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Topkaya Ş, Çelik A, Santosa AI, Jones RAC. Molecular Analysis of the Global Population of Potato Virus S Redefines Its Phylogeny, and Has Crop Biosecurity Implications. Viruses 2023; 15:v15051104. [PMID: 37243190 DOI: 10.3390/v15051104] [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: 01/18/2023] [Revised: 04/20/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
In 2020, 264 samples were collected from potato fields in the Turkish provinces of Bolu, Afyon, Kayseri and Niğde. RT-PCR tests, with primers which amplified its coat protein (CP), detected potato virus S (PVS) in 35 samples. Complete CP sequences were obtained from 14 samples. Phylogenetic analysis using non-recombinant sequences of (i) the 14 CP's, another 8 from Tokat province and 73 others from GenBank; and (ii) 130 complete ORF, RdRp and TGB sequences from GenBank, found that they fitted within phylogroups, PVSI, PVSII or PVSIII. All Turkish CP sequences were in PVSI, clustering within five subclades. Subclades 1 and 4 were in three to four provinces, whereas 2, 3 and 5 were in one province each. All four genome regions were under strong negative selection constraints (ω = 0.0603-0.1825). Considerable genetic variation existed amongst PVSI and PVSII isolates. Three neutrality test methods showed PVSIII remained balanced whilst PVSI and PVSII underwent population expansion. The high fixation index values assigned to all PVSI, PVSII and PVSIII comparisons supported subdivision into three phylogroups. As it spreads more readily by aphid and contact transmission, and may elicit more severe symptoms in potato, PVSII spread constitutes a biosecurity threat for countries still free from it.
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Affiliation(s)
- Şerife Topkaya
- Department of Plant Protection, Faculty of Agriculture, Tokat Gaziosmanpasa University, Tokat 60250, Turkey
| | - Ali Çelik
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant İzzet Baysal University, Bolu 14030, Turkey
| | - Adyatma Irawan Santosa
- Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Roger A C Jones
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA 6009, Australia
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Chaudhary P, Kaur A, Singh B, Kumar S, Hallan V, Nagpal AK. First report of tomato chlorosis virus (ToCV) and detection of other viruses in field-grown tomatoes in North-Western region of India. Virusdisease 2023; 34:56-75. [PMID: 37009255 PMCID: PMC10050630 DOI: 10.1007/s13337-022-00801-y] [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: 06/23/2022] [Accepted: 11/12/2022] [Indexed: 12/23/2022] Open
Abstract
Tomato crop is known to be infected by large number of viruses across the globe causing severe losses in its yield. Accurate information on the distribution and incidence of different viruses is essential to implement virus control strategies. This study provides information on prevalence and distribution of different viruses infecting tomato crop in North-western region of India. Leaf samples of 76 symptomatic tomato and 30 symptomatic and asymptomatic plants of Chenopodium sp. (weed) were collected from eight villages. DAS-ELISA and/or RT-PCR/PCR were used to detect occurrence of nineteen viruses and one viroid in tomatoes. Nine viruses viz. cucumber mosaic virus, groundnut bud necrosis virus, potato virus M, potato virus S, potato virus X, potato virus Y, tomato chlorosis virus, tomato leaf curl New Delhi virus and tomato mosaic virus were detected in 58 of 76 tomato samples. Detection of viruses was confirmed by cloning of specific amplicons followed by sequencing and submission of sequences to the GenBank database. None of the targeted pathogens were found in collected weed samples. Tomato leaf curl New Delhi virus (ToLCNDV) was the most prevalent virus (64.47%) followed by potato virus Y (PVY) (23.68%). Double, triple, quadruple and quintuple infections were also noticed. Phylogenetic analysis of nucleotide sequences was also carried out. Nine viruses infecting tomato crop from North-western region of India were detected. ToLCNDV was most prevalent with highest incidence. To the best of our knowledge, this is the first report of ToCV on tomato from India. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-022-00801-y.
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Affiliation(s)
- Poonam Chaudhary
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Amritpreet Kaur
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Balwinder Singh
- Post Graduate Department of Botany, Khalsa College, Amritsar, India
| | - Surender Kumar
- Institute of Himalayan Bioresource Technology, Palampur, India
| | - Vipin Hallan
- Institute of Himalayan Bioresource Technology, Palampur, India
| | - Avinash Kaur Nagpal
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
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Prevalence and molecular characterization of important potato viruses in the Tokat province of Turkey. Mol Biol Rep 2023; 50:2171-2181. [PMID: 36565419 DOI: 10.1007/s11033-022-08134-1] [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: 03/31/2022] [Accepted: 11/17/2022] [Indexed: 12/25/2022]
Abstract
BACKGROUND It is believed that viruses affect potato yield more than any other pathogens worldwide. METHOD AND RESULTS We report here on a survey of the four most common potato viruses in the Tokat Province of northern Turkey. Leaf samples were collected from potato plants showing signs of viral diseases in five districts of the province. Over 400 leaf samples were tested using RT-PCR with virus-specific primers. Among the one or more viruses detected in 218 (52%) leaf samples, Potato virus Y (PVY) was the most common (47.1%), followed by potato virus S (PVS; 16.7%), potato virus X (PVX; 6.0%) and potato leaf roll virus (PLRV; 5.3%). The most common mixed infections were PVY + PVS (6.9%). A phylogenetic analysis of the gene sequences showed all Turkish PVS isolates to be clustered with the PVSO group, two PVY isolates with the PVYN-WI group and one isolate with the PVYNTN group. Turkish PVX isolates are in the Type X group of the two major PVX isolate groups. The Turkish PLRV isolates were separated into two major groups depending on the results of the phylogenetic analysis, with six cases in Group 1 and one in Group 2. CONCLUSIONS PVY, PVX, PVS and PLRV were detected in potato production areas in Tokat. A phylogenetic comparison of the gene sequences revealed all Turkish isolates to be immigrant members of the world populations of these viruses. Our results emphasize the importance of the strict quarantine control of plant materials entering Turkey.
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Grbin D, Pecman A, Music M, Kutnjak D, Škorić D. First report of potato virus S and potato virus Y in tomatoes from Croatia. PLANT DISEASE 2022; 107:975. [PMID: 35852906 DOI: 10.1094/pdis-06-22-1390-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Potato virus Y (PVY, genus Potyvirus) is an economically important aphid-transmissible virus with a very wide host range reported in many tomato-growing areas (Rivarez et al. 2021). Potato virus S (PVS, genus Carlavirus) has a limited host range (Lin et al. 2014) and occurs in tomato (Predajňa et al. 2017), mostly in mixed infections with other viruses. In 2021, greenhouse tomatoes from Vidovec (46° 17' 3.4'' N, 16° 15' 37.0'' E) in the northwestern and Sedlarica (45° 54' 23.0'' N, 17° 12' 0.5'' E) in the eastern regions of Croatia were surveyed for virus-like diseases. In total, 30 plants were sampled (12 from Vidovec and 18 from Sedlarica) showing symptoms of mild mottling, leaf rugosity and mild bronzing followed by leaf necroses later in the season. Nucleic acids were extracted from leaves by adapted CTAB procedure (Murray and Thompson 1980) and DNase treated. Four representative samples from Vidovec and four from Sedlarica were pooled for high throughput sequencing (HTS). After rRNA depletion (RiboMinus™ Plant Kit for RNA-Seq, Invitrogen) and polyA tailing, two location specific libraries (PCR-cDNA sequencing kit, Oxford Nanopore Technologies) were prepared for nanopore HTS on MinION Mk1C device. From Vidovec samples, 459,285 raw reads (mean length 354 nt) were obtained and 206,718 (mean length 446 nt) from Sedlarica and mapped (Minimap2, v.2.17) against Kraken2 viral genome sequences database (https://benlangmead.github.io/aws-indexes/k2). The number of reads mapped to PVS genome was 1004 from Vidovec (coverage depth 1.56) and those mapped to PVY genome were 781 (coverage depth 0.99) and 57 (coverage depth 1), from Vidovec and Sedlarica, respectively. The PVS complete consensus genome from Vidovec (ON468562, 8485 nt) had 99.09% nucleotide identity (BLASTn) to a potato isolate from the Netherlands (MF418030). The PVY consensus genome sequences from Vidovec (ON505007, 9698 nt) and Sedlarica (ON505008, 9698 nt) had respectively 98.37% and 98.48% identities to a tomato isolate from Slovakia (MW685827). Reverse transcription polymerase chain reaction (RT-PCR) was performed for all 30 samples and amplicons were Sanger sequenced, with primers PVS-7773F/PVS-3'endR for a 720 nt PVS genome portion spanning the 3'-part of the CP and a complete 11K gene (Lin et al. 2014) and PVY-2F/2R primers for a 510 nt portion of PVY CP gene (Aramburu et al. 2006). Only one tomato out of 12 ('Borana') from Vidovec harbored PVS in the mixed infection with PVY. Two additional tomatoes from Vidovec and two from Sedlarica were infected solely by PVY. Amplicon sequences of PVS (ON651427) and PVY (ON707000-4, ON734067-8) had 100% identity with the HTS assembled sequences. The PVS isolate from Croatia grouped with PVSO (ordinary) strain in phylogenetic analysis and the PVY isolates from both sites grouped with the PVY-NTN strain (Cox and Jones 2010). Although PVY is considered to be widespread in tomato (Nikolić et al. 2018; Rivarez et al. 2021), this is its first report from Croatia. PVS, newly reported from Croatia here, is probably not associated with the symptoms recorded because the same symptomatology was observed in the singly and mixed infected 'Borana' tomato plants. The occurrence of PVY in the geographically distant (100 km apart) Vidovec and Sedlarica, suggests that it is widespread in the continental Croatia where tomatoes are commercially grown in plastic greenhouses. Further analyses are needed to elucidate PVY and PVS epidemiology and impact on the local tomato production.
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Affiliation(s)
- Dorotea Grbin
- University of Zagreb, Faculty of Science, Department of Biology, Zagreb, Croatia;
| | - Anja Pecman
- National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia;
| | - Martina Music
- Sveuciliste u Zagrebu Prirodoslovno-matematicki fakultet, 117036, Department of Biology, Marulicev trg 9A, Zagreb, Croatia, 10000;
| | - Denis Kutnjak
- National Institute of Biology, Vecna pot 111, Ljubljana, Slovenia, 1000;
| | - Dijana Škorić
- University of Zagreb, Faculty of Science, Department of Biology, Zagreb, Croatia;
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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, Vicent Civera A, Yuen J, Zappalà L, Candresse T, Lacomme C, Bottex B, Oplaat C, Roenhorst A, Schenk M, Di Serio F. Pest categorisation of potato virus S (non-EU isolates). EFSA J 2020; 18:e05855. [PMID: 32626479 PMCID: PMC7008841 DOI: 10.2903/j.efsa.2020.5855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] 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 S (PVS). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact compared to the current situation in the EU, and availability of control measures of non‐EU isolates of PVS has been evaluated with regard to the criteria to qualify as potential Union quarantine pest. Because non‐EU isolates of PVS are absent from the EU, they do not meet one of the requirements to be regulated as an RNQP (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. Populations of PVS can be subdivided into two strains: the ordinary strain (PVS‐O) with a worldwide distribution (including the EU), and the Andean strain (PVS‐A) which is absent from the EU or considered to have at most a limited distribution in the EU. Two additional divergent isolates (PVS‐A/PVS‐O recombinants and PVS‐arracacha) have also been categorised. Non‐EU isolates of PVS‐A are expected to have an additional impact as compared to the PVS isolates currently present in the EU, and therefore meet all the criteria to qualify as potential Union quarantine pests; the magnitude of the additional impact is, however, unknown. Non‐EU isolates of PVS‐A/PVS‐O recombinants and of PVS‐arracacha also meet these criteria, with the exception of the criterion regarding the potential additional consequences in the EU territory for which the Panel was unable to conclude. Non‐EU PVS‐O isolates are not expected to have an additional impact in the EU as compared to EU isolates and therefore do not meet the corresponding criterion.
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Li X, Hataya T. Construction and characterization of an infectious cDNA clone of potato virus S developed from selected populations that survived genetic bottlenecks. Virol J 2019; 16:18. [PMID: 30728059 PMCID: PMC6364481 DOI: 10.1186/s12985-019-1124-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 01/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Infectious cDNA clones are a powerful tool for studies on RNA viruses using reverse genetics. Potato virus S (PVS) is a carlavirus with a worldwide distribution. Although the complete genome sequences of many PVS isolates have been reported, the construction of an infectious cDNA clone of PVS is yet to be reported. The aim of this study is the development and molecular characterization of an infectious cDNA clone of PVS. METHODS A full-length cDNA clone pPVS-H-FL-AB was constructed by connecting eight cDNA clones of PVS isolate H95. Capped RNA transcripts from pPVS-H-FL-AB and a modified clone pPVS-H-FL-H, containing the consensus genome sequence of PVS-H95, proved to be non-infectious. Therefore, a full-length cDNA clone pPVS-H-FL-β was reconstructed from PVS-H00, isolated from PVS-H95 populations by repeating a single local lesion isolation in Chenopodium quinoa three times; PVS-H00 appeared to be a selected variant that survived genetic bottlenecks. The sequence of cDNA clone pPVS-H-FL-β was determined as the genome sequence of PVS-H00 and compared with the consensus sequence of PVS-H95 genome. RESULTS All Nicotiana occidentalis plants inoculated with ≥0.2 μg capped RNA transcripts from pPVS-H-FL-β developed symptoms on upper leaves, as observed with PVS-H00 inoculation. Similar levels of viral genomic and subgenomic RNAs and coat protein were detected in systemically infected leaves. Sequence comparison of PVS-H95 and PVS-H00 revealed 370 nucleotide polymorphisms (4.4% of the entire genome sequence), causing 91 amino acid substitutions in six open reading frames (ORFs). The infectivity of chimeric RNAs derived from recombinants between the two cDNA clones revealed that the lack of infectivity of pPVS-H-FL-H transcripts was due to ORF1, which encodes replicase and harbors 80 amino acid substitutions compared with pPVS-H-FL-β. Approximately 71.3% amino acid substitutions in replicase were located within the variable region of unknown function between the putative methyltransferase and ovarian tumor-like protease domains. CONCLUSIONS This is the first report of the development of an infectious cDNA clone of PVS. Our analyses suggest that PVS population within a plant exists as quasispecies and the replicase sequence diversity of PVS obstruct the construction of a full-length infectious cDNA clone.
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Affiliation(s)
- Xin Li
- Laboratory of Pathogen-Plant Interactions, Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Tatsuji Hataya
- Laboratory of Pathogen-Plant Interactions, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
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Duan G, Zhan F, Du Z, Ho SYW, Gao F. Europe was a hub for the global spread of potato virus S in the 19th century. Virology 2018; 525:200-204. [PMID: 30296680 DOI: 10.1016/j.virol.2018.09.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/26/2018] [Accepted: 09/26/2018] [Indexed: 12/31/2022]
Abstract
Potato virus S (PVS) is a major plant pathogen that causes considerable losses in global potato production. Knowledge of the evolutionary history and spatio-temporal dynamics of PVS is vital for developing sustainable management schemes. In this study, we investigated the phylodynamics of the virus by analysing 103 nucleotide sequences of the coat protein gene, sampled between 1985 and 2014. Our Bayesian phylogenetic analyses showed that PVS has been evolving at a rate of 3.32 × 10-4 substitutions/site/year (95% credibility interval 1.33 × 10-4-5.58 × 10-4). We dated the crown group to the year 1325 CE (95% credibility interval 762-1743 CE). Our phylogeographic analyses pointed to viral origins in South America and identified multiple migration pathways between Europe and other regions, suggesting that Europe has been a major hub for PVS transmission. The results of our study have potential implications for developing effective strategies for the control of this pathogen.
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Affiliation(s)
- Guohua Duan
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Fangfang Zhan
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Zhenguo Du
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Fangluan Gao
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
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Santillan FW, Fribourg CE, Adams IP, Gibbs AJ, Boonham N, Kehoe MA, Maina S, Jones RAC. The Biology and Phylogenetics of Potato virus S Isolates from the Andean Region of South America. PLANT DISEASE 2018; 102:869-885. [PMID: 30673374 DOI: 10.1094/pdis-09-17-1414-re] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biological characteristics of 11 Potato virus S (PVS) isolates from three cultivated potato species (Solanum spp.) growing in five Andean countries and 1 from Scotland differed in virulence depending on isolate and host species. Nine isolates infected Chenopodium quinoa systemically but two others and the Scottish isolate remained restricted to inoculated leaves; therefore, they belonged to biologically defined strains PVSA and PVSO, respectively. When nine wild potato species were inoculated, most developed symptomless systemic infection but Solanum megistacrolobum developed systemic hypersensitive resistance (SHR) with one PVSO and two PVSA isolates. Andean potato cultivars developed mostly asymptomatic primary infection but predominantly symptomatic secondary infection. In both wild and cultivated potato plants, PVSA and PVSO elicited similar foliage symptoms. Following graft inoculation, all except two PVSO isolates were detected in partially PVS-resistant cultivar Saco, while clone Snec 66/139-19 developed SHR with two isolates each of PVSA and PVSO. Myzus persicae transmitted all nine PVSA isolates but none of the three PVSO isolates. All 12 isolates were transmitted by plant-to-plant contact. In infective sap, all isolates had thermal inactivation points of 55 to 60°C. Longevities in vitro were 25 to 40 days with six PVSA isolates but less than 21 days for the three PVSO isolates. Dilution end points were 10-3 for two PVSO isolates but 10-4 to 10-6 with the other isolates. Complete new genome sequences were obtained from seven Andean PVS isolates; seven isolates from Africa, Australia, or Europe; and single isolates from S. muricatum and Arracacia xanthorhiza. These 17 new genomes and 23 from GenBank provided 40 unique sequences; however, 5 from Eurasia were recombinants. Phylogenetic analysis of the 35 nonrecombinants revealed three major lineages, two predominantly South American (SA) and evenly branched and one non-SA with a single long basal branch and many distal subdivisions. Using least squares dating and nucleotide sequences, the two nodes of the basal PVS trifurcation were dated at 1079 and 1055 Common Era (CE), the three midphylogeny nodes of the SA lineages at 1352, 1487, and 1537 CE, and the basal node to the non-SA lineage at 1837 CE. The Potato rough dwarf virus/Potato virus P (PVS/PRDV/PVP) cluster was sister to PVS and diverged 5,000 to 7,000 years ago. The non-SA PVS lineage contained 18 of 19 isolates from S. tuberosum subsp. tuberosum but the two SA lineages contained 6 from S. tuberosum subsp. andigena, 4 from S. phureja, 3 from S. tuberosum subsp. tuberosum, and 1 each from S. muricatum, S. curtilobum, and A. xanthorrhiza. This suggests that a potato-infecting proto-PVS/PRDV/PVP emerged in South America at least 5,000 years ago, became endemic, and diverged into a range of local Solanum spp. and other species, and one early lineage spread worldwide in potato. Preventing establishment of the SA lineages is advised for all countries still without them.
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Affiliation(s)
- Franklin W Santillan
- Departamento de Fitopatologia, Universidad Nacional Agraria, La Molina, Lima, Peru; and Universidad de Cuenca, Cuenca, Azuay, Ecuador
| | - Cesar E Fribourg
- Departamento de Fitopatologia, Universidad Nacional Agraria, Peru
| | | | - Adrian J Gibbs
- Emeritus Faculty, Australian National University, ACT, Australia
| | - Neil Boonham
- Fera Ltd.; and Institute for Agrifood Research Innovations, Newcastle University, Newcastle upon Tyne, UK
| | - Monica A Kehoe
- Diagnostic Laboratory Services, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Solomon Maina
- Department of Agriculture and Environment and Institute of Agriculture, University of Western Australia, Crawley, Perth, WA, Australia
| | - Roger A C Jones
- Institute of Agriculture, University of Western Australia; and Crop Protection Branch, Department of Primary Industries and Regional Development, South Perth, WA, Australia
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Su X, Wu K, Zhang LZ, Rahman MS, Zheng K, Li T, Zhang Z, Dong J. Complete genome sequence of a new isolate of potato virus M in Yunnan, China. Arch Virol 2017; 162:2485-2488. [PMID: 28455669 DOI: 10.1007/s00705-017-3380-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/20/2017] [Indexed: 11/25/2022]
Abstract
The complete genome sequence of a new potato virus M (PVM) isolate (PVM-YN), collected from potato (Solanum tuberosum) in Yunnan, China, was determined. It was 8,530 nucleotides (nt) in length, excluding the poly(A) tail at the 3' end, and shared 71.4-72.0% nucleotide sequence identity with available PVM isolates in the NCBI database. The coat proteins (CP) of PVM-YN shared 79.0-97.4% amino acid sequence identity with that of other isolates. It is the first report of the complete genomic sequence of a new PVM isolate infecting S. tuberosum in China.
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Affiliation(s)
- Xiaoxia Su
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China
| | - Kuo Wu
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China
| | - Li Zhen Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China
| | - Mohammad Siddiqur Rahman
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China.,Bangladesh Agricultural Research Institute, Gazipur, 1701, Bangladesh
| | - Kuanyu Zheng
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China
| | - Ting Li
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China
| | - Zhongkai Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China.
| | - Jiahong Dong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, 9# Xueyun Rd, Wuhua Prefecture, Kunming, 650223, Yunnan, People's Republic of China.
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Wang J, Meng F, Chen R, Liu J, Nie X, Nie B. RT-PCR Differentiation, Molecular and Pathological Characterization of Andean and Ordinary Strains of Potato virus S in Potatoes in China. PLANT DISEASE 2016; 100:1580-1585. [PMID: 30686236 DOI: 10.1094/pdis-11-15-1257-re] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A survey of potatoes in a field in Hubei, China, for common potato viruses revealed that Potato virus S (PVS) was the most abundant virus. To unveil the strain identity of the virus, primers specific to the ordinary and/or Andean strains of PVS (i.e., PVSO and PVSA) were designed. RT-PCR using these primers successfully detected PVSO and PVSA in the samples. Sequence analysis of the amplicons confirmed the correctness of the RT-PCR assay. Two isolates, PVS HB24 and PVS HB7, representing PVSO and PVSA, respectively, were chosen for molecular and biological characterization. Both isolates contained a genome of 8,453 nt in length with six open reading frames. They shared a sequence identity of 79.5% at the complete genome sequence level. Phylogenetic analysis placed PVS HB24 and PVS HB7 to PVSO and PVSA clades, respectively. PVS HB24 induced chlorotic local lesions on the inoculated leaves but no visible symptom on the upper uninoculated leaves of Chenopodium quinoa after mechanical inoculation, whereas PVS HB7 induced both local and systemic symptoms on C. quinoa. ELISA and RT-PCR confirmed that PVS HB7 infected C. quinoa systemically whereas PVS HB24 failed to do so. Both isolates infected potato cv. Shepody and Solanum chacoense asymptomatically, but did not infect Nicotiana occidentalis and N. tobaccum cv. Samsun.
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Affiliation(s)
- Jinghui Wang
- MOE Key Laboratory of Horticultural Plant Biology, National Center for Vegetable Improvement, Potato Engineering and Technology Research Center of Hubei Province, and Huazhong Agricultural University, Wuhan 430070, China
| | - Fanye Meng
- MOE Key Laboratory of Horticultural Plant Biology, National Center for Vegetable Improvement, Potato Engineering and Technology Research Center of Hubei Province, and Huazhong Agricultural University, Wuhan 430070, China
| | - Ruhao Chen
- MOE Key Laboratory of Horticultural Plant Biology, National Center for Vegetable Improvement, Potato Engineering and Technology Research Center of Hubei Province, and Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Liu
- MOE Key Laboratory of Horticultural Plant Biology, National Center for Vegetable Improvement, Potato Engineering and Technology Research Center of Hubei Province, and Huazhong Agricultural University, Wuhan 430070, China
| | - Xianzhou Nie
- Potato Research Center, Agriculture and Agri-Food Canada, Fredericton, New Brunswick E3B4Z7, Canada
| | - Bihua Nie
- MOE Key Laboratory of Horticultural Plant Biology, National Center for Vegetable Improvement, Potato Engineering and Technology Research Center of Hubei Province, and Huazhong Agricultural University, Wuhan 430070, China
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11
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Blouin AG, Ross HA, Hobson-Peters J, O'Brien CA, Warren B, MacDiarmid R. A new virus discovered by immunocapture of double-stranded RNA, a rapid method for virus enrichment in metagenomic studies. Mol Ecol Resour 2016; 16:1255-63. [PMID: 26990372 DOI: 10.1111/1755-0998.12525] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 02/24/2016] [Accepted: 02/26/2016] [Indexed: 11/30/2022]
Abstract
Next-generation sequencing technologies enable the rapid identification of viral infection of diseased organisms. However, despite a consistent decrease in sequencing costs, it is difficult to justify their use in large-scale surveys without a virus sequence enrichment technique. As the majority of plant viruses have an RNA genome, a common approach is to extract the double-stranded RNA (dsRNA) replicative form, to enrich the replicating virus genetic material over the host background. The traditional dsRNA extraction is time-consuming and labour-intensive. We present an alternative method to enrich dsRNA from plant extracts using anti-dsRNA monoclonal antibodies in a pull-down assay. The extracted dsRNA can be amplified by reverse transcriptase-polymerase chain reaction and sequenced by next-generation sequencing. In our study, we have selected three distinct plant hosts: Māori potato (Solanum tuberosum), rengarenga (Arthropodium cirratum) and broadleaved dock (Rumex obtusifolius) representing a cultivated crop, a New Zealand-native ornamental plant and a weed, respectively. Of the sequence data obtained, 31-74% of the reads were of viral origin, and we identified five viruses including Potato virus Y and Potato virus S in potato; Turnip mosaic virus in rengarenga (a new host record); and in the dock sample Cherry leaf roll virus and a novel virus belonging to the genus Macluravirus. We believe that this new assay represents a significant opportunity to upscale virus ecology studies from environmental, primary industry and/or medical samples.
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Affiliation(s)
- Arnaud G Blouin
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, P.O. Box 92019, Auckland, New Zealand
| | - Howard A Ross
- School of Biological Sciences, University of Auckland, P.O. Box 92019, Auckland, New Zealand
| | - Jody Hobson-Peters
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
| | - Caitlin A O'Brien
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
| | - Ben Warren
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Robin MacDiarmid
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, P.O. Box 92019, Auckland, New Zealand
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12
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Tabasinejad F, Jafarpour B, Zakiaghl M, Siampour M, Rowhani H, Mehrvar M. Molecular variability in the cysteine rich protein of potato virus M. Virusdisease 2015; 26:117-22. [PMID: 26396977 PMCID: PMC4571596 DOI: 10.1007/s13337-015-0258-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/10/2015] [Indexed: 10/23/2022] Open
Abstract
The potato virus M (PVM), belonging to the genus Carlavirus, is a worldwide endemic pathogen in potato fields. p11 is an 11-16 kDa protein encoded by the last open reading frame of PVM which contains cysteine rich proteins (CRPs) motif. CRPs have been identified as suppressors of gene silencing. In this study the p11 gene from 28 PVM isolates, including 16 new isolates from Iran, were used to determine the global genetic structure of PVM populations. Pairwise nucleotide sequence identity scores showed that global PVM CRP sequence similarity was between 69.3 and 100 %. This genetic diversity divided the 28 isolates into two main divergent phylogenetic clades. The rate of genetic diversity and non-synonymous to synonymous mutations (dN/dS) were significantly different between these two clades. Analysis showed that PVM CP is under significant negative selection pressure with the global ω value of 0.260.
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Affiliation(s)
- Fatemeh Tabasinejad
- />Department of Plant Pathology, College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Behrooz Jafarpour
- />Department of Plant Pathology, College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Zakiaghl
- />Department of Plant Pathology, College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Majid Siampour
- />Department of Plant Protection, College of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Hamid Rowhani
- />Department of Plant Pathology, College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohsen Mehrvar
- />Department of Plant Pathology, College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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13
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Genetic structure and molecular variability of potato virus M populations. Arch Virol 2014; 159:2081-90. [DOI: 10.1007/s00705-014-2037-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 02/27/2014] [Indexed: 10/25/2022]
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14
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Molecular characterization of domestic and exotic potato virus S isolates and a global analysis of genomic sequences. Arch Virol 2014; 159:2115-22. [DOI: 10.1007/s00705-014-2022-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
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15
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Complete genome sequence of a novel potato virus S strain infecting Solanum phureja in Colombia. Arch Virol 2013; 158:2205-8. [DOI: 10.1007/s00705-013-1730-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/09/2013] [Indexed: 10/26/2022]
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16
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Lambert SJ, Scott JB, Pethybridge SJ, Hay FS. Strain Characterization of Potato virus S Isolates from Tasmania, Australia. PLANT DISEASE 2012; 96:813-819. [PMID: 30727348 DOI: 10.1094/pdis-07-11-0573] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Potato virus S (PVS) is prevalent within potato (Solanum tuberosum) production worldwide. Traditionally, PVS has been split into two strains, Ordinary (PVSO) and Andean (PVSA), based on reaction in herbaceous indicator species such as Chenopodium quinoa. However, recent research has identified further strain designations, such as PVSO-CS (Ordinary and Chenopodium systemic). Forty-four isolates of PVS were collected from potato seed lines in different geographical regions within Tasmania, Australia. Isolates were initially characterized by reactions in C. quinoa. Nineteen isolates were characterized as PVSO, based on the development of local lesions and serological detection in inoculated leaves only. Three isolates were identified as PVSA-like, based on local lesion development in inoculated leaves, mild mottling or chlorotic spots on noninoculated leaves, and serological detection in both inoculated and noninoculated leaves. Thirteen isolates produced no symptoms, and were detected serologically in inoculated leaves only (PVSO-like). Four isolates produced no symptoms but were detected serologically in both inoculated and noninoculated leaves (PVSA-like). Five isolates produced symptoms in inoculated leaves only but were detected serologically in both inoculated and noninoculated leaves (also PVSA-like). The ability of isolates to infect tomato has also been used as a criterion to assist in PVS strain differentiation. A subsample of isolates (n = 16) was unable to infect tomato 'Grosse Lisse'. Seventeen isolates representative of these groupings based on reactions in C. quinoa were also characterized by coat-protein sequencing. Phylogenetic comparisons suggested that all isolates were PVSO rather than PVSA. Therefore, whereas some of these PVS isolates were systemic in C. quinoa, findings from this study suggest that they were not PVSA, and that only PVSO and PVSO-CS isolates are present in Tasmania. The implications of this finding for disease management are discussed.
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Affiliation(s)
- Susan J Lambert
- Tasmanian Institute of Agricultural Research (TIAR), University of Tasmania-Cradle Coast campus, Burnie, Tasmania, 7320, Australia
| | - Jason B Scott
- Tasmanian Institute of Agricultural Research (TIAR), University of Tasmania-Cradle Coast campus, Burnie, Tasmania, 7320, Australia
| | - Sarah J Pethybridge
- Botanical Resources Australia-Agricultural Services Pty. Ltd., Ulverstone, Tasmania, 7315, Australia
| | - Frank S Hay
- TIAR, University of Tasmania-Cradle Coast campus
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17
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de Sousa Geraldino Duarte P, Galvino-Costa SBF, de Paula Ribeiro SRR, Figueira ADR. Complete genome sequence of the first Andean strain of potato virus S from Brazil and evidence of recombination between PVS strains. Arch Virol 2012; 157:1357-64. [PMID: 22456909 DOI: 10.1007/s00705-012-1289-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 02/14/2012] [Indexed: 11/24/2022]
Abstract
An isolate of the Andean strain of potato virus S (PVS), named BB-AND, was detected for the first time in a Brazilian potato crop, fully sequenced and analyzed. A comparison of BB-AND with other PVS isolates (Andean and Ordinary) showed that BB-AND is quite distinct. The lowest amino acid sequence identity to the only other fully sequenced Andean isolate was found in ORF 1 (82%) and ORF 6 (87%). Recombination analysis showed that the isolate Vltava (AJ863510), from Germany, is a recombinant between PVS(O) and PVS(A) isolates, with the recombination event located between nucleotides 6125 and 8324.
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18
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Nyalugwe EP, Wilson CR, Coutts BA, Jones RAC. Biological Properties of Potato virus X in Potato: Effects of Mixed Infection with Potato virus S and Resistance Phenotypes in Cultivars from Three Continents. PLANT DISEASE 2012; 96:43-54. [PMID: 30731851 DOI: 10.1094/pdis-04-11-0305] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Interactions between Potato virus X (PVX) and Potato virus S (PVS) were studied in potato plants, and isolates of PVX were inoculated to potato cultivars from four continents to identify occurrence of PVX resistance genes. Mixed infection with PVX and PVS increased the titer of PVS and enhanced expression of foliar symptoms in primarily and secondarily infected plants of 'Royal Blue'. PVX isolates belonging to strain groups 1 and 3 (WA1+3) or 3 (XK3 and TAS3) were sap and graft inoculated (1 to 3 isolates each) to 38 cultivars and one breeding line. Presence of extreme PVX resistance gene Rx was identified in four Australian ('Auski', 'Billabong', 'Flame', and 'Ruby Lou') and two European ('Mondial' and 'Rodeo') cultivars, and in a clone of North American 'Atlantic'. PVX hypersensitivity gene Nx was identified for the first time in two Australian ('Bliss' and 'MacRusset'), four European ('Almera', 'Harmony', 'Maxine', and 'Nadine'), and one North American ('Ranger Russet') cultivars, and in Australian breeding line 98-10713. PVX hypersensitivity gene Nb was identified for the first time in one Australian ('White Star'), five European ('Innovator', 'Kestrel', 'Kipfler', 'Laurine', and 'Royal Blue'), and one North American ('Shepody') cultivars. Probable ancestral sources of the resistance genes found in different cultivars were identified. Thus, although PVX resistance genes often occur in parents used in crosses, knowledge of their occurrence in parents and cultivars is often lacking. On sap inoculation, systemic hypersensitive phenotypes that caused shoot death often developed in cultivars with Nx but not necessarily in all shoots. This phenotype caused severe necrotic symptoms in infected tubers. In some instances, passage through cultivars with Nb separated strain group 3 from mixed isolate WA1+3.
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Affiliation(s)
- Eviness P Nyalugwe
- School of Plant Biology, Faculty of Natural and Agricultural Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Calum R Wilson
- Tasmanian Institute of Agricultural Research, University of Tasmania, New Town Research Laboratories, New Town, TAS 7008, Australia
| | - Brenda A Coutts
- Department of Agriculture and Food, Baron-Hay Court, South Perth, WA 6151, Australia; and School of Plant Biology, Faculty of Natural and Agricultural Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Roger A C Jones
- Department of Agriculture and Food, Baron-Hay Court, South Perth, WA 6151, Australia; and School of Plant Biology, Faculty of Natural and Agricultural Sciences, University of Western Australia, Crawley, WA 6009, Australia
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19
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Kerlan C, Nikolaeva OV, Hu X, Meacham T, Gray SM, Karasev AV. Identification of the molecular make-up of the Potato virus Y strain PVY(Z): genetic typing of PVY(Z)-NTN. PHYTOPATHOLOGY 2011; 101:1052-60. [PMID: 21834725 DOI: 10.1094/phyto-11-10-0317] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Potato virus Y (PVY) strains were originally defined by interactions with different resistance genes in standard potato cultivars. Five distinct strain groups are defined that cause local or systemic hypersensitive responses (HRs) in genetic background with a corresponding N gene: PVY(O), PVY(N), PVY(C), PVY(Z), and PVY(E). The nucleotide sequences of multiple isolates of PVY(O) and PVY(N) differ from each other by ≈8% along their genomes. Additionally, complete genome sequences of multiple recombinant isolates are composed of segments of parental PVY(O) and PVY(N) sequences. Here, we report that recombinant isolate PVY-L26 induces an HR in potato 'Maris Bard' carrying the putative Nz gene, and is not recognized by two other resistance genes, Nc and Ny(tbr). These genetic responses in potato, combined with the inability of PVY-L26 to induce vein necrosis in tobacco, clearly define it as an isolate from the PVY(Z) strain group and provide the first information on genome structure and sequence of PVY(Z). The genome of PVY-L26 displays typical features of European NTN-type isolates with three recombinant junctions (PVY(EU-NTN)), and the PVY-L26 is named PVY(Z)-NTN. Three typical PVY(NTN) isolates and two PVY(N) isolates, all inducing vein necrosis in tobacco, were compared with PVY-L26. One PVY(NTN) isolate elicited HR reactions in Maris Bard, similar to PVY-L26, while two induced a severe systemic HR-like reaction quite different from the quasi-symptomless reaction induced by two PVY(N) isolates. 'Yukon Gold' potato from North America produced HR against several PVY(NTN) isolates, including PVY-L26, but only late and limited systemic necrosis against one PVY(N) isolate. Consequently, according to symptoms in potato indicators, both PVY(Z) and PVY(NTN) isolates appeared biologically very close and clearly distinct from PVY(O) and PVY(N) strain groups.
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Affiliation(s)
- Camille Kerlan
- Department of PSES, University of Idaho, Moscow, ID, USA
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20
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Analysis of Iranian Potato virus S isolates. Virus Genes 2011; 43:281-8. [DOI: 10.1007/s11262-011-0619-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 04/28/2011] [Indexed: 10/18/2022]
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21
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Wylie S, Jones M. Hardenbergia virus A, a novel member of the family Betaflexiviridae from a wild legume in Southwest Australia. Arch Virol 2011; 156:1245-50. [DOI: 10.1007/s00705-011-0963-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 02/26/2011] [Indexed: 10/18/2022]
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