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Parrella G, Moury B. A new point mutation in the HC-Pro of potato virus Y is involved in tobacco vein necrosis. PLoS One 2024; 19:e0302692. [PMID: 38722893 PMCID: PMC11081373 DOI: 10.1371/journal.pone.0302692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/08/2024] [Indexed: 05/13/2024] Open
Abstract
Tobacco vein necrosis (TVN) is a complex phenomenon regulated by different genetic determinants mapped in the HC-Pro protein (amino acids N330, K391 and E410) and in two regions of potato virus Y (PVY) genome, corresponding to the cytoplasmic inclusion (CI) protein and the nuclear inclusion protein a-protease (NIa-Pro), respectively. A new determinant of TVN was discovered in the MK isolate of PVY which, although carried the HC-Pro determinants associated to TVN, did not induce TVN. The HC-Pro open reading frame (ORF) of the necrotic infectious clone PVY N605 was replaced with that of the non-necrotic MK isolate, which differed only by one amino acid at position 392 (T392 instead of I392). The cDNA clone N605_MKHCPro inoculated in tobacco induced only weak mosaics at the systemic level, demostrating that the amino acid at position 392 is a new determinant for TVN. No significant difference in accumulation in tobacco was observed between N605 and N605_MKHCPro. Since phylogenetic analyses showed that the loss of necrosis in tobacco has occurred several times independently during PVY evolution, these repeated evolutions strongly suggest that tobacco necrosis is a costly trait in PVY.
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Affiliation(s)
- Giuseppe Parrella
- Institute for Sustainable Plant Protection of The National Research Council (IPSP-CNR), Portici, Italy
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2
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Daniel J, Chikh-Ali M. Dynamics of Potato Virus Y Infection Pressure and Strain Composition in the San Luis Valley, Colorado. PLANT DISEASE 2024; 108:1146-1151. [PMID: 38736172 DOI: 10.1094/pdis-10-23-2166-sr] [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: 05/14/2024]
Abstract
The San Luis Valley (SLV), Colorado, is the second-largest fresh-potato-growing region in the United States, which accounts for about 95% of the total production in Colorado. Potato virus Y (PVY) is the leading cause of seed potato rejection in the SLV, which has caused a constant decline in seed potato production over the past two decades. To help potato growers control PVY, we monitored the dynamics of PVY infection pressure over the growing seasons of 2022 and 2023 (May through August) using tobacco bait plants exposed to field infection weekly. PVY infection dynamics were slightly different between the two seasons, but July and August had the highest infection in both years. The first PVY infection was detected in the second half of June, which coincides with the emergence of potato crops in the valley. PVY infection increased toward the beginning of August and declined toward the end of the season. Three PVY strains were identified in tobacco bait plants and potato fields, namely PVYO, PVYN-Wi, and PVYNTN. Unlike other producing areas of the United States, PVYO is still the major strain infecting potato crops in Colorado, comprising ∼40% of total PVY strain composition. This could be explained by the prevalence of the potato cultivar Russet Norkotah that lacks any identified N genes, including the Nytbr that controls PVYO, which imposes no negative selection against this strain. The current study demonstrated the usefulness of bait plants to understand PVY epidemiology and develop more targeted control practices of PVY.
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Affiliation(s)
- Jeremy Daniel
- San Luis Valley Research Center, Colorado State University, Center, CO 81125
| | - Mohamad Chikh-Ali
- San Luis Valley Research Center, Colorado State University, Center, CO 81125
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523
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3
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Rodriguez-Rodriguez M, Chikh-Ali M, Feng X, Karasev AV. Genome sequences of six recombinant variants of potato virus Y identified in North American potato cultivars grown in China. Microbiol Resour Announc 2024; 13:e0051223. [PMID: 38133347 PMCID: PMC10868197 DOI: 10.1128/mra.00512-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
Six genome sequences for potato virus Y (PVY) recombinants are reported from two North American potato cultivars grown in China. The coding complete sequences encode a single open reading frame characteristic of potyviruses. The six sequenced PVY isolates represent three distinct recombinants of PVY, namely N-Wi, SYR-I, and SYR-II.
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Affiliation(s)
| | - Mohamad Chikh-Ali
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, Idaho, USA
| | - Xue Feng
- Shanxi Agricultural University, College of Plant Protection, Taigu, Shanxi, China
| | - Alexander V. Karasev
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, Idaho, USA
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Samarskaya VO, Ryabov EV, Gryzunov N, Spechenkova N, Kuznetsova M, Ilina I, Suprunova T, Taliansky ME, Ivanov PA, Kalinina NO. The Temporal and Geographical Dynamics of Potato Virus Y Diversity in Russia. Int J Mol Sci 2023; 24:14833. [PMID: 37834280 PMCID: PMC10573581 DOI: 10.3390/ijms241914833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Potato virus Y, an important viral pathogen of potato, has several genetic variants and geographic distributions which could be affected by environmental factors, aphid vectors, and reservoir plants. PVY is transmitted to virus-free potato plants by aphids and passed on to the next vegetative generations through tubers, but the effects of tuber transmission in PVY is largely unknown. By using high-throughput sequencing, we investigated PVY populations transmitted to potato plants by aphids in different climate zones of Russia, namely the Moscow and Astrakhan regions. We analyzed sprouts from the tubers produced by field-infected plants to investigate the impact of tuber transmission on PVY genetics. We found a significantly higher diversity of PVY isolates in the Astrakhan region, where winters are shorter and milder and summers are warmer compared to the Moscow region. While five PVY types, NTNa, NTNb, N:O, N-Wi, and SYR-I, were present in both regions, SYRI-II, SYRI-III, and 261-4 were only found in the Astrakhan region. All these recombinants were composed of the genome sections derived from PVY types O and N, but no full-length sequences of such types were present. The composition of the PVY variants in the tuber sprouts was not always the same as in their parental plants, suggesting that tuber transmission impacts PVY genetics.
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Affiliation(s)
- Viktoriya O. Samarskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.O.S.); (N.G.); (N.S.); (M.K.); (I.I.); (M.E.T.)
| | - Eugene V. Ryabov
- Department of Entomology, University of Maryland, College Park, MD 20742, USA;
| | - Nikita Gryzunov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.O.S.); (N.G.); (N.S.); (M.K.); (I.I.); (M.E.T.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Nadezhda Spechenkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.O.S.); (N.G.); (N.S.); (M.K.); (I.I.); (M.E.T.)
| | - Maria Kuznetsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.O.S.); (N.G.); (N.S.); (M.K.); (I.I.); (M.E.T.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Irina Ilina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.O.S.); (N.G.); (N.S.); (M.K.); (I.I.); (M.E.T.)
| | | | - Michael E. Taliansky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.O.S.); (N.G.); (N.S.); (M.K.); (I.I.); (M.E.T.)
| | - Peter A. Ivanov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Natalia O. Kalinina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (V.O.S.); (N.G.); (N.S.); (M.K.); (I.I.); (M.E.T.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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5
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Guo H, Xu C, Wang F, Jiang L, Lei X, Zhang M, Li R, Lan X, Xia Z, Wang Z, Wu Y. Transcriptome sequencing and functional verification revealed the roles of exogenous magnesium in tobacco anti-PVY infection. Front Microbiol 2023; 14:1232279. [PMID: 37577430 PMCID: PMC10414187 DOI: 10.3389/fmicb.2023.1232279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/13/2023] [Indexed: 08/15/2023] Open
Abstract
Potato virus Y (PVY) infection causes necrosis and curling of leaves, which seriously affect the yield and quality of Solanaceous crops. The roles of nutrient elements in the regulation of plant resistance to virus infection has been widely reported, while the mechanisms are poorly studied. Previous studies in our laboratory have demonstrated that foliar spraying of MgSO4 could induce Nicotiana tabacum resistance to PVY by increasing the activity of defense-related enzymes. Consistent with the results, we found that exogenous magnesium (Mg) had a certain effect on N. tabacum anti-PVY infection. Meanwhile, Illumina RNA sequencing revealed that Mg induced resistance to PVY infection was mainly by regulating carbohydrate metabolism and transportation, nitrogen metabolism, Ca2+ signal transduction and oxidative phosphorylation. Moreover, we used virus-induced gene silencing assays to verify the function of homologs of five N. tabacum genes involved in above pathways in N. benthamiana. The results showed that NbTPS and NbGBE were conducive to PVY infection, while NbPPases and NbNR were related to resistance to PVY infection. These results suggested a novel strategy for resistance to PVY infection and provided a theoretical basis for virus-resistance breeding.
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Affiliation(s)
- Huiyan Guo
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Chuantao Xu
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
- Luzhou Branch of Sichuan Province Tobacco Company, Luzhou, China
| | - Fei Wang
- Luzhou Branch of Sichuan Province Tobacco Company, Luzhou, China
| | - Lianqiang Jiang
- Liangshan Branch of Sichuan Province Tobacco Company, Xichang, China
| | - Xiao Lei
- Luzhou Branch of Sichuan Province Tobacco Company, Luzhou, China
| | - Mingjin Zhang
- Luzhou Branch of Sichuan Province Tobacco Company, Luzhou, China
| | - Rui Li
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Xinyu Lan
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Zihao Xia
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Zhiping Wang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Yuanhua Wu
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
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6
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Mondal S, Wintermantel WM, Gray SM. Infection Dynamics of Potato Virus Y Isolate Combinations in Three Potato Cultivars. PLANT DISEASE 2023; 107:157-166. [PMID: 35657714 DOI: 10.1094/pdis-09-21-1980-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The United States potato industry has recently experienced a strain shift; recombinant potato virus Y (PVY) strains (e.g., PVYNTN) have emerged as the predominant strains over the long dominant ordinary strain (PVYO), yet both are often found as single infections within the same field and as mixed infections within individual plants. To understand mixed infection dynamics in potato plants and in daughter tubers, three potato varieties varying for PVY resistance, 'Red Maria', 'CalWhite', and 'Pike', were mechanically inoculated either at the pre- or postflowering stage with all possible heterologous isolate combinations of two PVYO and two PVYNTN isolates. Virus titer was determined from leaves collected at different positions on the plant at different times, and tuber-borne infection was determined for two successive generations. PVYNTN accumulated to higher levels than PVYO at nearly all sampling time points in 'Pike' potato. However, both virus strains accumulated to similar amounts in 'Red Maria' and 'CalWhite' potato early in the infection when inoculated preflowering; however, PVYNTN dominated at later stages and in plants inoculated postflowering. Regardless of inoculation time, both virus strains were transmitted to daughter plants raised from the tubers for most isolate combinations. The relative titer of PVYNTN and PVYO isolates at the later stages of mother plant development was indicative of what was found in the daughter plants. Although virus titer differed among cultivars depending on their genetics and virus isolates, it did not change the strain outcome in tuber-borne infection in subsequent generations. Differential virus accumulation in these cultivars suggests isolate-specific resistance to PVY accumulation.
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Affiliation(s)
- Shaonpius Mondal
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853-5904
- USDA-ARS, Crop Improvement and Protection Research Unit, Salinas, CA 93905
| | | | - Stewart M Gray
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853-5904
- USDA-ARS, Emerging Pests and Pathogen Research Unit and Plant Pathology, Ithaca, NY 14853-5904
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Ding P, Chen D, Feng H, Li J, Cao H, Tang M, Li J, Hao X, Han P, Meng Z, Karasev AV, Feng X. Prevalence and Strain Composition of Potato virus Y Circulating in Potato Fields in China's North-Central Province of Shanxi. PLANT DISEASE 2022; 106:1434-1445. [PMID: 34813711 DOI: 10.1094/pdis-09-21-1950-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Potato is an important crop in Shanxi province, located in north-central China. In 2019 to 2020, 319 potato leaf samples were collected from eight locations distributed in three major potato production areas in Shanxi. BioChip testing revealed the presence of several potato viruses, of which Potato virus Y (PVY) was the most common, reaching an incidence of 87.8% of all symptomatic samples. Immunocaptured multiplex reverse transcription (RT) PCR was used to identify strains for all 280 PVY-positive samples, unveiling 242 samples infected with a single strain of PVY (86.4%) and 38 (13.6%) with a mixed infection. Of samples with a single-strain infection, PVY-SYR-II accounted for 102 (42.1%), followed by PVYN-Wi (33, 13.6%), PVY-SYR-I (28, 11.6%), 261-4 (22, 9.1%), PVYNTNa (20, 8.3%), PVYNTNb (19, 7.9%), and PVY-SYR-III (18, 7.4%). Seven isolates representing different recombinants were selected for whole genome sequencing. Phylogenetic and recombination analyses confirmed the RT-PCR-based strain typing for all seven strains of PVY found in Shanxi. SXKL-12 is the first SYR-III strain from potato reported from China. However, unlike that in other known SYR-III isolates, the region positioned from 1,764 to 1,902 nt in SXKL-12 shared the highest sequence identity of 82.2% with an uncharacterized PVY isolate, JL-23, from China. Interestingly, PVYN-Wi isolate SXZY-40 also possessed a more divergent sequence for the region positioned from 6,156 to 6,276 nt than other N-Wi isolates known to date, sharing the highest identity of 86.6% with an uncharacterized Chinese PVY isolate, JL-11. Pathogenicity analysis of dominant strains PVY-SYR-II and PVYN-Wi in six local popular potato cultivars revealed that 'Kexin 13', 'Helan 15', and 'Jizhangshu 12' were susceptible to these two strains, with mild mottling or mosaic symptom expression, and three cultivars, 'Jinshu 16', 'Qingshu 9', and 'Xisen 6', were fully resistant.
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Affiliation(s)
- Pengcheng Ding
- Shanxi Agricultural University, College of Agriculture, Taigu, Shanxi 030800, China
| | - Dexin Chen
- Haikou Cigar Research Institute, Haikou, Hainan, 571100, China
| | - Haixu Feng
- Shanxi Agricultural University, College of Plant Protection, Taigu, Shanxi 030800, China
| | - Jiao Li
- Shanxi Agricultural University, College of Plant Protection, Taigu, Shanxi 030800, China
| | - Hui Cao
- Shanxi Agricultural University, College of Plant Protection, Taigu, Shanxi 030800, China
| | - Muning Tang
- Shanxi Agricultural University, College of Plant Protection, Taigu, Shanxi 030800, China
| | - Juan Li
- Shanxi Agricultural University, College of Plant Protection, Taigu, Shanxi 030800, China
| | - Xiaojuan Hao
- Shanxi Agricultural University, College of Plant Protection, Taigu, Shanxi 030800, China
| | - Pengjie Han
- Shanxi Agricultural University, College of Plant Protection, Taigu, Shanxi 030800, China
| | - Ze Meng
- Shanxi Agricultural University, College of Plant Protection, Taigu, Shanxi 030800, China
| | - Alexander V Karasev
- University of Idaho, Department of Entomology, Plant Pathology and Nematology, Moscow, ID 83843, U.S.A
| | - Xue Feng
- Shanxi Agricultural University, College of Plant Protection, Taigu, Shanxi 030800, China
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Tran LT, Green KJ, Rodriguez-Rodriguez M, Orellana GE, Funke CN, Nikolaeva OV, Quintero-Ferrer A, Chikh-Ali M, Woodell L, Olsen N, Karasev AV. Prevalence of Recombinant Strains of Potato Virus Y in Seed Potato Planted in Idaho and Washington States Between 2011 and 2021. PLANT DISEASE 2022; 106:810-817. [PMID: 34698520 DOI: 10.1094/pdis-08-21-1852-sr] [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
Potato virus Y (PVY) has emerged as the main reason for potato seed lot rejections, seriously affecting seed potato production in the United States throughout the past 20 years. The dynamics of PVY strain abundance and composition in various potato growing areas of the United States has not been well documented or understood up to now. The objective of this study was to find out the prevalence of PVY strains in potato fields in the Pacific Northwest (PNW), including seed potato production systems in the State of Idaho and commercial potato fields in the Columbia Basin of Washington State between 2011 and 2021. Based on the testing of >10,000 foliar samples during Idaho seed certification winter grow-out evaluations of seed potato lots and seed lot trials in Washington State, a dramatic shift in the PVY strain composition was revealed in the PNW between 2011 and 2016. During this time period, the prevalence of the ordinary, PVYO strain in seed potato dropped 8- to 10-fold, concomitantly with the rise of recombinant strains PVYN-Wi and PVYNTNa, which together accounted for 98% of all PVY positives by 2021. In Idaho seed potato, PVYNTNa strain associated with the potato tuber necrotic ringspot disease (PTNRD) was found to increase threefold between 2011 and 2019, accounting for 24% of all PVY positives in 2019. Mild foliar symptoms induced by recombinant PVY strains may be partially responsible for the proliferation of PVYN-Wi and PVYNTNa in potato crops. A spike of another PTNRD-associated recombinant, PVY-NE11, was recorded in the PNW between 2012 and 2016, but after reaching a 7 to 10% level in 2012 to 2013 this recombinant disappeared from the PNW potato by 2019. Whole genome sequence analysis of the PVY-NE11 suggested this recombinant was introduced in the United States at least three times. The data on PVY strain abundance in the PNW potato crops suggest that virus management strategies must consider the current dominance of the two recombinant PVY strains, PVYN-Wi and PVYNTNa.
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Affiliation(s)
- Lisa T Tran
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID 83844-2329
| | - Kelsie J Green
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID 83844-2329
| | | | - Gardenia E Orellana
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID 83844-2329
| | - Cassandra N Funke
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID 83844-2329
| | - Olga V Nikolaeva
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID 83844-2329
| | - Arturo Quintero-Ferrer
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID 83844-2329
| | - Mohamad Chikh-Ali
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID 83844-2329
| | - Lynn Woodell
- Department of Plant Science, University of Idaho, Kimberly Research and Extension Center, Kimberly, ID 83844-2333
| | - Nora Olsen
- Department of Plant Science, University of Idaho, Kimberly Research and Extension Center, Kimberly, ID 83844-2333
| | - Alexander V Karasev
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID 83844-2329
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Cassedy A, Della Bartola M, Parle-McDermott A, Mullins E, O'Kennedy R. A one-step reverse transcription recombinase polymerase amplification assay for lateral flow-based visual detection of PVY. Anal Biochem 2021; 642:114526. [PMID: 34922917 DOI: 10.1016/j.ab.2021.114526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/07/2021] [Accepted: 12/11/2021] [Indexed: 12/12/2022]
Abstract
Potato virus Y (PVY) is an abundant and damaging virus which reduces crop yield and marketability. Accurate detection of this economically important virus both in-field and in seed potato is considered essential in the control of PVY spread. Current detection methods are focused on immunodetection and PCR-based methods, however, identification of PVY through isothermal amplification is a promising avenue for developing accessible, on-site diagnostics with quick turnaround times. In this work, a rapid recombinase polymerase amplification assay was developed which could readily amplify PVY nucleic acids with good sensitivity and specificity. Additionally, this assay was shown to be capable of amplification directly from RNA in a one-step amplification process, without the need for prior reverse transcription. The assay was coupled with lateral flow technology to provide a rapid visual confirmation of amplification. This nucleic-acid lateral flow immunoassay could feasibly be employed in-field, or at any location where testing is required, to aid in the detection and control of PVY.
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Affiliation(s)
- Arabelle Cassedy
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | | | | | - Ewen Mullins
- Crop Science Department, Teagasc, Oak Park, Carlow, Ireland
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland; Hamad Bin Khalifa University, Education City, Doha, Qatar; Qatar Foundation, Education City, Doha, Qatar.
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10
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Jones RAC, Barbetti MJ, Fox A, Adams IP. Potato Virus Y Biological Strain Group Y D: Hypersensitive Resistance Genes Elicited and Phylogenetic Placement. PLANT DISEASE 2021; 105:3600-3609. [PMID: 34080887 DOI: 10.1094/pdis-03-21-0534-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: 06/12/2023]
Abstract
Potato virus Y (PVY) disrupts healthy seed potato production and causes tuber yield and quality losses globally. Its subdivisions consist of strain groups defined by potato hypersensitive resistance (HR) genes and whether necrosis occurs in tobacco, and phylogroups defined by sequencing. When PVY isolate PP was inoculated to potato cultivar differentials with HR genes, the HR phenotype pattern obtained resembled that caused by strain group PVYD isolate KIP1. A complete genome of isolate PP was obtained by high-throughput sequencing. After removal of its short terminal recombinant segment, it was subjected to phylogenetic analysis together with 30 complete nonrecombinant PVY genomes. It fitted within the same minor phylogroup PVYO3 subclade as KIP1. Putative HR gene Nd was proposed previously to explain the unique HR phenotype pattern that developed when differential cultivars were inoculated with PVYD. However, an alternative explanation was that PVYD elicits HR with HR genes Nc and Ny instead. To establish which gene(s) it elicits, isolates KIP1 and PP were inoculated to F1 potato seedlings from (i) crossing 'Kipfler' and 'White Rose' with 'Ruby Lou' and (ii) self-pollinated 'Desiree' and 'Ruby Lou', where 'Kipfler' is susceptible (S) but 'White Rose', 'Desiree', and 'Ruby Lou' develop HR. With both isolates, the HR:S segregation ratios obtained fitted 5:1 for 'Kipfler' × 'Ruby Lou', 11:1 for 'White Rose' × 'Ruby Lou', and 3:1 for 'Desiree'. Those for 'Ruby Lou' were 68:1 (isolate PP) and 52:0 (isolate KIP1). Because potato is tetraploid, these ratios suggest PVYD elicits HR with Ny from 'Ruby Lou' (duplex condition) and 'Desiree' (simplex condition) and Nc from 'White Rose' (simplex condition) but provide no evidence that Nd exists. Therefore, our differential cultivar inoculations and inheritance studies highlight that PVYD isolates elicit an HR phenotype in potato cultivars with either of two HR genes Nc or Ny, so putative gene Nd can be discounted. Moreover, phylogenetic analysis placed isolate PP within the same minor phylogroup PVYO3 subclade as KIP1, which constitutes the most basal divergence within overall major phylogroup PVYO.
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Affiliation(s)
- Roger A C Jones
- The University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, WA 6009, Australia
| | - Martin J Barbetti
- The University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, WA 6009, Australia
- School of Agriculture and Environment, University of Western Australia, Crawley, WA 6009, Australia
| | - Adrian Fox
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK
| | - Ian P Adams
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK
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11
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Rodriguez-Rodriguez M, Quintero-Ferrer A, Green KJ, Robles-Hernández L, Gonzalez-Franco AC, Karasev AV. Molecular and Biological Characterization of Recombinant Isolates of Potato virus Y Circulating in Potato Fields in Mexico. PLANT DISEASE 2021; 105:2688-2696. [PMID: 33267640 DOI: 10.1094/pdis-10-20-2215-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: 06/12/2023]
Abstract
Potato virus Y (PVY) is a significant threat to potato (Solanum tuberosum) production in Mexico. The presence of recombinant strains of PVY circulating in potato has been reported in the country, but no systematic study on the genetic diversity of PVY in potato and prevalence of PVY strains has been conducted yet. We report on a series of surveys in seed potato production areas in two states in Mexico, namely, Chihuahua and Jalisco, between 2011 and 2019. PVY was detected through the period of nine years in multiple potato cultivars in both states, often remaining asymptomatic in the most popular cultivars, such as 'Fianna' and 'Agata'. When typed to strain, all PVY samples studied were found to have N-serotype, and were all identified molecularly as isolates of the same recombinant strain, PVYNTN. Five of these PVY isolates were tested on tobacco (Nicotiana tabacum), where they induced vein necrosis supporting the molecular typing. This identification was also confirmed biologically on differential potato cultivars, where one PVYNTN isolate from the 2013 survey triggered the hypersensitive resistance conferred by the Nztbr gene in the cv. Maris Bard. Seven of these Mexican PVYNTN isolates, collected between 2013 and 2019, including two PVY isolates from potato tubers exhibiting potato tuber necrotic ringspot disease, were subjected to whole genome sequencing and found to show a typical PVYNTNa recombinant structure. When subjected to phylogenetic analysis, Mexican PVYNTN sequences clustered in more than three separate clades, suggesting multiple introductions of PVYNTN in the country. The wide circulation of the PVYNTN strain in Mexican potato should be considered by potato producers, to develop mitigation strategies for this PVY strain associated with tuber necrotic symptoms.
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Affiliation(s)
- Mariana Rodriguez-Rodriguez
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844-2329, U.S.A
- Facultad de Ciencias Agrotecnológicas, Universidad Autónoma de Chihuahua, Chihuahua, 31310 Mexico
| | - Arturo Quintero-Ferrer
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844-2329, U.S.A
| | - Kelsie J Green
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844-2329, U.S.A
| | - Loreto Robles-Hernández
- Facultad de Ciencias Agrotecnológicas, Universidad Autónoma de Chihuahua, Chihuahua, 31310 Mexico
| | - Ana C Gonzalez-Franco
- Facultad de Ciencias Agrotecnológicas, Universidad Autónoma de Chihuahua, Chihuahua, 31310 Mexico
| | - Alexander V Karasev
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844-2329, U.S.A
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12
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Yanagisawa H, Matsushita Y, Khiutti A, Mironenko N, Ohto Y, Afanasenko O. Occurrence and distribution of viruses infecting potato in Russia. Lett Appl Microbiol 2021; 73:64-72. [PMID: 33825200 DOI: 10.1111/lam.13476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/14/2021] [Accepted: 03/14/2021] [Indexed: 11/28/2022]
Abstract
Potato viral disease has been a major problem in potato production worldwide including Russia. Here, we detected Potato Virus M (PVM), P (PVP), S (PVS), Y (PVY), and X (PVX) and Potato Leaf Roll Virus (PLRV) by RT-PCR on potato leaves and tubers from the Northwestern (NW), Volga (VF), and Far Eastern (FE) federal districts of Russia. Each sample was co-infected with up to five viruses. RT-PCR disclosed all six viruses in NW, three in VF, and five in FE. Phylogenetic analyses of PVM and PVS strains resolved all PVM isolates in Group O (ordinary) and all PVS isolates in Group O. Seven PVY strains were detected, and they included only recombinants. PVY recombinants were thus the dominant potato virus strains in Russia, although they widely varied among the regions. Our research provides insights into the geographical distribution and genetic variability of potato viruses in Russia.
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Affiliation(s)
- H Yanagisawa
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Y Matsushita
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - A Khiutti
- Federal State Budget Scientific Institution, All-Russian Institute of Plant Protection (FSBSI VIZR), Saint Petersburg, Russia
| | - N Mironenko
- Federal State Budget Scientific Institution, All-Russian Institute of Plant Protection (FSBSI VIZR), Saint Petersburg, Russia
| | - Y Ohto
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - O Afanasenko
- Federal State Budget Scientific Institution, All-Russian Institute of Plant Protection (FSBSI VIZR), Saint Petersburg, Russia
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13
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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:plants10040753. [PMID: 33921504 PMCID: PMC8069754 DOI: 10.3390/plants10040753] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/30/2021] [Accepted: 04/10/2021] [Indexed: 12/28/2022]
Abstract
In recent years, high throughput sequencing (HTS) has brought new possibilities to the study of the diversity and complexity of plant viromes. Mixed infection of a single plant with several viruses is frequently observed in such studies. We analyzed the virome of 10 tomato and sweet pepper samples from Slovakia, all showing the presence of potato virus Y (PVY) infection. Most datasets allow the determination of the nearly complete sequence of a single-variant PVY genome, belonging to one of the PVY recombinant strains (N-Wi, NTNa, or NTNb). However, in three to-mato samples (T1, T40, and T62) the presence of N-type and O-type sequences spanning the same genome region was documented, indicative of mixed infections involving different PVY strains variants, hampering the automated assembly of PVY genomes present in the sample. The N- and O-type in silico data were further confirmed by specific RT-PCR assays targeting UTR-P1 and NIa genomic parts. Although full genomes could not be de novo assembled directly in this situation, their deep coverage by relatively long paired reads allowed their manual re-assembly using very stringent mapping parameters. These results highlight the complexity of PVY infection of some host plants and the challenges that can be met when trying to precisely identify the PVY isolates involved in mixed infection.
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14
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Mondal S, Ghanim M, Roberts A, Gray SM. Different potato virus Y strains frequently co-localize in single epidermal leaf cells and in the aphid stylet. J Gen Virol 2021; 102. [PMID: 33709906 DOI: 10.1099/jgv.0.001576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Single aphids can simultaneously or sequentially acquire and transmit multiple potato virus Y (PVY) strains. Multiple PVY strains are often found in the same field and occasionally within the same plant, but little is known about how PVY strains interact in plants or in aphid stylets. Immuno-staining and confocal microscopy were used to examine the spatial and temporal dynamics of PVY strain mixtures (PVYO and PVYNTN or PVYO and PVYN) in epidermal leaf cells of 'Samsun NN' tobacco and 'Goldrush' potato. Virus binding and localization was also examined in aphid stylets following acquisition. Both strains systemically infected tobacco and co-localized in cells of all leaves examined; however, the relative amounts of each virus changed over time. Early in the tobacco infection, when mosaic symptoms were observed, PVYO dominated the infection although PVYNTN was detected in some cells. As the infection progressed and vein necrosis developed, PVYNTN was prevalent. Co-localization of PVYO and PVYN was also observed in epidermal cells of potato leaves with most cells infected with both viruses. Furthermore, two strains could be detected binding to the distal end of aphid stylets following virus acquisition from a plant infected with a strain mixture. These data are in contrast with the traditional belief of spatial separation of two closely related potyviruses and suggest apparent non-antagonistic interaction between PVY strains that could help explain the multitude of emerging recombinant PVY strains discovered in potato in recent years.
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Affiliation(s)
- Shaonpius Mondal
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853-5904, USA
- Present address: USDA-ARS, Crop Improvement and Protection Research Unit, Salinas, CA. 93905, USA
| | - Murad Ghanim
- Department of Entomology, Volcani Center, P.O Box 155, Bet Dagan 5025001, Israel
| | - Alison Roberts
- Cellular and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, DD2 5DA, UK
| | - Stewart M Gray
- USDA-ARS, Emerging Pests and Pathogen Research Unit, Ithaca, NY 14853-5904, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853-5904, USA
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15
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Rodriguez-Rodriguez M, Chikh-Ali M, Johnson SB, Gray SM, Malseed N, Crump N, Karasev AV. The Recombinant Potato virus Y (PVY) Strain, PVY NTN, Identified in Potato Fields in Victoria, Southeastern Australia. PLANT DISEASE 2020; 104:3110-3114. [PMID: 33058718 DOI: 10.1094/pdis-05-20-0961-sc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Potato virus Y (PVY) is one of the main viruses affecting potato in Australia. However, molecular characterization of PVY isolates circulating in potato in different states of Australia has not yet been thoroughly conducted. Only nonrecombinant isolates of three biological PVY strains collected from potato were reported previously from Western Australia and one from Queensland. Here, PVY isolates collected from seed potato originating in Victoria, Australia, and printed on FTA cards, were subjected to strain typing by RT-PCR, with three isolates subjected to whole genome sequencing. All the 59 PVY isolates detected during two growing seasons were identified to be recombinants based on two RT-PCR assays. No nonrecombinant PVY isolates were identified. All the RT-PCR typed isolates belonged to the PVYNTN strain. Sequence analysis of the whole genomes of three isolates suggested a single introduction of the PVYNTN strain to Australia but provided no clues as to where this introduction originated. Given the association of the PVYNTN strain with potato tuber damage, growers in Australia should implement appropriate strategies to manage PVYNTN in potato.
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Affiliation(s)
| | - Mohamad Chikh-Ali
- University of Idaho, Department of EPPN, Moscow, ID 83844-2329, U.S.A
| | - Steven B Johnson
- University of Maine Cooperative Extension, Orono, ME 04469, U.S.A
| | - Stewart M Gray
- USDA-ARS and Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
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16
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Gao F, Kawakubo S, Ho SYW, Ohshima K. The evolutionary history and global spatio-temporal dynamics of potato virus Y. Virus Evol 2020; 6:veaa056. [PMID: 33324488 PMCID: PMC7724251 DOI: 10.1093/ve/veaa056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Potato virus Y (PVY) is a destructive plant pathogen that causes considerable losses to global potato and tobacco production. Although the molecular structure of PVY is well characterized, the evolutionary and global transmission dynamics of this virus remain poorly understood. We investigated the phylodynamics of the virus by analysing 253 nucleotide sequences of the genes encoding the third protein (P3), cylindrical inclusion protein (CI), and the nuclear inclusion protein (NIb). Our Bayesian phylogenetic analyses showed that the mean substitution rates of different regions of the genome ranged from 8.50 × 10-5 to 1.34 × 10-4 substitutions/site/year, whereas the time to the most recent common ancestor of PVY varied with the length of the genomic regions and with the number of viral isolates being analysed. Our phylogeographic analysis showed that the PVY population originated in South America and was introduced into Europe in the 19th century, from where it spread around the globe. The migration pathways of PVY correlate well with the trade routes of potato tubers, suggesting that the global spread of PVY is associated with human activities.
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Affiliation(s)
- Fangluan Gao
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shusuke Kawakubo
- Laboratory of Plant Virology, Department of Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Department of Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan.,The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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17
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Green KJ, Funke CN, Chojnacky J, Alvarez-Quinto RA, Ochoa JB, Quito-Avila DF, Karasev AV. Potato Virus Y (PVY) Isolates from Solanum betaceum Represent Three Novel Recombinants Within the PVY N Strain Group and Are Unable to Systemically Spread in Potato. PHYTOPATHOLOGY 2020; 110:1588-1596. [PMID: 32370660 DOI: 10.1094/phyto-04-20-0111-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Tamarillo, or tree tomato (Solanum betaceum), is a perennial small tree or shrub species cultivated in subtropical areas for fresh fruit and juice production. In Ecuador, tamarillo orchards are affected by several viruses, with one previously identified as potato virus Y (PVY); however, the specific strain composition of PVY in tamarillo was not determined. In 2015 and 2016, eight tamarillo plants exhibiting symptoms of leaf drop, mosaic, and mottled fruit were sampled near Tumbaco and Quito, Ecuador. These tamarillo PVY isolates were able to systemically infect tobacco, Nicotiana benthamiana, naranjilla, and tamarillo. Seven of the eight PVY isolates from tamarillo exhibited N-serotype, while one of the PVY isolates studied, Tam15, had no identifiable serotype. One isolate, Tam17, had N-serotype but produced asymptomatic systemic infection in tobacco. In tamarillo, four tamarillo isolates induced mosaic and slight growth retardation and were unable to systemically infect pepper or potato. Tamarillo, on the other hand, was unable to support systemic infection of PVY isolates belonging to the PVYO and PVYEu-N strains. The whole genomes of eight PVY isolates were sequenced from a series of overlapping RT-PCR fragments. Phylogenetically, tamarillo PVY isolates were found to belong to the large PVYN lineage, in a new tamarillo clade. Recombination analysis revealed that these tamarillo PVY isolates represent at least three novel recombinant types not reported before. The combination of the biological and molecular properties found in these eight PVY isolates suggested the existence of a new tamarillo strain of PVY that may have coevolved with S. betaceum.
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Affiliation(s)
| | | | | | - Robert A Alvarez-Quinto
- Centro de Investigaciones Biotecnologicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Ecuador
| | - Jose B Ochoa
- Instituto Nacional Autónomo de Investigaciones Agropecuarias (INIAP), Quito, Ecuador
| | - Diego F Quito-Avila
- Centro de Investigaciones Biotecnologicas del Ecuador (CIBE), Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Ecuador
| | - Alexander V Karasev
- Department of EPPN, University of Idaho, Moscow, ID
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID
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18
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Green KJ, Quintero-Ferrer A, Chikh-Ali M, Jones RAC, Karasev AV. Genetic Diversity of Nine Non-Recombinant Potato virus Y Isolates From Three Biological Strain Groups: Historical and Geographical Insights. PLANT DISEASE 2020; 104:2317-2323. [PMID: 32692623 DOI: 10.1094/pdis-02-20-0294-sc] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Potato virus Y (PVY) isolates from potato currently exist as a complex of six biologically defined strain groups all containing nonrecombinant isolates and at least 14 recombinant minor phylogroups. Recent studies on eight historical UK potato PVY isolates preserved since 1984 found only nonrecombinants. Here, four of five PVY isolates from cultivated potato or wild Solanum spp. collected recently in Australia, Mexico, and the U.S.A. were typed by inoculation to tobacco plants and/or serological testing using monoclonal antibodies. Next, these five modern isolates and four additional historical UK isolates belonging to biological strain groups PVYC, PVYZ, or PVYN obtained from cultivated potato in 1943 to 1984 were sequenced. None of the nine complete PVY genomes obtained were recombinants. Phylogenetic analysis revealed that the four historical UK isolates were in minor phylogroups PVYC1 (YC-R), PVYO-O (YZ-CM1), PVYNA-N (YN-M), or PVYEu-N (YN-RM), Australian isolate YO-BL2 was in minor phylogroup PVYO-O5, and both Mexican isolate YN-Mex43 and U.S.A. isolates YN-MT12_Oth288, YN-MT12_Oth295, and YN-WWAA150131G42 were in minor phylogroup PVYEu-N. When combined, these new findings and those from the eight historical UK isolates sequenced earlier provide important historical insights concerning the diversity of early PVY populations in Europe and the appearance of recombinants in that part of the world. They and four recent Australian isolates sequenced earlier also provide geographical insights about the geographical distribution and diversity of PVY populations in Australia and North America.
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Affiliation(s)
- Kelsie J Green
- Department of EPPN, University of Idaho, Moscow, ID, U.S.A
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID, U.S.A
| | | | | | - Roger A C Jones
- Institute of Agriculture, University of Western Australia, Crawley, WA 6009, Australia
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia
| | - Alexander V Karasev
- Department of EPPN, University of Idaho, Moscow, ID, U.S.A
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID, U.S.A
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19
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Gómez MM, de Mello Volotão E, Assandri IR, Peyrou M, Cristina J. Analysis of codon usage bias in potato virus Y non-recombinant strains. Virus Res 2020; 286:198077. [PMID: 32619560 DOI: 10.1016/j.virusres.2020.198077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 11/30/2022]
Abstract
Potato virus Y (PVY) is a member of the genus Potyvirus, family Potyviridae, is considered one of the most devastating pest affecting economically important crops, such as potato, tobacco, tomato and pepper, representing a serious threat due to high incidence and worldwide distribution. Its economic significance as well as it biological and molecular complexities have aroused great attention, thus several studies have explore it genetic characteristics. However, little is known about PVY codon usage. To shed light on the relation of codon usage among viruses and their hosts is extremely important to understand virus survival, fitness and evolution. In this study, we performed a comprehensive analysis of codon usage and composition of PVY non-recombinant strains (PVYN-NA, PVYEu-N, PVYO, PVYO5, PVYC) based on 130 complete open reading frame sequences extracted from public databases. Furthermore, similarities between the synonymous codon usage of PVY and its main hosts were investigated. The results obtained in the current study suggest that the overall codon usage among PVY genotypes is similar and slightly biased. PVY codon usage is strongly influenced by mutational bias, but also by G + C compositional constraint and dinucleotide composition. Furthermore, similarities among codon usage preferences between PVY strains and analyzed hosts were observed.
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Affiliation(s)
- Mariela Martínez Gómez
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, 11600, Montevideo, Uruguay.
| | - Eduardo de Mello Volotão
- Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, 11600, Montevideo, Uruguay
| | - Isabel Rodríguez Assandri
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, 11600, Montevideo, Uruguay
| | - Mercedes Peyrou
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, 11600, Montevideo, Uruguay
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400, Montevideo, Uruguay
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20
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Desbiez C, Wipf-Scheibel C, Millot P, Berthier K, Girardot G, Gognalons P, Hirsch J, Moury B, Nozeran K, Piry S, Schoeny A, Verdin E. Distribution and evolution of the major viruses infecting cucurbitaceous and solanaceous crops in the French Mediterranean area. Virus Res 2020; 286:198042. [PMID: 32504705 DOI: 10.1016/j.virusres.2020.198042] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/19/2020] [Accepted: 05/31/2020] [Indexed: 12/20/2022]
Abstract
Plant viral diseases represent a significant burden to plant health, and their highest impact in Mediterranean agriculture is on vegetables grown under intensive horticultural practices. In order to understand better virus evolution and emergence, the most prevalent viruses were mapped in the main cucurbitaceous (melon, squashes) and solanaceous (tomato, pepper) crops and in some wild hosts in the French Mediterranean area, and virus diversity, evolution and population structure were studied through molecular epidemiology approaches. Surveys were performed in summer 2016 and 2017, representing a total of 1530 crop samples and 280 weed samples. The plant samples were analysed using serological and molecular approaches, including high-throughput sequencing (HTS). The viral species and their frequency in crops were quite similar to those of surveys conducted ten years before in the same areas. Contrary to other Mediterranean countries, aphid-transmitted viruses remain the most prevalent in France whereas whitefly-transmitted ones have not yet emerged. However, HTS analysis of viral evolution revealed the appearance of undescribed viral variants, especially for watermelon mosaic virus (WMV) in cucurbits, or variants not present in France before, as for cucumber mosaic virus (CMV) in solanaceous crops. Deep sequencing also revealed complex virus populations within individual plants with frequent recombination or reassortment. The spatial genetic structure of cucurbit aphid-borne yellows virus (CABYV) was related to the landscape structure, whereas in the case of WMV, the recurrence of introduction events and probable human exchanges of plant material resulted in complex spatial pattern of genetic variation.
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Affiliation(s)
| | | | | | | | | | | | - Judith Hirsch
- INRAE, Pathologie Végétale, F-84140, Montfavet, France
| | - Benoît Moury
- INRAE, Pathologie Végétale, F-84140, Montfavet, France
| | | | - Sylvain Piry
- INRAE, Pathologie Végétale, F-84140, Montfavet, France; CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | | | - Eric Verdin
- INRAE, Pathologie Végétale, F-84140, Montfavet, France
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21
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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:E478. [PMID: 32340210 PMCID: PMC7232445 DOI: 10.3390/v12040478] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 02/06/2023] Open
Abstract
Potato virus Y (PVY) is the most economically important virus infecting cultivated potato (Solanum tuberosum L.). Accurate diagnosis is crucial to regulate the trade of tubers and for the sanitary selection of plant material for propagation. However, high genetic diversity of PVY represents a challenge for the detection and classification of isolates. Here, the diversity of Irish PVY isolates from a germplasm collection and commercial sites was investigated using conventional molecular and serological techniques. Recombinant PVY isolates were prevalent, with PVYNTNa being the predominant genotype. In addition, we evaluated Nanopore sequencing to detect and reconstruct the whole genome sequence of four viruses (PVY, PVX, PVS, PLRV) and five PVY genotypes in a subset of eight potato plants. De novo assembly of Nanopore sequencing reads produced single contigs covering greater than 90% of the viral genome and sharing greater than 99.5% identity to the consensus sequences obtained with Illumina sequencing. Interestingly, single near full genome contigs were obtained for different isolates of PVY co-infecting the same plant. Mapping reads to available reference viral genomes enabled us to generate near complete genome sequences sharing greater than 99.90% identity to the Illumina-derived consensus. This is the first report describing the use of Oxford Nanopore's MinION to detect and genotype potato viruses. We reconstructed the genome of PVY and other RNA viruses; indicating the technologies potential for virus detection in potato production systems, and for the study of genetic diversity of highly heterogeneous viruses such as PVY.
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Affiliation(s)
| | | | - Ewen Mullins
- Crop Science Department, Teagasc, Oak Park, R93XE12 Carlow, Ireland; (M.D.B.); (S.B.)
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22
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Bragard C, Dehnen-Schmutz K, Gonthier P, Jacques MA, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, van der Werf W, Civera AV, Yuen J, Zappalà L, Candresse T, Lacomme C, Bottex B, Oplaat C, Roenhorst A, Schenk M, Di Serio F. Pest categorisation of potato virus Y (non-EU isolates). EFSA J 2020; 18:e05938. [PMID: 32626492 PMCID: PMC7008826 DOI: 10.2903/j.efsa.2020.5938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non‐EU isolates of potato virus Y (PVY). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways and potential additional impact of non‐EU isolates of PVY, has been evaluated with regard to the criteria to qualify as a potential Union quarantine pest. Because non‐EU isolates of PVY are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non‐quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. Populations of PVY can be subdivided into several strains and groups of isolates: strain C (PVY‐C), strain N (PVY‐N), strain O (PVY‐O) and a wide range of recombinant isolates (PVY‐recombinants) which have a worldwide distribution (including the EU). Two groups of isolates, i.e. the Brazilian (PVY‐Br) and Chilean (PVY‐Ch) isolates, are considered absent from the EU. Non‐EU isolates of PVY‐C, PVY‐N, PVY‐O and PVY‐recombinants identified so far are not expected to have an additional impact in the EU compared to the PVY isolates already present and, therefore, do not meet the corresponding criterion to qualify as a potential Union quarantine pest. The Panel is unable to conclude on the potential additional impact of isolates of PVY‐Br and PVY‐Ch in the EU territory, but these isolates meet all the other criteria to qualify as potential Union quarantine pests.
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Gutierrez Sanchez PA, Babujee L, Jaramillo Mesa H, Arcibal E, Gannon M, Halterman D, Jahn M, Jiang J, Rakotondrafara AM. Overexpression of a modified eIF4E regulates potato virus Y resistance at the transcriptional level in potato. BMC Genomics 2020; 21:18. [PMID: 31906869 PMCID: PMC6945410 DOI: 10.1186/s12864-019-6423-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/22/2019] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Potato virus Y (PVY) is a major pathogen of potatoes with major impact on global agricultural production. Resistance to PVY can be achieved by engineering potatoes to express a recessive, resistant allele of eukaryotic translation initiation factor eIF4E, a host dependency factor essential to PVY replication. Here we analyzed transcriptome changes in eIF4E over-expressing potatoes to shed light on the mechanism underpinning eIF4E-mediated recessive PVY resistance. RESULTS As anticipated, modified eIF4E-expressing potatoes demonstrated a high level of resistance, eIF4E expression, and an unexpected suppression of the susceptible allele transcript, likely explaining the bulk of the potent antiviral phenotype. In resistant plants, we also detected marked upregulation of genes involved in cell stress responses. CONCLUSIONS Our results reveal a previously unanticipated second layer of signaling attributable to eIF4E regulatory control, and potentially relevant to establishment of a broader, more systematic antiviral host defense.
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Affiliation(s)
- Pablo A Gutierrez Sanchez
- Laboratorio de Microbiología Industrial, Facultad de Ciencias, Universidad Nacional de Colombia Sede Medellín, Calle 59 A N 63-20, Medellín, Colombia
| | - Lavanya Babujee
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA
| | - Helena Jaramillo Mesa
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA
| | - Erica Arcibal
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA
| | - Megan Gannon
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA
| | - Dennis Halterman
- U.S. Department of Agriculture-Agricultural Research Service, Madison, WI, 53726, USA
| | - Molly Jahn
- Department of Agronomy, University of Wisconsin-Madison, Moore Hall, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Aurélie M Rakotondrafara
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA.
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24
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Chikh-Ali M, Tran LT, Price WJ, Karasev AV. Effects of the Age-Related Resistance to Potato virus Y in Potato on the Systemic Spread of the Virus, Incidence of the Potato Tuber Necrotic Ringspot Disease, Tuber Yield, and Translocation Rates Into Progeny Tubers. PLANT DISEASE 2020; 104:269-275. [PMID: 31746695 DOI: 10.1094/pdis-06-19-1201-re] [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] [Indexed: 06/10/2023]
Abstract
The recombinant strain of potato virus Y (PVY), PVYNTN, is the main cause of the potato tuber necrotic ringspot disease (PTNRD) in susceptible potato cultivars, which reduces the quality of potato tubers, in addition to the yield loss. Control of PVY has been the main challenge in most potato-producing areas. Here, the effects of the age-related resistance (ARR) were investigated in transplants of a potato cultivar Yukon Gold to the infection with PVYNTN strain in greenhouse experiments. Within the first 3 weeks after transplanting into soil (week 1 [W1] to W3), Yukon Gold plants developed ARR that impaired the systemic movement of PVYNTN into upper noninoculated leaves and concomitant translocation into progeny tubers starting from W4 after transplanting. The yield and quality of tubers from PVY-infected plants with the established ARR (W5 to W8) were comparable with the healthy controls, suggesting that late PVY infection would not significantly affect commercial potato production. Plants inoculated early (W1 to W2), before the establishment of the ARR, exhibited a 100% primary systemic infection with PVYNTN and produced fewer tubers of smaller sizes, exhibiting PTNRD; this resulted ≤70% yield reduction compared with plants inoculated later in the season (W5 to W8). This ARR greatly restricted the systemic movement of PVYNTN in the foliage and resulted in very limited translocation rates of the virus into tested progeny tubers: 7.8 and 4.1% in 2017 and 2018, respectively, of all plants inoculated later in the season (W5 to W8). This study suggests that PVYNTN management programs in Yukon Gold seed potato should focus more on the early stages of the potato development before the onset of the ARR.
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Affiliation(s)
- Mohamad Chikh-Ali
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID 83844-2329
| | - Lisa T Tran
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID 83844-2329
| | - William J Price
- Statistical Programs, College of Agricultural and Life Sciences, Moscow, ID 83844-2337
| | - Alexander V Karasev
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID 83844-2329
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID 83844-3050
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25
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Khelifa M. Detection and Quantification of Potato virus Y Genomes in Single Aphid Stylets. PLANT DISEASE 2019; 103:2315-2321. [PMID: 31322977 DOI: 10.1094/pdis-02-19-0398-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: 06/10/2023]
Abstract
Typically, the detection of a plant virus within its vector is carried out on the entire insect body. This process can be a possible source of confusion in the quantification of transmissible virus particles for styletborne viruses such as Potato virus Y (PVY), since the transmissible virus fraction is the one only retained in the aphid vector's mouthparts. The objective of this study was to develop and validate the quantitative PCR method for the detection and quantification of PVY in the vector's stylet. Using a specific method based on TaqMan chemistry with higher sensitivity than conventional reverse transcription PCR, this study reveals that a significant amount of the virus is enclosed within the dissected stylets of Myzus persicae. Because this quantification only concerns the portion of the virus attached to the stylets, uniformity was observed in the recorded numbers of virus targets. This novel assay is applicable to several PVY strains as a rapid and sensitive detection method for use in PVY research and offers a convenient tool for deciphering the mechanism of Potyvirus acquisition.
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Affiliation(s)
- M Khelifa
- Fédération Nationale des Producteurs de Plants de Pomme de Terre/ Recherche, Développement et Promotion du Plant de Pomme de Terre (FN3PT/RD3PT), 75008 Paris, France
- Centre de Ressources Régionales en Biologie Moléculaire, Université de Picardie Jules Verne, 80039 Amiens Cedex 1, France
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26
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Rogozina EV, Mironenko NV, Chalaya NA, Matsushita Y, Yanagisawa H. Potato mosaic viruses which infect plants of tuber-bearing Solanum spp. growing in the VIR field gene bank. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Potato crop is particularly affected by virus diseases, and potato virus Y (PVY) currently considered the most important pathogen distributed worldwide as a diversity of strains. Wild and cultivated tuber-bearing species of the genus Solanum L., stored in the VIR collection, are used as the initial material in creation domestic potato varieties (Solanum tuberosum L.) resistant to virus diseases. The preservation and rational utilization of the potato collection is based on regular phytosanitary monitoring, including quarantine objects, foremost PSTVd (potato spindle tuber viroid). The aim of the work is to examine plants of tuber-bearing Solanum species in the field gene bank of VIR for the presence of PSTVd and PVX (potato virus X), PVS (potato virus S), PVM (potato virus M) and PVY, which are the most common viruses on potatoes in the North-West District of Russia. We examined clonal plants of 137 genotypes representing 31 species of the section Petota of the genus Solanum L. A diagnostic was carried out using ELISA, RT-PCR and indicator plants. No PSTVd was found in the studied plants, but a plural infestation by mosaic viruses was detected, more than half of the tested clones are infected with two or more viruses. In the studied samples, only 17 genotypes (12 %) are not infected by PVX, PVS, PVM and PVY according to the ELISA test. There are statistically significant differences in the virus infestation of Solanum species with different origins, according to Pearson’s chi-squared test. Among the studied genotypes of wild relatives of potatoes, the proportion of those affected by PVY was significantly higher in the South American than in the North American species (χ2 = 4.56, p = 0.03); the proportion of genotypes affected by PVХ was significantly higher in the North American species (χ2 = 8.81, p = 0.003), the critical value was χ2 = 3.841. PVY strains were identified by multiplex RT-PCR in 37 genotypes of Solanum spp. We found that 27 genotypes are infected by a common PVYO strain, two genotypes are infected by PVYNW (A) and PVYNW (B) strains, respectively, seven genotypes are infected by a mixture of PVYO +PVYNW (A) strains, and one is infected by a mixture of PVYO +PVYNTN-NW (SYRI)+SYRIII strains. The recombinant strains of PVY are detected in the North-West District of Russia for the first time. Coherency of the results of PVY strains detection by various (immunological, molecular and biological) methods is discussed.
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Affiliation(s)
- E. V. Rogozina
- The N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | | | - N. A. Chalaya
- The N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - Yu. Matsushita
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization
| | - H. Yanagisawa
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization
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27
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Characterization of potato virus Y populations in potato in Israel. Arch Virol 2019; 164:1691-1695. [PMID: 30968213 DOI: 10.1007/s00705-019-04250-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 03/15/2019] [Indexed: 10/27/2022]
Abstract
Potato virus Y (PVY) is the most common virus infecting potato worldwide. We analysed potato tuber PVY infections from the major Israeli growing region in 2014-2017. Isolates were characterized by multiplex PCR according to Chikh-Ali et al. (Plant Disease 97, 1370, 2013), whose primers were not fully compatible with the Israeli isolates. New primers were designed for a multiplex PCR assay to differentiate the Israeli isolates. Three recombinant strains were observed: PVYNTNa (72% of the isolates), PVYNWi (24%) and PVYSyr-III (found only in 2015). The archetypal PVYO strain was found only once. The classical PVY strains have recently been displaced by recombinant forms, with PVYNTNa dominating. The Israeli isolates appear very similar to those of Europe (the seed tuber source), except for PVYSyr-III.
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28
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Babujee L, Witherell RA, Mikami K, Aiuchi D, Charkowski AO, Rakotondrafara AM. Optimization of an isothermal recombinase polymerase amplification method for real-time detection of Potato virus Y O and N types in potato. J Virol Methods 2019; 267:16-21. [PMID: 30796947 DOI: 10.1016/j.jviromet.2019.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 11/16/2022]
Abstract
Potato virus Y (PVY) is a global challenge for potato production and the leading cause of seed crop downgrading and rejection for certification. Accurate and timely diagnosis is key to effective control of PVY. Here we optimized the isothermal recombinase polymerase amplification (RPA) for accurate detection of different PVY O and N types that were tested, present in different tissues of potato plants including tubers with a primer set that specifically targets the highly conserved pipo region within the viral genome. Combined with a simplified preparation of the template by tissue homogenization, we established a rapid RPA procedure, which can allow real time detection in less than 10 min with a fluorescent probe. Specificity of the reaction was determined by the lack of cross-reactivity with other common potato viruses. Although RPA reagents remain more expensive than PCR reagents, RPA technology is equivalent in that results can be visualized by gel electrophoresis or with a fluorescent probe with greater sensitivity; and it is superior to the common PCR-based assay in its versatility, speed, and lack of need for a highly purified RNA template.
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Affiliation(s)
- Lavanya Babujee
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA
| | - Robert A Witherell
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA
| | - Kakeru Mikami
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Inada-cho, Obihiro, 0808555, Japan
| | - Daigo Aiuchi
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Inada-cho, Obihiro, 0808555, Japan
| | - Amy O Charkowski
- Bioagricultural Sciences and Pest Management, C129 Plant Science Building, 307 University Avenue, Colorado State University, Fort Collins, CO, 80523, USA
| | - Aurélie M Rakotondrafara
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA.
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29
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Bai Y, Han S, Gao Y, Zhang W, Fan G, Qiu C, Nie X, Wen J. Genetic Diversity of Potato virus Y in Potato Production Areas in Northeast China. PLANT DISEASE 2019; 103:289-297. [PMID: 30501466 DOI: 10.1094/pdis-04-18-0687-re] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In 2011-2014, ELISA or nucleic acid spot hybridization (NASH) testing for common potato viruses or Potato spindle tuber viroid (PSTVd) was performed on 500 leaf samples collected in potato fields in the northeast provinces Heilongjiang and Inner Mongolia, China. The results revealed that 38.4% (Heilongjiang) and 27.7% (Inner Mongolia) were positive for Potato virus Y (PVY). To unveil the strain composition and population structure of PVY in the region, the multiplex RT-PCR described by Chikh-Ali et al. was performed on all of the ELISA-PVY-positive samples. Of the 158 samples whose PVY strain scenarios could be determined, PVYNTN-NW-SYR-II and PVYN-Wi were the most abundant strains, occurring in 58.9 and 47.5% samples, followed by PVYNTN-NW-SYR-I (31.0%), PVYN:O (19.6%), Eu-PVYNTN (7.6%), NA-PVYN (1.3%), and PVYO (0.6%). In the 84 single-strain-infected samples, PVYN-Wi accounted for 41.7%, PVYNTN-NW-SYR-II for 40.5%, PVYNTN-NW-SYR-I for 14.3%, and PVYN:O and Eu-PVYNTN for 3.6% each. Seven isolates representing PVYNTN-NW-SYR-I (HLJ-6-1 and HLJ-9-4), PVYNTN-NW-SYR-II (INM-W-369-12 and SC-1-1-2), PVYN:O (HLJ-30-2), and PVYN-Wi (HLJ-BDH-2 and HLJ-C-429) were sequenced and analyzed molecularly. Whereas the sequence identities for isolates belonging to the same strain group were >98.5%, they fell for isolates belonging to different strain groups to 92.7-98.1% at the genome level and 96.1-98.4% at the polyprotein level. Interestingly, the exact location of the recombination events varied among isolates within a strain group. Phylogenetic analysis of all 42 full length PVY sequences from China indicated that most clustered to various recombinant groups, despite the fact that the PVY isolates were isolated from at least five host species. Pathological analysis of four isolates representing PVYN:O, PVYN-Wi, PVYNTN-NW-SYR-I, and PVYNTN-NW-SYR-II revealed that the PVYNTN-NW-SYR-II isolate incited the most severe symptoms on potato cultivar Kexin 13, followed by PVYNTN-NW-SYR-I, PVYN:O and PVYN-Wi. The PVYNTN-NW-SYR-I and PVYNTN-NW-SYR-II isolates also caused necrotic ringspots on the tubers of Kexin 13, indicating their ability to induce the potato tuber necrotic ringspot disease in potato.
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Affiliation(s)
- Yanju Bai
- Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang 150086, China
| | - Shuxin Han
- Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Yanling Gao
- Northeast Agricultural University, Harbin, Heilongjiang 150030, China; Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang 150086, China
| | - Wei Zhang
- Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang 150086, China
| | - Guoquan Fan
- Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang 150086, China
| | - Cailing Qiu
- Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang 150086, China
| | - Xianzhou Nie
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, Canada E3B 4Z7
| | - Jingzhi Wen
- Northeast Agricultural University, Harbin, Heilongjiang 150030, China
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30
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Chikh-Ali M, Rodriguez-Rodriguez M, Green KJ, Kim DJ, Chung SM, Kuhl JC, Karasev AV. Identification and Molecular Characterization of Recombinant Potato Virus Y (PVY) in Potato from South Korea, PVY NTN Strain. PLANT DISEASE 2019; 103:137-142. [PMID: 30412456 DOI: 10.1094/pdis-05-18-0715-re] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Potato is an important source of food in South Korea, and viruses represent a significant threat to sustainable and profitable potato production. However, information about viruses affecting the potato crop in South Korea is limited. In 2017, potato plants of five cultivars exhibiting foliar mosaic, crinkling, and mottle were collected in two seed potato production areas, in Gangwon-do and Jeollabuk-do Provinces, and subjected to virus testing and characterization. Potato virus Y (PVY) was found associated with mosaic symptoms, and samples were characterized using reverse transcription polymerase chain reaction (RT-PCR) and whole genome sequencing. All analyzed PVY-positive samples were found to represent the same recombinant PVY strain: PVYNTN. Three PVY isolates were subjected to whole genome sequencing using overlapping RT-PCR fragments and Sanger methodology, and all three were confirmed to represent strain PVYNTNa after a recombination analysis of the complete genomes. In phylogenetic analysis, the three South Korean isolates were placed most closely to several PVYNTNa isolates reported from Japan and Vietnam, suggesting a common source of infection. This is the first report and complete molecular characterization of a PVYNTN strain present in the country, and because this strain induces tuber necrotic ringspot disease in susceptible cultivars of potato, appropriate management tools need to be implemented to mitigate potential tuber quality losses.
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Affiliation(s)
- Mohamad Chikh-Ali
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, 83844-2329
| | | | - Kelsie J Green
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, 83844-2329
| | - Dong-Jun Kim
- Inno Seed Co., Dong-myeon Chuncheon-si Gangwon-do, 24210, South Korea
| | - Sang-Min Chung
- Life Science Department, Dongguk University-Seoul, Seoul, 04620, South Korea
| | - Joseph C Kuhl
- Department of Plant Science, University of Idaho, Moscow, 83844-2333
| | - Alexander V Karasev
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, 83844-2329, and Bioinformatics and Computational Biology Program, University of Idaho, Moscow, 83844-3050
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31
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Anthropogenic influences on emergence of vector-borne plant viruses: the persistent problem of Potato virus Y. Curr Opin Virol 2018; 33:177-183. [PMID: 30428411 DOI: 10.1016/j.coviro.2018.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/08/2018] [Accepted: 10/14/2018] [Indexed: 11/23/2022]
Abstract
Potato virus Y (PVY) has reemerged as a serious impediment to seed potato production, responsible for reduced yields and tuber quality, as well as the majority of seed lot rejections by certification programs due to excessive virus incidence. This has led to seed shortages, especially in cultivars highly susceptible to infection. While seed certification programs have been effective at managing many virus diseases below economic thresholds, PVY has rapidly evolved in recent decades to become a complex of strains that evade many certification and farm management practices. The evolution of PVY strains is naturally occurring, but several human influences can be linked to the rapid change in PVY populations affecting the potato crop. Here we highlight the recent history and current status of PVY in potatoes and suggest some approaches for managing the virus moving forward.
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32
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Shakir N, Hameed S, Karasev AV, Zafar Y. Occurrence of Potato virus Y Recombinants, Strain PVY NTN, Infecting Tobacco in Pakistan. PLANT DISEASE 2018; 102:PDIS03180449PDN. [PMID: 30192174 DOI: 10.1094/pdis-03-18-0449-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- N Shakir
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - S Hameed
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - A V Karasev
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow 83844-2339
| | - Y Zafar
- Pakistan Agricultural Research Council, Islamabad, Pakistan
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