidemiological characterization of PPV. However, elucidating the genetic determinants underlying intra-strain biological variation among populations or isolates remains a relevant but unexamined aspect of the epidemiology of the virus. In this study, based on complete nucleotide sequence information of 210 Japanese and 47 non-Japanese isolates of the PPV-Dideron (D) strain, we identified five positively selected sites in the PPV-D genome. Among them, molecular studies showed that amino acid substitutions at position 2,635 in viral replicase correlate with viral titre and competitiveness at the systemic level, suggesting that amino acid position 2,635 is involved in aphid transmission efficiency and symptom severity. Estimation of ancestral genome sequences indicated that substitutions at amino acid position 2,635 were reversible and peculiar to one of two genetically distinct PPV-D populations in Japan. The reversible amino acid evolution probably contributes to the dissemination of the virus population. This study provides the first genomic insight into the evolutionary epidemiology of PPV based on intra-strain biological variation ascribed to positive selection.
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Affiliation(s)
- Kensaku Maejima
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Masayoshi Hashimoto
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Yuka Hagiwara‐Komoda
- Department of Sustainable AgricultureCollege of Agriculture, Food and Environment SciencesRakuno Gakuen UniversityEbetsuHokkaidoJapan
| | - Akio Miyazaki
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Masanobu Nishikawa
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Ryosuke Tokuda
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Kohei Kumita
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Noriko Maruyama
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Shigetou Namba
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
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Hajizadeh M, Gibbs AJ, Amirnia F, Glasa M. The global phylogeny o f Plum pox virus is emerging. J Gen Virol 2019; 100:1457-1468. [PMID: 31418674 DOI: 10.1099/jgv.0.001308] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The 206 complete genomic sequences of Plum pox virus in GenBank (January 2019) were downloaded. Their main open reading frames (ORF)s were compared by phylogenetic and population genetic methods. All fell into the nine previously recognized strain clusters; the PPV-Rec and PPV-T strain ORFs were all recombinants, whereas most of those in the PPV-C, PPV-CR, PPV-CV, PPV-D, PPV-EA, PPV-M and PPV-W strain clusters were not. The strain clusters ranged in size from 2 (PPV-CV and PPV-EA) to 74 (PPV-D). The isolates of eight of the nine strains came solely from Europe and the Levant (with an exception resulting from a quarantine breach), but many PPV-D strain isolates also came from east and south Asia and the Americas. The estimated time to the most recent common ancestor (TMRCA) of all 134 non-recombinant ORFs was 820 (865-775) BCE. Most strain populations were only a few decades old, and had small intra-strain, but large inter-strain, differences; strain PPV-W was the oldest. Eurasia is clearly the 'centre of emergence' of PPV and the several PPV-D strain populations found elsewhere only show evidence of gene flow with Europe, so have come from separate introductions from Europe. All ORFs and their individual genes show evidence of strong negative selection, except the positively selected pipo gene of the recently migrant populations. The possible ancient origins of PPV are discussed.
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Affiliation(s)
- Mohammad Hajizadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Adrian J Gibbs
- Emeritus Faculty Australian National University, Canberra, Australia
| | - Fahimeh Amirnia
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovakia
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Nováková S, Danchenko M, Skultety L, Fialová I, Lešková A, Beke G, Flores-Ramírez G, Glasa M. Photosynthetic and Stress Responsive Proteins Are Altered More Effectively in Nicotiana benthamiana Infected with Plum pox virus Aggressive PPV-CR versus Mild PPV-C Cherry-Adapted Isolates. J Proteome Res 2018; 17:3114-3127. [PMID: 30084641 DOI: 10.1021/acs.jproteome.8b00230] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plum pox virus (PPV, family Potyviridae) is one of the most important viral pathogens of Prunus spp. causing considerable damage to stone-fruit industry worldwide. Among the PPV strains identified so far, only PPV-C, PPV-CR, and PPV-CV are able to infect cherries under natural conditions. Herein, we evaluated the pathogenic potential of two viral isolates in herbaceous host Nicotiana benthamiana. Significantly higher accumulation of PPV capsid protein in tobacco leaves infected with PPV-CR (RU-30sc isolate) was detected in contrast to PPV-C (BY-101 isolate). This result correlated well with the symptoms observed in the infected plants. To further explore the host response upon viral infection at the molecular level, a comprehensive proteomic profiling was performed. Using reverse-phase ultra-high-performance liquid chromatography followed by label-free mass spectrometry quantification, we identified 38 unique plant proteins as significantly altered due to the infection. Notably, the abundances of photosynthesis-related proteins, mainly from the Calvin-Benson cycle, were found more aggressively affected in plants infected with PPV-CR isolate than those of PPV-C. This observation was accompanied by a significant reduction in the amount of photosynthetic pigments extracted from the leaves of PPV-CR infected plants. Shifts in the abundance of proteins that are involved in stimulation of photosynthetic capacity, modification of amino acid, and carbohydrate metabolism may affect plant growth and initiate energy formation via gluconeogenesis in PPV infected N. benthamiana. Furthermore, we suggest that the higher accumulation of H2O2 in PPV-CR infected leaves plays a crucial role in plant defense and development by activating the glutathione synthesis.
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Affiliation(s)
- Slavomíra Nováková
- Biomedical Research Center, Institute of Virology , Slovak Academy of Sciences , Dubravska cesta 9 , 845 05 Bratislava , Slovak Republic
| | - Maksym Danchenko
- Biomedical Research Center, Institute of Virology , Slovak Academy of Sciences , Dubravska cesta 9 , 845 05 Bratislava , Slovak Republic
| | - Ludovit Skultety
- Biomedical Research Center, Institute of Virology , Slovak Academy of Sciences , Dubravska cesta 9 , 845 05 Bratislava , Slovak Republic
- Institute of Microbiology , The Czech Academy of Sciences , Videnska 1083 , 142 20 Prague , Czech Republic
| | - Ivana Fialová
- Plant Science and Biodiversity Center, Institute of Botany , Slovak Academy of Sciences , Dubravska cesta 9 , 845 23 Bratislava , Slovak Republic
| | - Alexandra Lešková
- Plant Science and Biodiversity Center, Institute of Botany , Slovak Academy of Sciences , Dubravska cesta 9 , 845 23 Bratislava , Slovak Republic
| | - Gábor Beke
- Institute of Molecular Biology , Slovak Academy of Sciences , Dúbravská cesta 21 , 845 51 Bratislava , Slovak Republic
| | - Gabriela Flores-Ramírez
- Biomedical Research Center, Institute of Virology , Slovak Academy of Sciences , Dubravska cesta 9 , 845 05 Bratislava , Slovak Republic
| | - Miroslav Glasa
- Biomedical Research Center, Institute of Virology , Slovak Academy of Sciences , Dubravska cesta 9 , 845 05 Bratislava , Slovak Republic
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Sheveleva A, Ivanov P, Gasanova T, Osipov G, Chirkov S. Sequence Analysis of Plum pox virus Strain C Isolates from Russia Revealed Prevalence of the D96E Mutation in the Universal Epitope and Interstrain Recombination Events. Viruses 2018; 10:E450. [PMID: 30142962 PMCID: PMC6164383 DOI: 10.3390/v10090450] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/13/2018] [Accepted: 08/22/2018] [Indexed: 12/01/2022] Open
Abstract
The understanding of genetic diversity, geographic distribution, and antigenic properties of Plum pox virus (PPV) is a prerequisite to improve control of sharka, the most detrimental viral disease of stone fruit crops worldwide. Forty new PPV strain C isolates were detected in sour cherry (Prunus cerasus) from three geographically distant (700⁻1100 km) regions of European Russia. Analysis of their 3'-terminal genomic sequences showed that nineteen isolates (47.5%) bear the D96E mutation in the universal epitope of the coat protein. Almost all of them cannot be detected by the monoclonal antibody 5B in triple antibody sandwich enzyme-linked immunosorbent assayand Western blot analysis that may potentially compromise serological PPV detection in cherries. Full-length genomes of seven PPV-C isolates were determined employing next-generation sequencing. Using the Recombination Detection Program (RDP4), the recombination event covering the region from (Cter)P1 to the middle of the HcPro gene was predicted in all the available PPV-C complete genomes. The isolates Tat-4, belonging to the strain CV, and RU-17sc (PPV-CR) were inferred as major and minor parents, respectively, suggesting possible pathways of evolution of the cherry-adapted strains. Downy cherry (P. tomentosa) was identified as the natural PPV-C host for the first time.
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Affiliation(s)
- Anna Sheveleva
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
| | - Peter Ivanov
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
| | - Tatiana Gasanova
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
| | - Gennady Osipov
- Tatar Research Institute of Agriculture, Kazan 420059, Russia.
| | - Sergei Chirkov
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
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Chirkov S, Sheveleva A, Ivanov P, Zakubanskiy A. Analysis of Genetic Diversity of Russian Sour Cherry Plum pox virus Isolates Provides Evidence of a New Strain. PLANT DISEASE 2018; 102:569-575. [PMID: 30673474 DOI: 10.1094/pdis-07-17-1104-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Plum pox virus (PPV) exists as a complex of nine strains adapted to different Prunus hosts. Unusual PPV isolates that do not belong to the known cherry-adapted strains were discovered on sour cherry in Russia. Here, two complete genomes of isolates Tat-2 and Tat-4 were determined by sequencing on the Illumina HiSeq 2500 platform. Both were composed of 9,792 nucleotides, excluding the poly(A) tail, with the organization typical of PPV and had 99.4 and 99.7% identity between each other at the nucleotide and amino acid levels. The sequence identities between Tat-2/Tat-4 and known PPV strains ranged from 77.6 to 83.3% for genomic RNA and from 80.0 to 93.8% for polyprotein. Phylogenetic analysis placed Tat-2 and Tat-4 in a separate clade, distinct from the C and CR strains. Three more Tat-2/Tat-4-like isolates were detected in local cherry plantings using the newly developed, specific RT-PCR assay. Based on the phylogenetic analysis, sequence identities, and environmental distribution, Tat-2, Tat-4, and related isolates represent a new cherry-adapted PPV strain for which the name PPV-CV (Cherry Volga) is proposed.
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Affiliation(s)
- Sergei Chirkov
- Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Anna Sheveleva
- Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Peter Ivanov
- Lomonosov Moscow State University, 119234 Moscow, Russia
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Chirkov S, Ivanov P, Sheveleva A, Kudryavtseva A, Mitrofanova I. Molecular characterization of Plum pox virus Rec isolates from Russia suggests a new insight into evolution of the strain. Virus Genes 2018; 54:328-332. [PMID: 29460128 DOI: 10.1007/s11262-018-1541-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/11/2018] [Indexed: 11/29/2022]
Abstract
Field isolates of Plum pox virus (PPV), belonging to the strain Rec, have been found for the first time in Russia. Full-size genomes of the isolates K28 and Kisl-1pl from myrobalan and plum, respectively, were sequenced on the 454 platform. Analysis of all known PPV-Rec complete genomes using the Recombination Detection Program (RDP4) revealed yet another recombination event in the 5'-terminal region. This event was detected by seven algorithms, implemented in the RDP4, with statistically significant P values and supported by a phylogenetic analysis with the bootstrap value of 87%. A putative PPV-M-derived segment, encompassing the C-terminus of the P1 gene and approximately two-thirds of the HcPro gene, is bordered by breakpoints at positions 760-940 and 1838-1964, depending on the recombinant isolate. The predicted 5'-distal breakpoint for the isolate Valjevka is located at position 2804. The Dideron (strain D) and SK68 (strain M) isolates were inferred as major and minor parents, respectively. Finding of another recombination event suggests more complex evolutionary history of PPV-Rec than previously assumed. Perhaps the first recombination event led to the formation of a PPV-D variant harboring the PPV-M-derived fragment within the 5'-proximal part of the genome. Subsequent recombination of its descendant with PPV-M in the 3'-proximal genomic region resulted in the emergence of the evolutionary successful strain Rec.
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Affiliation(s)
- Sergei Chirkov
- Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Peter Ivanov
- Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anna Sheveleva
- Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Irina Mitrofanova
- Nikita Botanical Gardens - National Scientific Center, Yalta, 298648, Russia
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11
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New highly divergent Plum pox virus isolates infecting sour cherry in Russia. Virology 2016; 502:56-62. [PMID: 28006670 DOI: 10.1016/j.virol.2016.12.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 11/21/2022]
Abstract
Unusual Plum pox virus (PPV) isolates (named Tat isolates) were discovered on sour cherry (Prunus cerasus) in Russia. They failed to be recognized by RT-PCR using commonly employed primers specific to the strains C or CR (the only ones that proved able to infect sour cherry) as well as to the strains M and W. Some of them can be detected by RT-PCR using the PPV-D-specific primers P1/PD or by TAS-ELISA with the PPV-C-specific monoclonal antibody AC. Phylogenetic analysis of the 3'-terminal genomic region assigned the Tat isolates into the cluster of cherry-adapted strains. However, they grouped separately from the C and CR strains and from each other as well. The sequence divergence of the Tat isolates is comparable to the differences between the known PPV strains. They may represent new group(s) of cherry-adapted isolates which do not seem to belong to any known strain of the virus.
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12
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Kimura K, Usugi T, Hoshi H, Kato A, Ono T, Koyano S, Kagiwada S, Nishio T, Tsuda S. Surveys of Viruliferous Alate Aphid of Plum pox virus in Prunus mume Orchards in Japan. PLANT DISEASE 2016; 100:40-48. [PMID: 30688586 DOI: 10.1094/pdis-05-15-0540-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Plum pox virus (PPV) is transmitted by infected buds and aphids. It is important to analyze the outbreak trends and viruliferous rate of aphids in areas where the occurrence of PPV is reported, so as to develop strategies for disease control. Between April 2011 and December 2012, yellow insect-trapping adhesive plates were placed for 2 days at a time each week in an area where PPV is occurring in Japan. Outbreak trends were analyzed based on the trapped alate aphid samples, and up to 50 of them were tested per week to identify species and determine the rate of viruliferous specimens. Although the number of aphids varied according to survey year, three peaks were noticeable in each year. Based on the sequence data for the mitochondrial cytochrome c oxidase I region, approximately 40 different species of aphid were trapped in both years. Of the five dominant species of aphids identified during the 2 years, Aphis spiraecola was trapped in large numbers. PPV-positive aphids were higher in fall onward, when the total number of trapped aphids decreased, than in spring and summer, when a larger number of aphids was caught. PPV transmission tests using the most abundant species revealed that A. spiraecola, A. craccivora, A. gossypii, and Rhopalosiphum maidis were transmitters, although A. spiraecola is likely of epidemiological significance.
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Affiliation(s)
- Kota Kimura
- NARO Agricultural Research Center, Kan-nondai, Tsukuba, Ibaraki 305-8666, Japan; and Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Kajino-cho, Koganei, Tokyo 184-8584
| | | | - Hideo Hoshi
- Tokyo Metropolitan Agriculture and Forestry Research Center, Fujimi-cho, Tachikawa, Tokyo 190-0013
| | - Ayana Kato
- Tokyo Metropolitan Agriculture and Forestry Research Center, Fujimi-cho, Tachikawa, Tokyo 190-0013
| | - Tsuyoshi Ono
- Tokyo Metropolitan Agriculture and Forestry Research Center, Fujimi-cho, Tachikawa, Tokyo 190-0013
| | - Shinji Koyano
- Tokyo Metropolitan Agriculture and Forestry Research Center, Fujimi-cho, Tachikawa, Tokyo 190-0013
| | - Satoshi Kagiwada
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University
| | - Takeshi Nishio
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University
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13
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Chirkov S, Ivanov P, Sheveleva A, Kudryavtseva A, Prikhodko Y, Mitrofanova I. Occurrence and characterization of plum pox virus strain D isolates from European Russia and Crimea. Arch Virol 2015; 161:425-30. [PMID: 26530833 DOI: 10.1007/s00705-015-2658-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/21/2015] [Indexed: 10/22/2022]
Abstract
Numerous plum pox virus (PPV) strain D isolates have been found in geographically distant regions of European Russia and the Crimean peninsula on different stone fruit hosts. Phylogenetic analysis of their partial and complete genomes suggests multiple introductions of PPV-D into Russia. Distinct natural isolates from Prunus tomentosa were found to bear unique amino acid substitutions in the N-terminus of the coat protein (CP) that may contribute to the adaptation of PPV-D to this host. Serological analysis using the PPV-D-specific monoclonal antibody 4DG5 provided further evidence that mutations at positions 58 and 59 of the CP are crucial for antibody binding.
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Affiliation(s)
| | - Peter Ivanov
- Lomonosov Moscow State University, Moscow, Russia
| | | | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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14
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Rimbaud L, Dallot S, Gottwald T, Decroocq V, Jacquot E, Soubeyrand S, Thébaud G. Sharka epidemiology and worldwide management strategies: learning lessons to optimize disease control in perennial plants. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:357-78. [PMID: 26047559 DOI: 10.1146/annurev-phyto-080614-120140] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Many plant epidemics that cause major economic losses cannot be controlled with pesticides. Among them, sharka epidemics severely affect prunus trees worldwide. Its causal agent, Plum pox virus (PPV; genus Potyvirus), has been classified as a quarantine pathogen in numerous countries. As a result, various management strategies have been implemented in different regions of the world, depending on the epidemiological context and on the objective (i.e., eradication, suppression, containment, or resilience). These strategies have exploited virus-free planting material, varietal improvement, surveillance and removal of trees in orchards, and statistical models. Variations on these management options lead to contrasted outcomes, from successful eradication to widespread presence of PPV in orchards. Here, we present management strategies in the light of sharka epidemiology to gain insights from this worldwide experience. Although focused on sharka, this review highlights more general levers and promising approaches to optimize disease control in perennial plants.
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Affiliation(s)
- Loup Rimbaud
- Montpellier SupAgro, UMR 385 BGPI (Biology and Genetics of Plant-Pathogen Interactions), 34398 Montpellier Cedex 5, France;
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15
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Zhang S, Ravelonandro M, Russell P, McOwen N, Briard P, Bohannon S, Vrient A. Rapid diagnostic detection of plum pox virus in Prunus plants by isothermal AmplifyRP(®) using reverse transcription-recombinase polymerase amplification. J Virol Methods 2014; 207:114-20. [PMID: 25010790 DOI: 10.1016/j.jviromet.2014.06.026] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/23/2014] [Accepted: 06/27/2014] [Indexed: 01/12/2023]
Abstract
Plum pox virus (PPV) causes the most destructive viral disease known as plum pox or Sharka disease in stone fruit trees. As an important regulated pathogen, detection of PPV is thus of critical importance to quarantine and eradication of the spreading disease. In this study, the innovative development of two AmplifyRP(®) tests is reported for a rapid isothermal detection of PPV using reverse transcription-recombinase polymerase amplification. In an AmplifyRP(®) test, all specific recombination and amplification reactions occur at a constant temperature without thermal cycling and the test results are either recorded in real-time with a portable fluorescence reader or displayed using a lateral flow strip contained inside an amplicon detection chamber. The major improvement of this assay is that the entire test from sample preparation to result can be completed in as little as 20min and can be performed easily both in laboratories and in the field. The results from this study demonstrated the ability of the AmplifyRP(®) technique to detect all nine PPV strains (An, C, CR, D, EA, M, Rec, T, or W). Among the economic benefits to pathogen surveys is the higher sensitivity of the AmplifyRP(®) to detect PPV when compared to the conventional ELISA and ImmunoStrip(®) assays. This is the first report describing the use of such an innovative technique to detect rapidly plant viruses affecting perennial crops.
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Affiliation(s)
- Shulu Zhang
- Agdia Inc., 52642 County Road 1, Elkhart, IN 46514, USA.
| | - Michel Ravelonandro
- UMR-1332, Biologie du Fruit et Pathologie, Virologie, INRA-Bordeaux, BP-81, CS20032, Villenave d'Ornon 33882, France
| | - Paul Russell
- Agdia Inc., 52642 County Road 1, Elkhart, IN 46514, USA
| | - Nathan McOwen
- Agdia Inc., 52642 County Road 1, Elkhart, IN 46514, USA
| | - Pascal Briard
- UMR-1332, Biologie du Fruit et Pathologie, Virologie, INRA-Bordeaux, BP-81, CS20032, Villenave d'Ornon 33882, France
| | | | - Albert Vrient
- Agdia Inc., 52642 County Road 1, Elkhart, IN 46514, USA
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16
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Transcriptomic analysis of Prunus domestica undergoing hypersensitive response to plum pox virus infection. PLoS One 2014; 9:e100477. [PMID: 24959894 PMCID: PMC4069073 DOI: 10.1371/journal.pone.0100477] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 05/25/2014] [Indexed: 12/03/2022] Open
Abstract
Plum pox virus (PPV) infects Prunus trees around the globe, posing serious fruit production problems and causing severe economic losses. One variety of Prunus domestica, named ‘Jojo’, develops a hypersensitive response to viral infection. Here we compared infected and non-infected samples using next-generation RNA sequencing to characterize the genetic complexity of the viral population in infected samples and to identify genes involved in development of the resistance response. Analysis of viral reads from the infected samples allowed reconstruction of a PPV-D consensus sequence. De novo reconstruction showed a second viral isolate of the PPV-Rec strain. RNA-seq analysis of PPV-infected ‘Jojo’ trees identified 2,234 and 786 unigenes that were significantly up- or downregulated, respectively (false discovery rate; FDR≤0.01). Expression of genes associated with defense was generally enhanced, while expression of those related to photosynthesis was repressed. Of the total of 3,020 differentially expressed unigenes, 154 were characterized as potential resistance genes, 10 of which were included in the NBS-LRR type. Given their possible role in plant defense, we selected 75 additional unigenes as candidates for further study. The combination of next-generation sequencing and a Prunus variety that develops a hypersensitive response to PPV infection provided an opportunity to study the factors involved in this plant defense mechanism. Transcriptomic analysis presented an overview of the changes that occur during PPV infection as a whole, and identified candidates suitable for further functional characterization.
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17
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García JA, Glasa M, Cambra M, Candresse T. Plum pox virus and sharka: a model potyvirus and a major disease. MOLECULAR PLANT PATHOLOGY 2014; 15:226-41. [PMID: 24102673 PMCID: PMC6638681 DOI: 10.1111/mpp.12083] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
TAXONOMIC RELATIONSHIPS Plum pox virus (PPV) is a member of the genus Potyvirus in the family Potyviridae. PPV diversity is structured into at least eight monophyletic strains. GEOGRAPHICAL DISTRIBUTION First discovered in Bulgaria, PPV is nowadays present in most of continental Europe (with an endemic status in many central and southern European countries) and has progressively spread to many countries on other continents. GENOMIC STRUCTURE Typical of potyviruses, the PPV genome is a positive-sense single-stranded RNA (ssRNA), with a protein linked to its 5' end and a 3'-terminal poly A tail. It is encapsidated by a single type of capsid protein (CP) in flexuous rod particles and is translated into a large polyprotein which is proteolytically processed in at least 10 final products: P1, HCPro, P3, 6K1, CI, 6K2, VPg, NIapro, NIb and CP. In addition, P3N-PIPO is predicted to be produced by a translational frameshift. PATHOGENICITY FEATURES PPV causes sharka, the most damaging viral disease of stone fruit trees. It also infects wild and ornamental Prunus trees and has a large experimental host range in herbaceous species. PPV spreads over long distances by uncontrolled movement of plant material, and many species of aphid transmit the virus locally in a nonpersistent manner. SOURCES OF RESISTANCE A few natural sources of resistance to PPV have been found so far in Prunus species, which are being used in classical breeding programmes. Different genetic engineering approaches are being used to generate resistance to PPV, and a transgenic plum, 'HoneySweet', transformed with the viral CP gene, has demonstrated high resistance to PPV in field tests in several countries and has obtained regulatory approval in the USA.
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Affiliation(s)
- Juan Antonio García
- Departmento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
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Calvo M, Malinowski T, García JA. Single amino acid changes in the 6K1-CI region can promote the alternative adaptation of Prunus- and Nicotiana-propagated Plum pox virus C isolates to either host. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:136-49. [PMID: 24200075 DOI: 10.1094/mpmi-08-13-0242-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plum pox virus (PPV) C is one of the less common PPV strains and specifically infects cherry trees in nature. Making use of two PPV-C isolates that display different pathogenicity features, i.e., SwCMp, which had been adapted to Nicotiana species, and BY101, which had been isolated from cherry rootstock L2 (Prunus lannesiana) and propagated only in cherry species, we have generated two infective full-length cDNA clones in order to determine which viral factors are involved in the adaptation to each host. According to our results, the C-P3(PIPO)/6K1/N-CI (cylindrical inclusion) region contains overlapping but not coincident viral determinants involved in symptoms development, local viral amplification, and systemic movement capacity. Amino acid changes in this region promoting the adaptation to N. benthamiana or P. avium have trade-off effects in the alternative host. In both cases, adaptation can be achieved through single amino acid changes in the NIapro protease recognition motif between 6K1 and CI or in nearby sequences. Thus, we hypothesize that the potyvirus polyprotein processing could depend on specific host factors and the adaptation of PPV-C isolates to particular hosts relies on a fine regulation of the proteolytic cleavage of the 6K1-CI junction.
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Rozák J, Predajňa L, Gálová Z, Glasa M. Detection and characterisation of Plum pox virus (PPV) isolates from Eastern Slovakia revealed the presence of three main viral strains. POTRAVINARSTVO 2013. [DOI: 10.5219/315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plum pox virus (PPV), the agent responsible for Sharka disease, is the most important viral pathogen of stone fruit trees world-wide, having an endemic status in Slovakia. To increase knowledge of PPV diversity in Slovakia, a set of 11 isolates, originated from the eastern part of the country, was characterised. The isolates were chip-budded from their original Prunus hosts to the susceptible GF305 indicators, exhibiting the symptoms of variable severity. A genomic region encompassing the partial NIb and the hypervariable 5´terminal region of the CP gene was amplified from all 11 isolates in RT-PCR and directly sequenced. The phylogenetic analysis revealed the grouping of the 11 Slovak isolates into 3 distinct clusters, representing the PPV-M (2 isolates), D (7 isolates) and Rec strains (2 isolates). The strain affiliation of isolates was further confirmed by strain-specific RT-PCR, using which the presence of additional mixed infection by minor PPV variants was detected in 2 samples. The results further contribute to the understanding of PPV diversity in Slovakia and confirm the specificity and sensitivity of molecular approaches used for the virus strain determination.
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