1
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Tsarmpopoulos I, Marais A, Faure C, Theil S, Candresse T. A new potyvirus from hedge mustard (Sisymbrium officinale (L.) Scop.) sheds light on the evolutionary history of turnip mosaic virus. Arch Virol 2022; 168:14. [PMID: 36576617 DOI: 10.1007/s00705-022-05682-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/09/2022] [Indexed: 12/29/2022]
Abstract
A novel potyvirus was identified in symptomatic hedge mustard (Sisymbrium officinale (L.) Scop.) and wild radish (Raphanus raphanistrum L.) in France. The nearly complete genome sequence of hedge mustard mosaic virus (HMMV) was determined, demonstrating that it belongs to a sister species to turnip mosaic virus (TuMV). HMMV readily infected several other members of the family Brassicaceae, including turnip, shepherd's purse (Capsella bursa-pastoris), and arabidopsis. The identification of HMMV as a Brassicaceae-infecting virus closely related to TuMV leads us to question the current scenario of TuMV evolution and suggests a possible alternative one in which transition from a monocot-adapted ancestral lifestyle to a Brassicaceae-adapted one could have occurred earlier than previously recognized.Please check and confirm that the authors and their respective affiliations have been correctly identified and amend if necessary.all OK.
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Affiliation(s)
- Iason Tsarmpopoulos
- Univ. Bordeaux, INRAE, UMR BFP, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Chantal Faure
- Univ. Bordeaux, INRAE, UMR BFP, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- Univ. Bordeaux, INRAE, UMR BFP, CS 20032, 33882, Villenave d'Ornon Cedex, France
- INRAE, UMRF, Aurillac, France
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR BFP, CS 20032, 33882, Villenave d'Ornon Cedex, France.
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2
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Qin L, Ding S, Wang Z, Jiang R, He Z. Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus. Viruses 2022; 14:v14102267. [PMID: 36298822 PMCID: PMC9607058 DOI: 10.3390/v14102267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 01/25/2023] Open
Abstract
Turnip mosaic virus (TuMV), an important pathogen that causes mosaic diseases in vegetable crops worldwide, belongs to the genus Potyvirus of the family Potyviridae. Previously, the areas of genetic variation, population structure, timescale, and migration of TuMV have been well studied. However, the codon usage pattern and host adaptation analysis of TuMV is unclear. Here, compositional bias and codon usage of TuMV were performed using 184 non-recombinant sequences. We found a relatively stable change existed in genomic composition and a slightly lower codon usage choice displayed in TuMV protein-coding sequences. Statistical analysis presented that the codon usage patterns of TuMV protein-coding sequences were mainly affected by natural selection and mutation pressure, and natural selection was the key influencing factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) revealed that TuMV genes were strongly adapted to Brassica oleracea from the present data. Similarity index (SiD) analysis also indicated that B. oleracea is potentially the preferred host of TuMV. Our study provides the first insights for assessing the codon usage bias of TuMV based on complete genomes and will provide better advice for future research on TuMV origins and evolution patterns.
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Affiliation(s)
- Lang Qin
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
| | - Shiwen Ding
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
| | - Zhilei Wang
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
| | - Runzhou Jiang
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
| | - Zhen He
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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3
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Fox A, Gibbs AJ, Fowkes AR, Pufal H, McGreig S, Jones RAC, Boonham N, Adams IP. Enhanced Apiaceous Potyvirus Phylogeny, Novel Viruses, and New Country and Host Records from Sequencing Apiaceae Samples. PLANTS 2022; 11:plants11151951. [PMID: 35956429 PMCID: PMC9370115 DOI: 10.3390/plants11151951] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022]
Abstract
The family Apiaceae comprises approximately 3700 species of herbaceous plants, including important crops, aromatic herbs and field weeds. Here we report a study of 10 preserved historical or recent virus samples of apiaceous plants collected in the United Kingdom (UK) import interceptions from the Mediterranean region (Egypt, Israel and Cyprus) or during surveys of Australian apiaceous crops. Seven complete new genomic sequences and one partial sequence, of the apiaceous potyviruses apium virus Y (ApVY), carrot thin leaf virus (CaTLV), carrot virus Y (CarVY) and celery mosaic virus (CeMV) were obtained. When these 7 and 16 earlier complete non-recombinant apiaceous potyvirus sequences were subjected to phylogenetic analyses, they split into 2 separate lineages: 1 containing ApVY, CeMV, CarVY and panax virus Y and the other CaTLV, ashitabi mosaic virus and konjac virus Y. Preliminary dating analysis suggested the CarVY population first diverged from CeMV and ApVY in the 17th century and CeMV from ApVY in the 18th century. They also showed the “time to most recent common ancestor” of the sampled populations to be more recent: 1997 CE, 1983 CE and 1958 CE for CarVY, CeMV and ApVY, respectively. In addition, we found a new family record for beet western yellows virus in coriander from Cyprus; a new country record for carrot torradovirus-1 and a tentative novel member of genus Ophiovirus as a co-infection in a carrot sample from Australia; and a novel member of the genus Umbravirus recovered from a sample of herb parsley from Israel.
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Affiliation(s)
- Adrian Fox
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (A.R.F.); (S.M.); (I.P.A.)
- Correspondence:
| | - Adrian J. Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia;
| | - Aimee R. Fowkes
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (A.R.F.); (S.M.); (I.P.A.)
| | - Hollie Pufal
- School of Natural and Environmental Sciences, Newcastle University, Agriculture Building, King’s Road, Newcastle upon Tyne NE1 7RU, UK; (H.P.); (N.B.)
| | - Sam McGreig
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (A.R.F.); (S.M.); (I.P.A.)
| | - Roger A. C. Jones
- UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009, Australia;
| | - Neil Boonham
- School of Natural and Environmental Sciences, Newcastle University, Agriculture Building, King’s Road, Newcastle upon Tyne NE1 7RU, UK; (H.P.); (N.B.)
| | - Ian P. Adams
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (A.R.F.); (S.M.); (I.P.A.)
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4
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Kawakubo S, Tomitaka Y, Tomimura K, Koga R, Matsuoka H, Uematsu S, Yamashita K, Ho SYW, Ohshima K. The Recombinogenic History of Turnip Mosaic Potyvirus Reveals its Introduction to Japan in the 19th Century. Virus Evol 2022; 8:veac060. [PMID: 35903148 PMCID: PMC9320297 DOI: 10.1093/ve/veac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/09/2022] [Accepted: 06/24/2022] [Indexed: 11/15/2022] Open
Abstract
Characterizing the detailed spatial and temporal dynamics of plant pathogens can provide
valuable information for crop protection strategies. However, the epidemiological
characteristics and evolutionary trajectories of pathogens can differ markedly from one
country to another. The most widespread and important virus of brassica vegetables, turnip
mosaic virus (TuMV), causes serious plant diseases in Japan. We collected 317 isolates of
TuMV from Raphanus and Brassica plants throughout Japan
over nearly five decades. Genomic sequences from these isolates were combined with
published sequences. We identified a total of eighty-eight independent recombination
events in Japanese TuMV genomes and found eighty-two recombination-type patterns in Japan.
We assessed the evolution of TuMV through space and time using whole and partial genome
sequences of both nonrecombinants and recombinants. Our results suggest that TuMV was
introduced into Japan after the country emerged from its isolationist policy (1639–1854)
in the Edo period and then dispersed to other parts of Japan in the 20th century. The
results of our analyses reveal the complex structure of the TuMV population in Japan and
emphasize the importance of identifying recombination events in the genome. Our study also
provides an example of surveying the epidemiology of a virus that is highly
recombinogenic.
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Affiliation(s)
- Shusuke Kawakubo
- Laboratory of Plant Virology, Department of Biological Resource Science, Faculty of Agriculture, Saga University , 1-banchi, Honjo-machi, Saga, Saga 840-8502, Japan
| | - Yasuhiro Tomitaka
- Laboratory of Plant Virology, Department of Biological Resource Science, Faculty of Agriculture, Saga University , 1-banchi, Honjo-machi, Saga, Saga 840-8502, Japan
- Institute for Plant Protection, National Agriculture and Food Research Organization , 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Kenta Tomimura
- Laboratory of Plant Virology, Department of Biological Resource Science, Faculty of Agriculture, Saga University , 1-banchi, Honjo-machi, Saga, Saga 840-8502, Japan
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization , 485-6 Okitsu Nakacho, Shimizu, Shizuoka 424-0292, Japan
| | - Ryoko Koga
- Laboratory of Plant Virology, Department of Biological Resource Science, Faculty of Agriculture, Saga University , 1-banchi, Honjo-machi, Saga, Saga 840-8502, Japan
| | - Hiroki Matsuoka
- Laboratory of Plant Virology, Department of Biological Resource Science, Faculty of Agriculture, Saga University , 1-banchi, Honjo-machi, Saga, Saga 840-8502, Japan
| | - Seiji Uematsu
- Laboratory of Agro-Environmental Science, Warm Region Horticulture Institute, Chiba Prefectural Agriculture and Forestry Research Center , 1762 Yamamoto, Tateyama, Chiba 294-0014, Japan
- Laboratory of Molecular and Cellular Biology, Department of Bioregulation and Bio- interaction, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Kazuo Yamashita
- Vegetable Research Institute, Aomori Prefectural Industrial Technology Research Center , 91 Yanagisawa, Inuotose, Rokunohe, Aomori 033-0071, Japan
- Fukuchi Garlic R&S, 4-92 Akane , Fukuda, Nanbu-machi, Aomori 039-0815, 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 Resource Science, Faculty of Agriculture, Saga University , 1-banchi, Honjo-machi, Saga, Saga 840-8502, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University , 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
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5
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Ohshima K, Kawakubo S, Muraoka S, Gao F, Ishimaru K, Kayashima T, Fukuda S. Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic. Front Microbiol 2021; 12:789596. [PMID: 34956155 PMCID: PMC8692251 DOI: 10.3389/fmicb.2021.789596] [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] [Received: 10/05/2021] [Accepted: 11/11/2021] [Indexed: 11/30/2022] Open
Abstract
Scallion mosaic virus (ScaMV) belongs to the turnip mosaic virus phylogenetic group of potyvirus and is known to infect domestic scallion plants (Allium chinense) in China and wild Japanese garlic (Allium macrostemon Bunge) in Japan. Wild Japanese garlic plants showing asymptomatic leaves were collected from different sites in Japan during 2012–2015. We found that 73 wild Japanese garlic plants out of 277 collected plants were infected with ScaMV, identified by partial genomic nucleotide sequences of the amplified RT-PCR products using potyvirus-specific primer pairs. Sixty-three ScaMV isolates were then chosen, and those full genomic sequences were determined. We carried out evolutionary analyses of the complete polyprotein-coding sequences and four non-recombinogenic regions of partial genomic sequences. We found that 80% of ScaMV samples have recombination-like genome structure and identified 12 recombination-type patterns in the genomes of the Japanese ScaMV isolates. Furthermore, we found two non-recombinant-type patterns in the Japanese population. Because the wild plants and weeds may often serve as reservoirs of viruses, it is important to study providing the exploratory investigation before emergence in the domestic plants. This is possibly the first epidemiological and evolutionary study of a virus from asymptomatic wild plants.
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Affiliation(s)
- Kazusato Ohshima
- Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan.,Institute of Wild Onion Science, Saga University, Saga, Japan.,The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Shusuke Kawakubo
- Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan
| | - Satoshi Muraoka
- Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan
| | - Fangluan Gao
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kanji Ishimaru
- Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan.,Institute of Wild Onion Science, Saga University, Saga, Japan.,The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Tomoko Kayashima
- Institute of Wild Onion Science, Saga University, Saga, Japan.,Department of School Education Course, Faculty of Education, Saga University, Saga, Japan
| | - Shinji Fukuda
- Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan.,Institute of Wild Onion Science, Saga University, Saga, Japan.,The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.,Saga University Center for Education and Research in Agricultural Innovation, Faculty of Agriculture, Saga University, Saga, Japan
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6
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Valouzi H, Shahmohammadi N, Golnaraghi A, Moosavi MR, Ohshima K. Genetic diversity and evolutionary analyses of potyviruses infecting narcissus in Iran. JOURNAL OF PLANT PATHOLOGY : AN INTERNATIONAL JOURNAL OF THE ITALIAN PHYTOPATHOLOGICAL SOCIETY 2021; 104:237-250. [PMID: 34866893 PMCID: PMC8628840 DOI: 10.1007/s42161-021-00985-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Potyviruses are among the most important pathogens of dicotyledonous and monocotyledonous ornamentals and crop plants. In this study, leaf samples were collected from symptomatic narcissus plants and weeds in Fars and Tehran provinces of Iran. Enzyme-linked immunosorbent assay using broad-spectrum potyvirus antibodies gave a positive reaction with 38 out of 61 narcissus samples tested (62.3%); the results were confirmed by reverse-transcription polymerase chain reaction using universal NIb primers, and for thirty samples, by sequencing and phylogenetic studies. The results suggested the infection of almost all positive samples with narcissus yellow stripe virus (NYSV); only one sample seemed to be infected with narcissus late season yellows virus (NLSYV). The 3'-end of the genome of the NLSYV isolate and six NYSV isolates, encompassing the complete coat protein gene, was amplified and sequenced using species-specific and universal potyvirus primers. Sequence analysis indicated the presence of NLSYV and NYSV, not previously identified from Western Asia. No evidence of recombination was found in Iranian isolates. Based on phylogenetic analyses, isolates of NLSYV and NYSV clustered into five and three phylogroups, respectively, where all the Iranian isolates fell into distinct subpopulations in groups NLSYV-I and NYSV-II. Multiple sequence alignments showed some phylogroup-specific amino acid substitutions for both viruses. Phylogroup IV and II populations had higher nucleotide diversities as compared with other populations of NLSYV and NYSV, respectively. Our findings revealed the presence of negative selection in the populations of both viruses. Almost no statistically significant gene flow was found between populations of these viruses. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s42161-021-00985-0.
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Affiliation(s)
- Hajar Valouzi
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Niayesh Shahmohammadi
- Department of Plant Protection, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Alireza Golnaraghi
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran, Iran
- Department of Biodiversity, BoomZista Institute, Vancouver, British Columbia Canada
| | - Mohammad Reza Moosavi
- Department of Plant Pathology, Marvdasht Branch, Islamic Azad University, Marvdasht, Iran
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, 1-banchi, Honjo-manchi, Saga, 804-8502 Japan
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7
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Genomic analysis of the brassica pathogen turnip mosaic potyvirus reveals its spread along the former trade routes of the Silk Road. Proc Natl Acad Sci U S A 2021; 118:2021221118. [PMID: 33741737 PMCID: PMC8000540 DOI: 10.1073/pnas.2021221118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Our article presents the most comprehensive reconstruction of the evolutionary and phylogeographic history of a major plant pathogen of brassica vegetables in Eurasia. Sampling across such a large landmass poses considerable challenges, and our study attempts to describe the spatial and temporal patterns of migration for a plant pathogen on a large scale. Our phylogeographic and molecular clock analyses show that the migration pathways of turnip mosaic potyvirus retrace some of the historical trade arteries of the Silk Road. This study demonstrates how a comprehensive genetic analysis can provide a large-scale view of the epidemiology and human-mediated spread of a plant pathogen across centuries of evolutionary history. Plant pathogens have agricultural impacts on a global scale and resolving the timing and route of their spread can aid crop protection and inform control strategies. However, the evolutionary and phylogeographic history of plant pathogens in Eurasia remains largely unknown because of the difficulties in sampling across such a large landmass. Here, we show that turnip mosaic potyvirus (TuMV), a significant pathogen of brassica crops, spread from west to east across Eurasia from about the 17th century CE. We used a Bayesian phylogenetic approach to analyze 579 whole genome sequences and up to 713 partial sequences of TuMV, including 122 previously unknown genome sequences from isolates that we collected over the past five decades. Our phylogeographic and molecular clock analyses showed that TuMV isolates of the Asian-Brassica/Raphanus (BR) and basal-BR groups and world-Brassica3 (B3) subgroup spread from the center of emergence to the rest of Eurasia in relation to the host plants grown in each country. The migration pathways of TuMV have retraced some of the major historical trade arteries in Eurasia, a network that formed the Silk Road, and the regional variation of the virus is partly characterized by different type patterns of recombinants. Our study presents a complex and detailed picture of the timescale and major transmission routes of an important plant pathogen.
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8
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Toribio R, Muñoz A, Sánchez F, Ponz F, Castellano MM. High overexpression of CERES, a plant regulator of translation, induces different phenotypical defence responses during TuMV infection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:256-267. [PMID: 33899980 DOI: 10.1111/tpj.15290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Mutations in the eukaryotic translation initiation factors eIF4E and eIF(iso)4E confer potyvirus resistance in a range of plant hosts. This supports the notion that, in addition to their role in translation of cellular mRNAs, eIF4E isoforms are also essential for the potyvirus cycle. CERES is a plant eIF4E- and eIF(iso)4E-binding protein that, through its binding to the eIF4Es, modulates translation initiation; however, its possible role in potyvirus resistance is unknown. In this article, we analyse if the ectopic expression of AtCERES is able to interfere with turnip mosaic virus replication in plants. Our results demonstrate that, during infection, the ectopic expression of CERES in Nicotiana benthamiana promotes the development of a mosaic phenotype when it is accumulated to moderate levels, but induces veinal necrosis when it is accumulated to higher levels. This necrotic process resembles a hypersensitive response (HR)-like response that occurs with different HR hallmarks. Remarkably, Arabidopsis plants inoculated with a virus clone that promotes high expression of CERES do not show signs of infection. These final phenotypical outcomes are independent of the capacity of CERES to bind to eIF4E. All these data suggest that CERES, most likely due to its leucine-rich repeat nature, could act as a resistance protein, able to promote a range of different defence responses when it is highly overexpressed from viral constructs.
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Affiliation(s)
- René Toribio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Alfonso Muñoz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Botánica, Ecología y Fisiología Vegetal, Campus de Rabanales, Edificio Severo Ochoa, Universidad de Córdoba, Córdoba, 14071, Spain
| | - Flora Sánchez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Fernando Ponz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - M Mar Castellano
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
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9
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Butković A, González R, Rivarez MPS, Elena SF. A genome-wide association study identifies Arabidopsis thaliana genes that contribute to differences in the outcome of infection with two Turnip mosaic potyvirus strains that differ in their evolutionary history and degree of host specialization. Virus Evol 2021; 7:veab063. [PMID: 34532063 PMCID: PMC8438913 DOI: 10.1093/ve/veab063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/23/2021] [Accepted: 06/30/2021] [Indexed: 01/14/2023] Open
Abstract
Viruses lie in a continuum between generalism and specialism depending on their ability to infect more or less hosts. While generalists are able to successfully infect a wide variety of hosts, specialists are limited to one or a few. Even though generalists seem to gain an advantage due to their wide host range, they usually pay a pleiotropic fitness cost within each host. On the contrary, a specialist has maximal fitness within its own host. A relevant yet poorly explored question is whether viruses differ in the way they interact with their hosts' gene expression depending on their degree of specialization. Using a genome-wide association study approach, we have identified host genes whose expression depends on whether hosts were infected with more or less specialized viral strains. Four hundred fifty natural accessions of Arabidopsis thaliana were inoculated with Turnip mosaic potyvirus strains with different past evolutionary histories and that shown different degrees of specialization. Three disease-related traits were measured and associated with different sets of host genes for each strain. The genetic architectures of these traits differed among viral strains and, in the case of the more specialized virus, also varied along the duration of infection. While most of the mapped loci were strain specific, one shared locus was mapped for both strains, a disease-resistance TIR-NBS-LRR class protein. Likewise, only putative cysteine-rich receptor-like protein kinases were involved in all three traits. The impact on disease progress of 10 selected genes was validated by studying the infection phenotypes of loss-of-function mutant plants. Nine of these mutants have altered the disease progress and/or symptoms intensity between both strains. Compared to wild-type plants six had an effect on both viral strains, three had an effect only on the more specialized, and two were significant during infection with the less specialized.
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10
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Roques L, Desbiez C, Berthier K, Soubeyrand S, Walker E, Klein EK, Garnier J, Moury B, Papaïx J. Emerging strains of watermelon mosaic virus in Southeastern France: model-based estimation of the dates and places of introduction. Sci Rep 2021; 11:7058. [PMID: 33782446 PMCID: PMC8007712 DOI: 10.1038/s41598-021-86314-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 02/16/2021] [Indexed: 11/09/2022] Open
Abstract
Where and when alien organisms are successfully introduced are central questions to elucidate biotic and abiotic conditions favorable to the introduction, establishment and spread of invasive species. We propose a modelling framework to analyze multiple introductions by several invasive genotypes or genetic variants, in competition with a resident population, when observations provide knowledge on the relative proportions of each variant at some dates and places. This framework is based on a mechanistic-statistical model coupling a reaction–diffusion model with a probabilistic observation model. We apply it to a spatio-temporal dataset reporting the relative proportions of five genetic variants of watermelon mosaic virus (WMV, genus Potyvirus, family Potyviridae) in infections of commercial cucurbit fields. Despite the parsimonious nature of the model, it succeeds in fitting the data well and provides an estimation of the dates and places of successful introduction of each emerging variant as well as a reconstruction of the dynamics of each variant since its introduction.
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Affiliation(s)
- L Roques
- INRAE, BioSP, 84914, Avignon, France.
| | - C Desbiez
- INRAE, Pathologie Végétale, 84140, Montfavet, France
| | - K Berthier
- INRAE, Pathologie Végétale, 84140, Montfavet, France
| | | | - E Walker
- INRAE, BioSP, 84914, Avignon, France
| | - E K Klein
- INRAE, BioSP, 84914, Avignon, France
| | - J Garnier
- Laboratoire de Mathématiques (LAMA), CNRS and Université de Savoie-Mont Blanc, Chambéry, France
| | - B Moury
- INRAE, Pathologie Végétale, 84140, Montfavet, France
| | - J Papaïx
- INRAE, BioSP, 84914, Avignon, France
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11
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Palukaitis P, Kim S. Resistance to Turnip Mosaic Virus in the Family Brassicaceae. THE PLANT PATHOLOGY JOURNAL 2021; 37:1-23. [PMID: 33551693 PMCID: PMC7847761 DOI: 10.5423/ppj.rw.09.2020.0178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 05/21/2023]
Abstract
Resistance to diseases caused by turnip mosaic virus (TuMV) in crop species of the family Brassicaceae has been studied extensively, especially in members of the genus Brassica. The variation in response observed on resistant and susceptible plants inoculated with different isolates of TuMV is due to a combination of the variation in the plant resistome and the variation in the virus genome. Here, we review the breadth of this variation, both at the level of variation in TuMV sequences, with one eye towards the phylogeny and evolution of the virus, and another eye towards the nature of the various responses observed in susceptible vs. different types of resistance responses. The analyses of the viral genomes allowed comparisons of pathotyped viruses on particular indicator hosts to produce clusters of host types, while the inclusion of phylogeny data and geographic location allowed the formation of the host/geographic cluster groups, the derivation of both of which are presented here. Various studies on resistance determination in particular brassica crops sometimes led to further genetic studies, in many cases to include the mapping of genes, and in some cases to the actual identification of the genes. In addition to summarizing the results from such studies done in brassica crops, as well as in radish and Arabidopsis (the latter as a potential source of candidate genes for brassica and radish), we also summarize work done using nonconventional approaches to obtaining resistance to TuMV.
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Affiliation(s)
- Peter Palukaitis
- Department of Horticultural Sciences, Seoul Women’s University, Seoul 0797, Korea
- Co-corresponding authors P. Palukaitis, Phone) +82-2-970-5614, FAX) +82-2-970-5610, E-mail) , S. Kim, Phone) +82-31-5182-8112, FAX) +82-31-5182-8113, E-mail) , ORCID, Peter Palukaitis https://orcid.org/0000-0001-8735-1273
| | - Su Kim
- Institute of Plant Analysis Technology Development, The Saeron Co., Suwon 16648, Korea
- Co-corresponding authors P. Palukaitis, Phone) +82-2-970-5614, FAX) +82-2-970-5610, E-mail) , S. Kim, Phone) +82-31-5182-8112, FAX) +82-31-5182-8113, E-mail) , ORCID, Peter Palukaitis https://orcid.org/0000-0001-8735-1273
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12
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Ágoston J, Almási A, Salánki K, Palkovics L. Genetic Diversity of Potyviruses Associated with Tulip Breaking Syndrome. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1807. [PMID: 33352796 PMCID: PMC7766433 DOI: 10.3390/plants9121807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/12/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022]
Abstract
Tulip breaking is economically the most important viral disease of modern-day tulip growing. It is characterized by irregular flame and feather-like patterns in the flowers and mosaic on the foliage. Thirty-two leaf samples were collected from cultivated tulip plants showing tulip breaking syndrome from Hungary in 2017 and 2018. Virus identification was performed by serological (ELISA) and molecular (RT-PCR) methods. All samples proved to be infected with a potyvirus and evidence was provided that three potyvirus species could be identified in the samples: Lily mottle virus (LMoV), Tulip breaking virus (TBV) and Rembrandt tulip-breaking virus (ReTBV). Recombination prediction accomplished with Recombination Detection Program (RDP) v4.98 revealed potential intraspecies recombination in the case of TBV and LMoV. Phylogenetic analyses of the coat protein (CP) regions proved the monophyletic origin of these viruses and verified them as three different species according to current International Committee on Taxonomy of Viruses (ICTV) species demarcation criteria. Based on these results, we analyzed taxonomic relations concerning potyviruses associated with tulip breaking syndrome. We propose the elevation of ReTBV to species level, and emergence of two new subgroups in ReTBV.
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Affiliation(s)
- János Ágoston
- Department of Plant Pathology, Faculty of Horticultural Science, Szent István University, 1118 Budapest, Hungary;
- Department of Agriculture, Faculty of Horticulture and Rural Development, John von Neumann University, 6000 Kecskemét, Hungary
| | - Asztéria Almási
- Plant Protection Institute, Centre for Agricultural Research, 1022 Budapest, Hungary; (A.A.); (K.S.)
| | - Katalin Salánki
- Plant Protection Institute, Centre for Agricultural Research, 1022 Budapest, Hungary; (A.A.); (K.S.)
| | - László Palkovics
- Department of Plant Pathology, Faculty of Horticultural Science, Szent István University, 1118 Budapest, Hungary;
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13
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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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14
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Cabrera Mederos D, Torres C, Bejerman N, Trucco V, Lenardon S, Leiva Mora M, Giolitti F. Phylodynamics of sunflower chlorotic mottle virus, an emerging pathosystem. Virology 2020; 545:33-39. [PMID: 32308196 DOI: 10.1016/j.virol.2020.02.003] [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: 11/05/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 10/24/2022]
Abstract
Distribution and epidemiological patterns of sunflower chlorotic mottle virus (SCMoV) in sunflower (Helianthus annuus L.) growing areas in Argentina were studied from 2006 to 2017. The virus was detected exclusively in the Pampas region (Entre Ríos, Santa Fe, Córdoba, La Pampa and Buenos Aires provinces). Phylodynamic analyses performed using the coat protein gene of SCMoV isolates from sunflower and weeds dated the most recent common ancestor (MRCA) back to 1887 (HPD95% = 1572-1971), which coincides with the dates of sunflower introduction in Argentina. The MRCA was located in the south of Buenos Aires province and was associated with sunflower host (posterior probability for the ancestral host, ppah = 0.98). The Bayesian phylodynamic analyses revealed the dispersal patterns of SCMoV, suggesting a link between natural host diversity, crop displacement by human activities and virus spread.
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Affiliation(s)
- Dariel Cabrera Mederos
- Instituto Nacional de Tecnología Agropecuaria, Centro de Investigaciones Agropecuarias, Instituto de Patología Vegetal Ing. Agr. Sergio Fernando Nome, Av. 11 de Septiembre 4755, X5020ICA, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Av. 11 de Septiembre 4755, X5020ICA, Córdoba, Argentina.
| | - Carolina Torres
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica, Cátedra de Virología, Junin 956, 4 Piso, C1113AAD, Ciudad Autónoma de Buenos Aires, Argentina
| | - Nicolás Bejerman
- Instituto Nacional de Tecnología Agropecuaria, Centro de Investigaciones Agropecuarias, Instituto de Patología Vegetal Ing. Agr. Sergio Fernando Nome, Av. 11 de Septiembre 4755, X5020ICA, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Av. 11 de Septiembre 4755, X5020ICA, Córdoba, Argentina
| | - Verónica Trucco
- Instituto Nacional de Tecnología Agropecuaria, Centro de Investigaciones Agropecuarias, Instituto de Patología Vegetal Ing. Agr. Sergio Fernando Nome, Av. 11 de Septiembre 4755, X5020ICA, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Av. 11 de Septiembre 4755, X5020ICA, Córdoba, Argentina
| | - Sergio Lenardon
- Instituto Nacional de Tecnología Agropecuaria, Centro de Investigaciones Agropecuarias, Instituto de Patología Vegetal Ing. Agr. Sergio Fernando Nome, Av. 11 de Septiembre 4755, X5020ICA, Córdoba, Argentina; Universidad Nacional de Río Cuarto, Facultad de Agronomía y Veterinaria, Ruta Nacional 36, Km. 601, X5804BYA, Río Cuarto, Córdoba, Argentina
| | - Michel Leiva Mora
- Escuela Superior Politécnica de Chimborazo, Facultad de Recursos Naturales, Laboratorio de Fitopatología, EC060155, Riobamba, Ecuador
| | - Fabián Giolitti
- Instituto Nacional de Tecnología Agropecuaria, Centro de Investigaciones Agropecuarias, Instituto de Patología Vegetal Ing. Agr. Sergio Fernando Nome, Av. 11 de Septiembre 4755, X5020ICA, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Av. 11 de Septiembre 4755, X5020ICA, Córdoba, Argentina.
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15
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Valouzi H, Hashemi SS, Wylie SJ, Ahadiyat A, Golnaraghi A. Wisteria Vein Mosaic Virus Detected for the First Time in Iran from an Unknown Host by Analysis of Aphid Vectors. THE PLANT PATHOLOGY JOURNAL 2020; 36:87-97. [PMID: 32089664 PMCID: PMC7012578 DOI: 10.5423/ppj.oa.10.2019.0268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/23/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
The development of reverse transcription-polymerase chain reaction using degenerate primers against conserved regions of most potyviral genomes enabled sampling of the potyvirome. However, these assays usually involve sampling potential host plants, but identifying infected plants when they are asymptomatic is challenging, and many plants, especially wild ones, contain inhibitors to DNA amplification. We used an alternative approach which utilized aphid vectors and indicator plants to identify potyviruses capable of infecting common bean (Phaseolus vulgaris). Aphids were collected from a range of asymptomatic leguminous weeds and trees in Iran, and transferred to bean seedlings under controlled conditions. Bean plants were tested serologically for potyvirus infections four-weeks post-inoculation. The serological assay and symptomatology together indicated the presence of one potyvirus, and symptomology alone implied the presence of an unidentified virus. The partial genome of the potyvirus, encompassing the complete coat protein gene, was amplified using generic potyvirus primers. Sequence analysis of the amplicon confirmed the presence of an isolate of Wisteria vein mosaic virus (WVMV), a virus species not previously identified from Western Asia. Phylogenetic analyses of available WVMV sequences categorized them into five groups: East Asian-1 to 3, North American and World. The Iranian isolate clustered with those in the World group. Multiple sequence alignment indicated the presence of some genogroup-specific amino acid substitutions among the isolates studied. Chinese isolates were sister groups of other isolates and showed higher nucleotide distances as compared with the others, suggesting a possible Eastern-Asian origin of WVMV, the main region where Wisteria might have originated.
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Affiliation(s)
- Hajar Valouzi
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran,
Iran
| | - Seyedeh-Shahrzad Hashemi
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran,
Iran
| | - Stephen J. Wylie
- Plant Biotechnology Research Group – Virology, State Agricultural Biotechnology Centre, Murdoch University, Perth, WA 6150,
Australia
| | - Ali Ahadiyat
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran,
Iran
| | - Alireza Golnaraghi
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran,
Iran
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16
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Gibbs AJ, Hajizadeh M, Ohshima K, Jones RA. The Potyviruses: An Evolutionary Synthesis Is Emerging. Viruses 2020; 12:E132. [PMID: 31979056 PMCID: PMC7077269 DOI: 10.3390/v12020132] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/28/2022] Open
Abstract
In this review, encouraged by the dictum of Theodosius Dobzhansky that "Nothing in biology makes sense except in the light of evolution", we outline the likely evolutionary pathways that have resulted in the observed similarities and differences of the extant molecules, biology, distribution, etc. of the potyvirids and, especially, its largest genus, the potyviruses. The potyvirids are a family of plant-infecting RNA-genome viruses. They had a single polyphyletic origin, and all share at least three of their genes (i.e., the helicase region of their CI protein, the RdRp region of their NIb protein and their coat protein) with other viruses which are otherwise unrelated. Potyvirids fall into 11 genera of which the potyviruses, the largest, include more than 150 distinct viruses found worldwide. The first potyvirus probably originated 15,000-30,000 years ago, in a Eurasian grass host, by acquiring crucial changes to its coat protein and HC-Pro protein, which enabled it to be transmitted by migrating host-seeking aphids. All potyviruses are aphid-borne and, in nature, infect discreet sets of monocotyledonous or eudicotyledonous angiosperms. All potyvirus genomes are under negative selection; the HC-Pro, CP, Nia, and NIb genes are most strongly selected, and the PIPO gene least, but there are overriding virus specific differences; for example, all turnip mosaic virus genes are more strongly conserved than those of potato virus Y. Estimates of dN/dS (ω) indicate whether potyvirus populations have been evolving as one or more subpopulations and could be used to help define species boundaries. Recombinants are common in many potyvirus populations (20%-64% in five examined), but recombination seems to be an uncommon speciation mechanism as, of 149 distinct potyviruses, only two were clear recombinants. Human activities, especially trade and farming, have fostered and spread both potyviruses and their aphid vectors throughout the world, especially over the past five centuries. The world distribution of potyviruses, especially those found on islands, indicates that potyviruses may be more frequently or effectively transmitted by seed than experimental tests suggest. Only two meta-genomic potyviruses have been recorded from animal samples, and both are probably contaminants.
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Affiliation(s)
- Adrian J. Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia
| | - Mohammad Hajizadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan;
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-2410 Korimoto, Kagoshima 890-0065, Japan
| | - Roger A.C. Jones
- Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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17
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Moury B, Desbiez C. Host Range Evolution of Potyviruses: A Global Phylogenetic Analysis. Viruses 2020; 12:v12010111. [PMID: 31963241 PMCID: PMC7020010 DOI: 10.3390/v12010111] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/28/2022] Open
Abstract
Virus host range, i.e., the number and diversity of host species of viruses, is an important determinant of disease emergence and of the efficiency of disease control strategies. However, for plant viruses, little is known about the genetic or ecological factors involved in the evolution of host range. Using available genome sequences and host range data, we performed a phylogenetic analysis of host range evolution in the genus Potyvirus, a large group of plant RNA viruses that has undergone a radiative evolution circa 7000 years ago, contemporaneously with agriculture intensification in mid Holocene. Maximum likelihood inference based on a set of 59 potyviruses and 38 plant species showed frequent host range changes during potyvirus evolution, with 4.6 changes per plant species on average, including 3.1 host gains and 1.5 host loss. These changes were quite recent, 74% of them being inferred on the terminal branches of the potyvirus tree. The most striking result was the high frequency of correlated host gains occurring repeatedly in different branches of the potyvirus tree, which raises the question of the dependence of the molecular and/or ecological mechanisms involved in adaptation to different plant species.
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18
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Evolutionary timescale and geographical movement of cucumber mosaic virus, with focus on Iranian strains. Arch Virol 2019; 165:185-192. [PMID: 31637514 DOI: 10.1007/s00705-019-04439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/16/2019] [Indexed: 10/25/2022]
Abstract
Cucumber mosaic virus (CMV) is a geographically widespread plant virus with a very broad host range. The virus has been detected in diverse crops all over Iran. In this study, we estimated the timescale of the evolution of CMV subgroup I and the geographical movement of the virus with a focus on Iranian strains. Analyses using the MP and CP genes and their concatenation revealed that the CMV population within subgroup I had a single ancestor dating back to about 450-550 years ago. The Iranian strains formed three clusters in a maximum-clade-credibility phylogenetic tree. It was found that the most recent common ancestor of the Iranian strains within each cluster dates back to less than 100 years ago. Our results also suggest that both short- and long-distance migration of Iranian CMV strains has occurred in the last 100 years.
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19
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Hajizadeh M, Gibbs AJ, Amirnia F, Glasa M. The global phylogeny o f Plum pox virus is emerging. J Gen Virol 2019; 100:1457-1468. [PMID: 31418674 DOI: 10.1099/jgv.0.001308] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The 206 complete genomic sequences of Plum pox virus in GenBank (January 2019) were downloaded. Their main open reading frames (ORF)s were compared by phylogenetic and population genetic methods. All fell into the nine previously recognized strain clusters; the PPV-Rec and PPV-T strain ORFs were all recombinants, whereas most of those in the PPV-C, PPV-CR, PPV-CV, PPV-D, PPV-EA, PPV-M and PPV-W strain clusters were not. The strain clusters ranged in size from 2 (PPV-CV and PPV-EA) to 74 (PPV-D). The isolates of eight of the nine strains came solely from Europe and the Levant (with an exception resulting from a quarantine breach), but many PPV-D strain isolates also came from east and south Asia and the Americas. The estimated time to the most recent common ancestor (TMRCA) of all 134 non-recombinant ORFs was 820 (865-775) BCE. Most strain populations were only a few decades old, and had small intra-strain, but large inter-strain, differences; strain PPV-W was the oldest. Eurasia is clearly the 'centre of emergence' of PPV and the several PPV-D strain populations found elsewhere only show evidence of gene flow with Europe, so have come from separate introductions from Europe. All ORFs and their individual genes show evidence of strong negative selection, except the positively selected pipo gene of the recently migrant populations. The possible ancient origins of PPV are discussed.
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Affiliation(s)
- Mohammad Hajizadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Adrian J Gibbs
- Emeritus Faculty Australian National University, Canberra, Australia
| | - Fahimeh Amirnia
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovakia
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20
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Hu WX, Kim BJ, Kwak Y, Seo EY, Kim JK, Han JY, Kim IH, Lim YP, Cho IS, Domier LL, Hammond J, Lim HS. Five Newly Collected Turnip Mosaic Virus (TuMV) Isolates from Jeju Island, Korea are Closely Related to Previously Reported Korean TuMV Isolates but Show Distinctive Symptom Development. THE PLANT PATHOLOGY JOURNAL 2019; 35:381-387. [PMID: 31481861 PMCID: PMC6706019 DOI: 10.5423/ppj.nt.11.2018.0238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 04/29/2019] [Accepted: 05/21/2019] [Indexed: 06/10/2023]
Abstract
For several years, temperatures in the Korean peninsula have gradually increased due to climate change, resulting in a changing environment for growth of crops and vegetables. An associated consequence is that emerging species of insect vector have caused increased viral transmission. In Jeju Island, Korea, occurrences of viral disease have increased. Here, we report characterization of five newly collected turnip mosaic virus (TuMV) isolates named KBJ1, KBJ2, KBJ3, KBJ4 and KBJ5 from a survey on Jeju Island in 2017. Full-length cDNAs of each isolate were cloned into the pJY vector downstream of cauliflower mosaic virus 35S and bacteriophage T7 RNA polymerase promoters. Their fulllength sequences share 98.9-99.9% nucleotide sequence identity and were most closely related to previously reported Korean TuMV isolates. All isolates belonged to the BR group and infected both Chinese cabbage and radish. Four isolates induced very mild symptoms in Nicotiana benthamiana but KBJ5 induced a hypersensitive response. Symptom differences may result from three amino acid differences uniquely present in KBJ5; Gly(382)Asp, Ile(891)Val, and Lys(2522)Glu in P1, P3, and NIb, respectively.
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Affiliation(s)
- Wen-Xing Hu
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134,
Korea
| | - Byoung-Jo Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134,
Korea
| | - Younghwan Kwak
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134,
Korea
| | - Eun-Young Seo
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134,
Korea
| | - Jung-Kyu Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134,
Korea
| | - Jae-Yeong Han
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134,
Korea
| | - Ik-Hyun Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134,
Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134,
Korea
| | - In-Sook Cho
- National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365,
Korea
| | - Leslie L Domier
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801,
USA
| | - John Hammond
- Floral and Nursery Plants Research Unit, United States National Arboretum, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705,
USA
| | - Hyoun-Sub Lim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134,
Korea
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21
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Hu WX, Seo EY, Cho IS, Kim JK, Ju HK, Kim IH, Choi GW, Kim B, Ahn CH, Domier LL, Oh SK, Hammond J, Lim HS. Amino acid differences in the N-terminal half of the polyprotein of Chinese turnip mosaic virus isolates affect symptom expression in Nicotiana benthamiana and radish. Arch Virol 2019; 164:1683-1689. [PMID: 30963304 DOI: 10.1007/s00705-019-04242-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 03/08/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Wen-Xing Hu
- Chungnam National University, 99 Daehak-ro, Daejeon, Republic of Korea
| | - Eun-Young Seo
- Chungnam National University, 99 Daehak-ro, Daejeon, Republic of Korea
| | - In-Sook Cho
- National Institute of Horticultural and Herbal Science, Rural Development Administration, 100, Jeonju, Jeollabuk-do, Republic of Korea
| | - Jung-Kyu Kim
- Chungnam National University, 99 Daehak-ro, Daejeon, Republic of Korea
| | - Hye-Kyoung Ju
- Chungnam National University, 99 Daehak-ro, Daejeon, Republic of Korea
| | - Ik-Hyun Kim
- Chungnam National University, 99 Daehak-ro, Daejeon, Republic of Korea
| | - Go-Woon Choi
- Chungnam National University, 99 Daehak-ro, Daejeon, Republic of Korea
| | - Boram Kim
- Chungnam National University, 99 Daehak-ro, Daejeon, Republic of Korea
| | - Chun-Hee Ahn
- Breeding Research Institute of Daeil Seed, Gimje, Jeollabuk-do, Republic of Korea
| | - Leslie L Domier
- Department of Crop Sciences, United States Department of Agriculture-Agricultural Research Service, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sang-Keun Oh
- Chungnam National University, 99 Daehak-ro, Daejeon, Republic of Korea.
| | - John Hammond
- Floral and Nursery Plants Research Unit, United States Department of Agriculture-Agricultural Research Service, U.S. National Arboretum, Beltsville, MD, 20705, USA.
| | - Hyoun-Sub Lim
- Chungnam National University, 99 Daehak-ro, Daejeon, Republic of Korea.
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Pepper veinal mottle virus in Japan is closely related to isolates from other Asian countries, but more distantly to most of those from Africa. Virus Genes 2019; 55:347-355. [PMID: 30895438 DOI: 10.1007/s11262-019-01656-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/11/2019] [Indexed: 10/27/2022]
Abstract
Pepper veinal mottle virus (PVMV) is known to infect chilli pepper and belongs to the Chilli veinal mottle virus phylogroup of potyviruses. PVMV has recently appeared in Japan. In this study, we report six complete genomic sequences of PVMV isolates from chilli pepper (i.e. Capsicum annuum) in Okinawa Islands in Japan, and we determined the evolutionary relationships between Japanese isolates and the isolates reported earlier from African and Asian countries. Complete genomic sequences of the six Japanese PVMV isolates were 9760 nucleotides in length, excluding the nucleotide primer sequences used for amplifying 5' end of the genomes. The major findings of this study are as follows: (1) all the Japanese isolates of PVMV have similar biological and molecular characteristics, indicating the presence of only one population in Japan; (2) there are at least three major phylogenetic groups of PVMV worldwide; (3) PVMV probably originated in East Africa; and (4) all the Asian isolates are closely related to the Ghanaian isolate.
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23
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Katsarou K, Mitta E, Bardani E, Oulas A, Dadami E, Kalantidis K. DCL-suppressed Nicotiana benthamiana plants: valuable tools in research and biotechnology. MOLECULAR PLANT PATHOLOGY 2019; 20:432-446. [PMID: 30343523 PMCID: PMC6637889 DOI: 10.1111/mpp.12761] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
RNA silencing is a universal mechanism involved in development, epigenetic modifications and responses to biotic and abiotic stresses. The major components of this mechanism are Dicer-like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) proteins. Understanding the role of each component is of great scientific and agronomic importance. Plants, including Nicotiana benthamiana, an important plant model, usually possess four DCL proteins, each of which has a specific role, namely being responsible for the production of an exclusive small RNA population. Here, we used RNA interference (RNAi) technology to target DCL proteins and produced single and combinatorial mutants for DCL. We analysed the phenotype for each DCL knockdown plant, together with the small RNA profile, by next-generation sequencing (NGS). We also investigated transgene expression, as well as viral infections, and were able to show that DCL suppression results in distinct developmental defects, changes in small RNA populations, increases in transgene expression and, finally, higher susceptibility in certain RNA viruses. Therefore, these plants are excellent tools for the following: (i) to study the role of DCL enzymes; (ii) to overexpress proteins of interest; and (iii) to understand the complex relationship between the plant silencing mechanism and biotic or abiotic stresses.
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Affiliation(s)
- Konstantina Katsarou
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
| | - Eleni Mitta
- Department of BiologyUniversity of CreteHeraklionGreece
| | | | - Anastasis Oulas
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
- Present address:
Bioinformatics Group, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Elena Dadami
- Department of BiologyUniversity of CreteHeraklionGreece
- Present address:
RLP AgroScience, AlPlantaNeustadtGermany
| | - Kriton Kalantidis
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
- Department of BiologyUniversity of CreteHeraklionGreece
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24
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Glasa M, Šoltys K, Predajňa L, Sihelská N, Nováková S, Šubr Z, Kraic J, Mihálik D. Molecular and Biological Characterisation of Turnip mosaic virus Isolates Infecting Poppy ( Papaversomniferum and P. rhoeas) in Slovakia. Viruses 2018; 10:E430. [PMID: 30110973 PMCID: PMC6116182 DOI: 10.3390/v10080430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/07/2018] [Accepted: 08/14/2018] [Indexed: 11/30/2022] Open
Abstract
In recent years, the accumulated molecular data of Turnip mosaic virus (TuMV) isolates from various hosts originating from different parts of the world considerably helped to understand the genetic complexity and evolutionary history of the virus. In this work, four complete TuMV genomes (HC9, PK1, MS04, MS15) were characterised from naturally infected cultivated and wild-growing Papaver spp., hosts from which only very scarce data were available previously. Phylogenetic analyses showed the affiliation of Slovak Papaver isolates to the world-B and basal-B groups. The PK1 isolate showed a novel intra-lineage recombination pattern, further confirming the important role of recombination in the shaping of TuMV genetic diversity. Biological assays indicated that the intensity of symptoms in experimentally inoculated oilseed poppy are correlated to TuMV accumulation level in leaves. This is the first report of TuMV in poppy plants in Slovakia.
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Affiliation(s)
- Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia.
| | - Katarína Šoltys
- Comenius University Science Park, Comenius University in Bratislava, Ilkovičova 8, 841 04 Bratislava, Slovakia.
| | - Lukáš Predajňa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia.
| | - Nina Sihelská
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia.
| | - Slavomíra Nováková
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia.
| | - Zdeno Šubr
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia.
| | - Ján Kraic
- Department of Biotechnologies, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, J. Herdu 2, 917 01 Trnava, Slovakia.
- National Agriculture and Food Centre, Research Institute of Plant Production, Bratislavská cesta 122, 921 68 Piešťany, Slovakia.
| | - Daniel Mihálik
- Department of Biotechnologies, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, J. Herdu 2, 917 01 Trnava, Slovakia.
- National Agriculture and Food Centre, Research Institute of Plant Production, Bratislavská cesta 122, 921 68 Piešťany, Slovakia.
- Institute of High Mountain Biology, University of Žilina, Univerzitná 8215/1, 010 26 Žilina, Slovakia.
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25
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Golnaraghi A, Shahraeen N, Nguyen HD. Characterization and Genetic Structure of a Tospovirus Causing Chlorotic Ring Spots and Chlorosis Disease on Peanut; Comparison with Iranian and Polish Populations of Tomato yellow fruit ring virus. PLANT DISEASE 2018; 102:1509-1519. [PMID: 30673421 DOI: 10.1094/pdis-09-17-1350-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A Tospovirus species was isolated from peanut plants showing chlorotic ring spots and chlorosis, and identified as Tomato yellow fruit ring virus (TYFRV) on the basis of its biological, serological, and molecular properties. In host range studies, a broad range of indicator plants was infected by the five isolates studied; all the isolates systemically infected Nicotiana tabacum cultivars and, thus, they were classified into the N-host-infecting type isolates of the virus. These isolates strongly reacted with TYFRV antibodies but not with the specific antibodies of other tospoviruses tested. Recombination analyses showed that the nucleoprotein gene of the peanut isolates and other isolates studied were nonrecombinant. In phylogenetic trees, the virus isolates were clustered in three genogroups: IRN-1, IRN-2, and a new group, POL; the peanut isolates fell into IRN-2 group. Multiple sequence alignments showed some genogroup-specific amino acid substitutions among the virus isolates studied. The results revealed the presence of negative selection in TYFRV populations. Also, the Iranian populations had higher nucleotide diversity compared with the Polish population. Genetic differentiation and gene flow analyses indicated that the populations from Iran and Poland and those belonging to different genogroups were partially differentiated populations. Our findings seem to suggest that there has been frequent gene flow between some populations of the virus in the mid-Eurasian region of Iran.
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Affiliation(s)
- A Golnaraghi
- Department of Plant Protection, Faculty of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, P.O. Box 14515-775, Tehran, Iran
| | - N Shahraeen
- Department of Plant Virus Research, Iranian Research Institute of Plant Protection, Agricultural Research, Education & Extension Organization, P.O. Box 19395-1454, Tehran, Iran
| | - H D Nguyen
- Department of Plant Pathology, Faculty of Agronomy, Vietnam National University of Agriculture, Trau Quy, Gia Lam, Hanoi, Vietnam
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26
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Pagán I. The diversity, evolution and epidemiology of plant viruses: A phylogenetic view. INFECTION GENETICS AND EVOLUTION 2018; 65:187-199. [PMID: 30055330 DOI: 10.1016/j.meegid.2018.07.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
During the past four decades, the scientific community has seen an exponential advance in the number, sophistication, and quality of molecular techniques and bioinformatics tools for the genetic characterization of plant virus populations. Predating these advances, the field of Phylogenetics has significantly contributed to understand important aspects of plant virus evolution. This review aims at summarizing the impact of Phylogenetics in the current knowledge on three major aspects of plant virus evolution that have benefited from the development of phylogenetic inference: (1) The identification and classification of plant virus diversity. (2) The mechanisms and forces shaping the evolution of plant virus populations. (3) The understanding of the interaction between plant virus evolution, epidemiology and ecology. The work discussed here highlights the important role of phylogenetic approaches in the study of the dynamics of plant virus populations.
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Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28223, Spain.
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27
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Adachi S, Honma T, Yasaka R, Ohshima K, Tokuda M. Effects of infection by Turnip mosaic virus on the population growth of generalist and specialist aphid vectors on turnip plants. PLoS One 2018; 13:e0200784. [PMID: 30016354 PMCID: PMC6049944 DOI: 10.1371/journal.pone.0200784] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 07/03/2018] [Indexed: 11/18/2022] Open
Abstract
Recent studies have revealed that relationships between plant pathogens and their vectors differ depending on species, strains and associated host plants. Turnip mosaic virus (TuMV) is one of the most important plant viruses worldwide and is transmitted by at least 89 aphid species in a non-persistent manner. TuMV is fundamentally divided into six phylogenetic groups; among which Asian-BR, basal-BR and world-B groups are known to occur in Japan. In Kyushu Japan, basal-BR has invaded approximately 2000 and immediately replaced the predominant world-B virus group. To clarify the relationships between TuMV and vector aphids, we examined the effects of the TuMV phylogenetic group on the population growth of aphid vectors in turnip plants. The population growth of a generalist aphid, Myzus persicae, was not significantly different between non-infected and TuMV-infected treatments. The population growth of a specialist aphid, Lipaphis erysimi, was higher in TuMV-infected plants than non-infected ones. Similar results were obtained in experiments using world-B and basal-BR groups of TuMV. Therefore, we conclude that L. erysimi is more mutualistic with TuMV than M. persicae, and differences in TuMV phylogenetic groups do not affect the growth of aphid vectors on turnip plants.
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Affiliation(s)
- Shuhei Adachi
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Laboratory of Systems Ecology, Faculty of Agriculture, Saga University, Saga, Japan
- * E-mail:
| | - Tomoki Honma
- Laboratory of Systems Ecology, Faculty of Agriculture, Saga University, Saga, Japan
| | - Ryosuke Yasaka
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga, Japan
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga, Japan
| | - Makoto Tokuda
- Laboratory of Systems Ecology, Faculty of Agriculture, Saga University, Saga, Japan
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28
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The genetic diversity of narcissus viruses related to turnip mosaic virus blur arbitrary boundaries used to discriminate potyvirus species. PLoS One 2018; 13:e0190511. [PMID: 29300751 PMCID: PMC5754079 DOI: 10.1371/journal.pone.0190511] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/15/2017] [Indexed: 11/19/2022] Open
Abstract
Narcissus plants (Narcissus tazetta var. chinensis) showing mosaic or striping leaves were collected from around Japan, and tested for virus infections using potyvirus-specific primers. Many were found to be infected with a macluravirus and mixtures of different potyviruses, one third of them narcissus yellow stripe virus (NYSV)-like viruses. Genomes of nine of the NYSV-like viruses were sequenced and, together with four already published, provided data for phylogenetic and pairwise identity analyses of their place in the turnip mosaic virus (TuMV) phylogenetic group. Using existing ICTV criteria for defining potyvirus species, the narcissus viruses in TuMV group were found to be from five species; the previously described NLSYV, and four new species we call narcissus virus 1 (NV-1) and narcissus yellow stripe-1 to -3 (NYSV-1, NYSV-2 and NYSV-3). However, as all are from a single host species, and natural recombinants with NV-1 and NYSV-3 'parents have been found in China and India, we also conclude that they could be considered to be members of a single mega-species, narcissus virus; the criteria for defining such a potyvirus species would then be that their polyprotein sequences have greater than 69% identical nucleotides and greater than 75% identical amino acids.
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29
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Parmar N, Thakur AK, Kumar P, Thakur PD, Bhardwaj SV. Molecular characterization of Turnip mosaic potyvirus ( TuMV)-infecting radish ( Raphanus sativus L.) crop in India. 3 Biotech 2017; 7:382. [PMID: 29134159 DOI: 10.1007/s13205-017-1016-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/24/2017] [Indexed: 11/30/2022] Open
Abstract
Nine isolates of Turnip mosaic potyvirus (TuMV)-infecting radish collected from different regions of Northern India were characterized. All isolates except for New Delhi and Rajasthan isolates resulted positive for TuMV in double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA). RNA was isolated from leaves of infected plants and used in reverse transcriptase-polymerase chain reaction (RT-PCR) with TuMV coat protein (CP) gene-specific primers. Viral amplicons of expected 1000 bp size were obtained, which were further subjected to cloning and sequencing. CP gene of all the seven isolates was 867 bp long, encoding 288 amino acid residues. Percent homology of CP gene of all the Indian isolates among themselves and with other TuMV isolates retrieved from NCBI was in the range of 87-99 and 92-100% at nucleotide and amino acid levels, respectively. Phylogenetic analysis based upon CP gene nucleotide and amino acid sequences with other TuMV isolates reported from across the globe using unweighted pair group method with arithmetic mean (UPGMA) inferred classification of test isolates into basal-BR group due to their occurrence nearest to the TuMV isolates belonging to the basal-BR group. Information generated about the characteristic features of TuMV and geographical distribution of particular virus genotype-infecting radish crop will provide a platform for formulating disease resistance strategies.
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Affiliation(s)
- Nehanjali Parmar
- Dr. Y.S. Parmar University of Horticulture and Forestry, Nauni, Solan, HP 173 230 India
| | - Ajay Kumar Thakur
- ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur, Rajasthan 321 303 India
| | - Pardeep Kumar
- Dr. Y.S. Parmar University of Horticulture and Forestry, Nauni, Solan, HP 173 230 India
| | - P D Thakur
- Dr. Y.S. Parmar University of Horticulture and Forestry, Nauni, Solan, HP 173 230 India
| | - Sat Vrat Bhardwaj
- Dr. Y.S. Parmar University of Horticulture and Forestry, Nauni, Solan, HP 173 230 India
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