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Verchot J, Herath V, Jordan R, Hammond J. Genetic Diversity among Rose Rosette Virus Isolates: A Roadmap towards Studies of Gene Function and Pathogenicity. Pathogens 2023; 12:pathogens12050707. [PMID: 37242377 DOI: 10.3390/pathogens12050707] [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: 02/01/2023] [Revised: 04/11/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
The phylogenetic relationships of ninety-five rose rosette virus (RRV) isolates with full-length genomic sequences were analyzed. These isolates were recovered mostly from commercial roses that are vegetatively propagated rather than grown from seed. First, the genome segments were concatenated, and the maximum likelihood (ML) tree shows that the branches arrange independent of their geographic origination. There were six major groups of isolates, with 54 isolates in group 6 and distributed in two subgroups. An analysis of nucleotide diversity across the concatenated isolates showed lower genetic differences among RNAs encoding the core proteins required for encapsidation than the latter genome segments. Recombination breakpoints were identified near the junctions of several genome segments, suggesting that the genetic exchange of segments contributes to differences among isolates. The ML analysis of individual RNA segments revealed different relationship patterns among isolates, which supports the notion of genome reassortment. We tracked the branch positions of two newly sequenced isolates to highlight how genome segments relate to segments of other isolates. RNA6 has an interesting pattern of single-nucleotide mutations that appear to influence amino acid changes in the protein products derived from ORF6a and ORF6b. The P6a proteins were typically 61 residues, although three isolates encoded P6a proteins truncated to 29 residues, and four proteins extended 76-94 residues. Homologous P5 and P7 proteins appear to be evolving independently. These results suggest greater diversity among RRV isolates than previously recognized.
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Affiliation(s)
- Jeanmarie Verchot
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77845, USA
| | - Venura Herath
- Department of Agriculture Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Ramon Jordan
- Floral and Nursery Plants Research Unit, US National Arboretum, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - John Hammond
- Floral and Nursery Plants Research Unit, US National Arboretum, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
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2
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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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3
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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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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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Bera S, Arena GD, Ray S, Flannigan S, Casteel CL. The Potyviral Protein 6K1 Reduces Plant Proteases Activity during Turnip mosaic virus Infection. Viruses 2022; 14:1341. [PMID: 35746814 PMCID: PMC9229136 DOI: 10.3390/v14061341] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/30/2022] [Accepted: 06/12/2022] [Indexed: 12/25/2022] Open
Abstract
Potyviral genomes encode just 11 major proteins and multifunctionality is associated with most of these proteins at different stages of the virus infection cycle. Some potyviral proteins modulate phytohormones and protein degradation pathways and have either pro- or anti-viral/insect vector functions. Our previous work demonstrated that the potyviral protein 6K1 has an antagonistic effect on vectors when expressed transiently in host plants, suggesting plant defenses are regulated. However, to our knowledge the mechanisms of how 6K1 alters plant defenses and how 6K1 functions are regulated are still limited. Here we show that the 6K1 from Turnip mosaic virus (TuMV) reduces the abundance of transcripts related to jasmonic acid biosynthesis and cysteine protease inhibitors when expressed in Nicotiana benthamiana relative to controls. 6K1 stability increased when cysteine protease activity was inhibited chemically, showing a mechanism to the rapid turnover of 6K1 when expressed in trans. Using RNAseq, qRT-PCR, and enzymatic assays, we demonstrate TuMV reprograms plant protein degradation pathways on the transcriptional level and increases 6K1 stability at later stages in the infection process. Moreover, we show 6K1 decreases plant protease activity in infected plants and increases TuMV accumulation in systemic leaves compared to controls. These results suggest 6K1 has a pro-viral function in addition to the anti-insect vector function we observed previously. Although the host targets of 6K1 and the impacts of 6K1-induced changes in protease activity on insect vectors are still unknown, this study enhances our understanding of the complex interactions occurring between plants, potyviruses, and vectors.
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Affiliation(s)
- Sayanta Bera
- School of Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14850, USA; (S.B.); (S.R.); (S.F.)
| | - Gabriella D. Arena
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo 04014-002, Brazil;
| | - Swayamjit Ray
- School of Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14850, USA; (S.B.); (S.R.); (S.F.)
| | - Sydney Flannigan
- School of Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14850, USA; (S.B.); (S.R.); (S.F.)
| | - Clare L. Casteel
- School of Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14850, USA; (S.B.); (S.R.); (S.F.)
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Rastgou M, Roumi V, Noris E, Matić S, Ercisli S. Phylogenetic Marker Selection and Protein Sequence Analysis of the ORF5 Gene Product of Grapevine Virus A. PLANTS (BASEL, SWITZERLAND) 2022; 11:1118. [PMID: 35567118 PMCID: PMC9104223 DOI: 10.3390/plants11091118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/17/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
Grapevine virus A (GVA), the type species of the Vitivirus genus, is one of the causal agents of the Kober stem grooving disease of the rugose wood complex and one of the most frequently detected viruses in grapevine. There is little information on GVA gene(s) marker useful for phylogenetic analysis. To this aim, a total of 403 leaf samples were collected from vineyards of East and West Azarbaijan provinces in the Northwestern provinces of Iran during 2014-2016 and tested by DAS-ELISA and RT-PCR using ORF5-specific primers. GVA was detected in 56 symptomatic samples, corresponding to 14% of infection, while it was not detected in asymptomatic samples. The ORF5 (p10) protein sequence of eight Iranian isolates was compared to other vitiviruses, showing that the most conserved region resides in the N-terminus, carrying an arginine-rich motif followed by a zinc-finger motif. Next, to define a robust phylogenetic marker representative of the whole genome sequence suitable for phylogenetic and evolutionary studies, phylogenetic trees based on the full genome sequences of all the available GVA isolates and on individual genomic regions were constructed and compared. ORF1, which encodes the RNA-dependent RNA polymerase, was found to be the best phylogenetic marker for GVA classification and evolution studies. These results can be used for further research on phylogenetic analyses, evolution history, epidemiology, and etiology of rugose wood complex, and to identify control measures against GVA and other vitiviruses.
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Affiliation(s)
- Mina Rastgou
- Department of Plant Protection, Faculty of Agriculture, Urmia University, Urmia 5756151818, Iran
| | - Vahid Roumi
- Department of Plant Protection, College of Agriculture, University of Maragheh, Maragheh 5518183111, Iran;
| | - Emanuela Noris
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), 10135 Turin, Italy; (E.N.); (S.M.)
| | - Slavica Matić
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), 10135 Turin, Italy; (E.N.); (S.M.)
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum 25240, Turkey;
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López-González S, Gómez-Mena C, Sánchez F, Schuetz M, Samuels AL, Ponz F. The Effects of Turnip Mosaic Virus Infections on the Deposition of Secondary Cell Walls and Developmental Defects in Arabidopsis Plants Are Virus-Strain Specific. FRONTIERS IN PLANT SCIENCE 2021; 12:741050. [PMID: 34691118 PMCID: PMC8531753 DOI: 10.3389/fpls.2021.741050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Two isolates of Turnip mosaic virus (UK 1 and JPN 1), representative of two different viral strains, induced differential alterations on secondary cell wall (SCW) development in Arabidopsis thaliana, suggesting cell-type specific effects of these viral infections. These potential effects were analyzed in inflorescence stems and flowers of infected plants, together with other possible cellular effects of the infections. Results obtained from macroscopic and histochemical analyses showed that infection with either virus significantly narrowed stem area, but defects in SCW were only found in JPN 1 infections. In flowers, reduced endothecium lignification was also found for JPN 1, while UK 1 infections induced severe floral cell and organ development alterations. A transcriptomic analysis focused on genes controlling and regulating SCW formation also showed notable differences between both viral isolates. UK 1 infections induced a general transcriptional decrease of most regulatory genes, whereas a more complex pattern of alterations was found in JPN 1 infections. The role of the previously identified viral determinant of most developmental alterations, the P3 protein, was also studied through the use of viral chimeras. No SCW alterations or creeping habit growth were found in infections by the chimeras, indicating that if the P3 viral protein is involved in the determination of these symptoms, it is not the only determinant. Finally, considerations as to the possibility of a taxonomical reappraisal of these TuMV viral strains are provided.
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Affiliation(s)
- Silvia López-González
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC, Madrid, Spain
| | - Concepción Gómez-Mena
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Flora Sánchez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC, Madrid, Spain
| | - Mathias Schuetz
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - A. Lacey Samuels
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Fernando Ponz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC, Madrid, Spain
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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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Chinnadurai C, Kollam M, Ramsubhag A, Jayaraman J. Genome characterization of zucchini yellow mosaic virus infecting cucurbits reveals the presence of a new genotype in Trinidad and Tobago in the Caribbean region. Arch Virol 2021; 166:1661-1669. [PMID: 33811529 DOI: 10.1007/s00705-021-05048-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/08/2021] [Indexed: 10/21/2022]
Abstract
Zucchini yellow mosaic virus (ZYMV) is a member of the genus Potyvirus that is becoming a serious pathogen of pumpkin and other cucurbits in Trinidad and Tobago and the entire Caribbean region. In this study, four ZYMV isolates infecting pumpkin in Trinidad and Tobago were characterized by complete genome sequencing. Phylogenetic analysis showed 5.9-6.0% nt and 7.7-7.9% aa sequence divergence in comparison to the most closely related isolates NAT and AG from Israel and SE04T from Slovakia. Based on the variations in the complete genome sequence as well as individual gene sequences, a new genotype, designated ZYMV-Trini, is proposed for these isolates. Among the gene sequences of ZYMV-Trini isolates, the greatest variation was observed in the HC-Pro gene, with 20.8% aa sequence divergence from their closest relatives, whereas the least variation was observed in the NIb, P3, and CP genes, with 1.8-2.2% aa sequence divergence. This study also showed that transmission of ZYMV can occur through seeds, but this was less common than transmission via the aphid Aphis gossypii. The progression of ZYMV in pumpkin seedlings was quantified by RT-qPCR, which showed a rapid surge in viral load after 37 days. From recombination analysis, it could be concluded that the isolates SE04T from Slovakia, NAT from Israel, and AG from Israel have made major contributions to the genome architecture of ZYMV-Trini isolates.
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Affiliation(s)
- Chinnaraja Chinnadurai
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, WI, Trinidad and Tobago
| | - Mounika Kollam
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, WI, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, WI, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, WI, Trinidad and Tobago.
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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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11
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Kim IH, Ju HK, Gong J, Han JY, Seo EY, Cho SW, Hu WX, Choi SR, Lim YP, Domier LL, Hammond J, Lim HS. A Turnip Mosaic Virus Determinant of Systemic Necrosis in Nicotiana benthamiana and a Novel Resistance-Breaking Determinant in Chinese Cabbage Identified from Chimeric Infectious Clones. PHYTOPATHOLOGY 2019; 109:1638-1647. [PMID: 31044662 DOI: 10.1094/phyto-08-18-0323-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Infectious clones of Korean turnip mosaic virus (TuMV) isolates KIH1 and HJY1 share 88.1% genomic nucleotides and 96.4% polyprotein amino acid identity, and they induce systemic necrosis or mild mosaic, respectively, in Nicotiana benthamiana. Chimeric constructs between these isolates exchanged the 5', central, and 3' domains of KIH1 (K) and HJY1 (H), where the order of the letters indicates the origin of these domains. KIH1 and chimeras KHH and KKH induced systemic necrosis, whereas HJY1 and chimeras HHK, HKK, and HKH induced mild symptoms, indicating the determinant of necrosis to be within the 5' 3.9 kb of KIH1; amino acid identities of the included P1, Helper component protease, P3, 6K1, and cylindrical inclusion N-terminal domain were 90.06, 98.91, 93.80, 100, and 100%, respectively. Expression of P1 or P3 from a potato virus X vector yielded symptom differences only between P3 of KIH1 and HJY1, implicating a role for P3 in necrosis in N. benthamiana. Chimera KKH infected Brassica rapa var. pekinensis 'Norang', which was resistant to both KIH1 and HJY1, indicating that two separate TuMV determinants are required to overcome the resistance. Ability of diverse TuMV isolates, chimeras, and recombinants to overcome resistance in breeding lines may allow identification of novel resistance genes.
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Affiliation(s)
- Ik-Hyun Kim
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Hye-Kyoung Ju
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Junsu Gong
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Jae-Yeong Han
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Eun-Young Seo
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Sang-Won Cho
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Wen-Xing Hu
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Su Ryun Choi
- Department of Horticulture, Chungnam National University, Daejeon, South Korea
| | - Yong Pyo Lim
- Department of Horticulture, Chungnam National University, Daejeon, South Korea
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, U.S.A
| | - John Hammond
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, U.S. Department of Agriculture-Agriculture Research Service, Beltsville, MD, U.S.A
| | - Hyoun-Sub Lim
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
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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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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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Gong J, Ju HK, Kim IH, Seo EY, Cho IS, Hu WX, Han JY, Kim JK, Choi SR, Lim YP, Hammond J, Lim HS. Sequence Variations Among 17 New Radish Isolates of Turnip mosaic virus Showing Differential Pathogenicity and Infectivity in Nicotiana benthamiana, Brassica rapa, and Raphanus sativus. PHYTOPATHOLOGY 2019; 109:904-912. [PMID: 30629482 DOI: 10.1094/phyto-12-17-0401-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Infectious clones were generated from 17 new Korean radish isolates of Turnip mosaic virus (TuMV). Phylogenetic analysis indicated that all new isolates, and three previously characterized Korean radish isolates, belong to the basal-BR group (indicating that the pathotype can infect both Brassica and Raphanus spp.). Pairwise analysis revealed genomic nucleotide and polyprotein amino acid identities of >87.9 and >95.7%, respectively. Five clones (HJY1, HJY2, KIH2, BE, and prior isolate R007) had lower sequence identities than other isolates and produced mild symptoms in Nicotiana benthamiana. These isolates formed three distinct sequence classes (HJY1/HJY2/R007, KIH2, and BE), and several differential amino acid residues (in P1, P3, 6K2, and VPg) were present only in mild isolates HJY1, HJY2, and R007. The remaining isolates all induced systemic necrosis in N. benthamiana. Four mild isolates formed a phylogenetic subclade separate from another subclade including all of the necrosis-inducing isolates plus mild isolate KIH2. Symptom severity in radish and Chinese cabbage genotypes was not correlated with pathogenicity in N. benthamiana; indeed, Chinese cabbage cultivar Norang was not infected by any isolate, whereas Chinese cabbage cultivar Chusarang was uniformly susceptible. Four isolates were unable to infect radish cultivar Iljin, but no specific amino acid residues were correlated with avirulence. These results may lead to the identification of new resistance genes against TuMV.
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Affiliation(s)
- Junsu Gong
- 1 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea
| | - Hye-Kyoung Ju
- 1 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea
| | - Ik-Hyun Kim
- 1 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea
| | - Eun-Young Seo
- 1 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea
| | - In-Sook Cho
- 2 Rural Development Administration, National Institute of Horticultural and Herbal Science, 100 Jeollabuk-do, Korea
| | - Wen-Xing Hu
- 1 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea
| | - Jae-Yeong Han
- 1 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea
| | - Jung-Kyu Kim
- 1 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea
| | - Su Ryun Choi
- 3 Department of Horticulture, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea; and
| | - Young Pyo Lim
- 3 Department of Horticulture, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea; and
| | - John Hammond
- 4 Floral and Nursery Plants Research Unit, U.S. National Arboretum, U.S. Department of Agriculture Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - Hyoun-Sub Lim
- 1 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 305-764, Korea
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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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Sardaru P, Sinausía L, López‐González S, Zindovic J, Sánchez F, Ponz F. The apparent non-host resistance of Ethiopian mustard to a radish-infecting strain of Turnip mosaic virus is largely determined by the C-terminal region of the P3 viral protein. MOLECULAR PLANT PATHOLOGY 2018; 19:1984-1994. [PMID: 29517848 PMCID: PMC6638043 DOI: 10.1111/mpp.12674] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 05/22/2023]
Abstract
Two different isolates of Turnip mosaic virus (TuMV: UK 1 and JPN 1) belonging to different virus strains were tested on three different Brassica species, namely turnip (Brassica rapa L.), Indian mustard (Brassica juncea L.) and Ethiopian mustard (Brassica carinata A. Braun). Although all three hosts were readily infected by isolate UK 1, isolate JPN 1 was able to establish a visible systemic infection only in the first two. Ethiopian mustard plants showed no local or systemic symptoms, and no virus antigens could be detected by enzyme-linked immunosorbent assay (ELISA). Thus, this species looks like a non-host for JPN 1, an apparent situation of non-host resistance (NHR). Through an experimental approach involving chimeric viruses made by gene interchange between two infectious clones of both virus isolates, the genomic region encoding the C-terminal domain of viral protein P3 was found to bear the resistance determinant, excluding any involvement of the viral fusion proteins P3N-PIPO and P3N-ALT in the resistance. A further determinant refinement identified two adjacent positions (1099 and 1100 of the viral polyprotein) as the main determinants of resistance. Green fluorescent protein (GFP)-tagged viruses showed that the resistance of Ethiopian mustard to isolate JPN 1 is only apparent, as virus-induced fluorescence could be found in discrete areas of both inoculated and non-inoculated leaves. In comparison with other plant-virus combinations of extreme resistance, we propose that Ethiopian mustard shows an apparent NHR to TuMV JPN 1, but not complete immunity or extreme resistance.
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Affiliation(s)
- Papaiah Sardaru
- Centro de Biotecnología y Genómica de Plantas (UPM‐INIA), Campus Montegancedo28223 MadridSpain
- Present address:
Department of Virology, College of SciencesSri Venkateswara UniversityTirupati 517502India
| | - Laura Sinausía
- Centro de Biotecnología y Genómica de Plantas (UPM‐INIA), Campus Montegancedo28223 MadridSpain
- Present address:
Celgene Institute for Translational Research Europe, Parque Científico y Tecnológico Cartuja 93, Centro de Empresas Pabellón de Italia, C/. Isaac Newton, 441092 SevillaSpain
| | - Silvia López‐González
- Centro de Biotecnología y Genómica de Plantas (UPM‐INIA), Campus Montegancedo28223 MadridSpain
| | - Jelena Zindovic
- Centro de Biotecnología y Genómica de Plantas (UPM‐INIA), Campus Montegancedo28223 MadridSpain
- Present address:
On leave of absence from Biotechnical Faculty, University of Montenegro, Mihajla Lalica 181000 PodgoricaMontenegro
| | - Flora Sánchez
- Centro de Biotecnología y Genómica de Plantas (UPM‐INIA), Campus Montegancedo28223 MadridSpain
| | - Fernando Ponz
- Centro de Biotecnología y Genómica de Plantas (UPM‐INIA), Campus Montegancedo28223 MadridSpain
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Li X, Zhu T, Yin X, Zhang C, Chen J, Tian Y, Liu J. The genetic structure of Turnip mosaic virus population reveals the rapid expansion of a new emergent lineage in China. Virol J 2017; 14:165. [PMID: 28851396 PMCID: PMC5575871 DOI: 10.1186/s12985-017-0832-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/21/2017] [Indexed: 11/21/2022] Open
Abstract
Background Turnip mosaic virus (TuMV) is one of the most widespread and economically important virus infecting both crop and ornamental species of the family Brassicaceae. TuMV isolates can be classified to five phylogenetic lineages, basal-B, basal-BR, Asian-BR, world-B and Orchis. Results To understand the genetic structure of TuMV from radish in China, the 3′-terminal genome of 90 TuMV isolates were determined and analyzed with other available Chinese isolates. The results showed that the Chinese TuMV isolates from radish formed three groups: Asian-BR, basal-BR and world-B. More than half of these isolates (52.54%) were clustered to basal-BR group, and could be further divided into three sub-groups. The TuMV basal-BR isolates in the sub-groups I and II were genetically homologous with Japanese ones, while those in sub-group III formed a distinct lineage. Sub-populations of TuMV basal-BR II and III were new emergent and in a state of expansion. The Chinese TuMV radish populations were under negative selection. Gene flow between TuMV populations from Tai’an, Weifang and Changchun was frequent. Conclusions The genetic structure of Turnip mosaic virus population reveals the rapid expansion of a new emergent lineage in China.
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Affiliation(s)
- Xiangdong Li
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Tiansheng Zhu
- College of Plant Science and Technology, Tarimu University, Alar, 843300, China
| | - Xiao Yin
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Chengling Zhang
- Xuzhou Sweet Potato Research Center of Jiangsu, Suzhou, 221121, China
| | - Jia Chen
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yanping Tian
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Jinliang Liu
- College of Plant Sciences, Jilin University, Changchun, 130062, China.
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Complete Nucleotide Sequence of an Australian Isolate of Turnip mosaic virus before and after Seven Years of Serial Passaging. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01269-16. [PMID: 27856582 PMCID: PMC5114374 DOI: 10.1128/genomea.01269-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The complete genome sequence of an Australian isolate of Turnip mosaic virus was determined by Sanger sequencing. After seven years of serial passaging by mechanical inoculation, the isolate was resequenced by RNA sequencing (RNA-Seq). Eighteen single nucleotide polymorphisms were identified between the isolates. Both isolates had 96% identity to isolate AUST10.
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19
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First Genome Sequence of Wild Onion Symptomless Virus, a Novel Member of Potyvirus in the Turnip Mosaic Virus Phylogenetic Group. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00851-16. [PMID: 27540073 PMCID: PMC4991718 DOI: 10.1128/genomea.00851-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The nearly complete genome sequence of a new species of potyvirus was obtained from the symptomless wild onion (Allium sp.) in Turkey. This virus has less than 67% nucleotide sequence identities over the polyprotein to other known potyviruses. We propose the name wild onion symptomless virus for this novel potyvirus.
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20
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Zhu F, Sun Y, Wang Y, Pan H, Wang F, Zhang X, Zhang Y, Liu J. Molecular Characterization of the Complete Genome of Three Basal-BR Isolates of Turnip mosaic virus Infecting Raphanus sativus in China. Int J Mol Sci 2016; 17:E888. [PMID: 27271614 PMCID: PMC4926422 DOI: 10.3390/ijms17060888] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/16/2016] [Accepted: 05/27/2016] [Indexed: 11/23/2022] Open
Abstract
Turnip mosaic virus (TuMV) infects crops of plant species in the family Brassicaceae worldwide. TuMV isolates were clustered to five lineages corresponding to basal-B, basal-BR, Asian-BR, world-B and OMs. Here, we determined the complete genome sequences of three TuMV basal-BR isolates infecting radish from Shandong and Jilin Provinces in China. Their genomes were all composed of 9833 nucleotides, excluding the 3'-terminal poly(A) tail. They contained two open reading frames (ORFs), with the large one encoding a polyprotein of 3164 amino acids and the small overlapping ORF encoding a PIPO protein of 61 amino acids, which contained the typically conserved motifs found in members of the genus Potyvirus. In pairwise comparison with 30 other TuMV genome sequences, these three isolates shared their highest identities with isolates from Eurasian countries (Germany, Italy, Turkey and China). Recombination analysis showed that the three isolates in this study had no "clear" recombination. The analyses of conserved amino acids changed between groups showed that the codons in the TuMV out group (OGp) and OMs group were the same at three codon sites (852, 1006, 1548), and the other TuMV groups (basal-B, basal-BR, Asian-BR, world-B) were different. This pattern suggests that the codon in the OMs progenitor did not change but that in the other TuMV groups the progenitor sequence did change at divergence. Genetic diversity analyses indicate that the PIPO gene was under the highest selection pressure and the selection pressure on P3N-PIPO and P3 was almost the same. It suggests that most of the selection pressure on P3 was probably imposed through P3N-PIPO.
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Affiliation(s)
- Fuxiang Zhu
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Ying Sun
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Yan Wang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Hongyu Pan
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Fengting Wang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Xianghui Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Yanhua Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Jinliang Liu
- College of Plant Sciences, Jilin University, Changchun 130062, China.
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21
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Han JY, Chung J, Kim J, Seo EY, Kilcrease JP, Bauchan GR, Lim S, Hammond J, Lim HS. Comparison of helper component-protease RNA silencing suppression activity, subcellular localization, and aggregation of three Korean isolates of Turnip mosaic virus. Virus Genes 2016; 52:592-6. [DOI: 10.1007/s11262-016-1330-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/29/2016] [Indexed: 11/29/2022]
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Sánchez F, Manrique P, Mansilla C, Lunello P, Wang X, Rodrigo G, López-González S, Jenner C, González-Melendi P, Elena SF, Walsh J, Ponz F. Viral Strain-Specific Differential Alterations in Arabidopsis Developmental Patterns. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1304-1315. [PMID: 26646245 DOI: 10.1094/mpmi-05-15-0111-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Turnip mosaic virus (TuMV) infections affect many Arabidopsis developmental traits. This paper analyzes, at different levels, the development-related differential alterations induced by different strains of TuMV, represented by isolates UK 1 and JPN 1. The genomic sequence of JPN 1 TuMV isolate revealed highest divergence in the P1 and P3 viral cistrons, upon comparison with the UK 1 sequence. Infectious viral chimeras covering the whole viral genome uncovered the P3 cistron as a major viral determinant of development alterations, excluding the involvement of the PIPO open reading frame. However, constitutive transgenic expression of P3 in Arabidopsis did not induce developmental alterations nor modulate the strong effects induced by the transgenic RNA silencing suppressor HC-Pro from either strain. This highlights the importance of studying viral determinants within the context of actual viral infections. Transcriptomic and interactomic analyses at different stages of plant development revealed large differences in the number of genes affected by the different infections at medium infection times but no significant differences at very early times. Biological functions affected by UK 1 (the most severe strain) included mainly stress response and transport. Most cellular components affected cell-wall transport or metabolism. Hubs in the interactome were affected upon infection.
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Affiliation(s)
- Flora Sánchez
- 1 Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Pozuelo de Alarcón, Madrid, Spain
| | - Pilar Manrique
- 1 Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Pozuelo de Alarcón, Madrid, Spain
| | - Carmen Mansilla
- 1 Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Pozuelo de Alarcón, Madrid, Spain
| | - Pablo Lunello
- 1 Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Pozuelo de Alarcón, Madrid, Spain
| | - Xiaowu Wang
- 1 Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Pozuelo de Alarcón, Madrid, Spain
| | - Guillermo Rodrigo
- 2 Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain
| | - Silvia López-González
- 1 Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Pozuelo de Alarcón, Madrid, Spain
| | - Carol Jenner
- 3 University of Warwick, Wellesbourne, Warwick, U.K.; and
| | - Pablo González-Melendi
- 1 Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Pozuelo de Alarcón, Madrid, Spain
| | - Santiago F Elena
- 2 Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain
- 4 The Santa Fe Institute, Santa Fe, New Mexico, U.S.A
| | - John Walsh
- 3 University of Warwick, Wellesbourne, Warwick, U.K.; and
| | - Fernando Ponz
- 1 Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Pozuelo de Alarcón, Madrid, Spain
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Yasaka R, Ohba K, Schwinghamer MW, Fletcher J, Ochoa-Corona FM, Thomas JE, Ho SYW, Gibbs AJ, Ohshima K. Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand. J Gen Virol 2014; 96:701-713. [PMID: 25481753 DOI: 10.1099/jgv.0.000007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Turnip mosaic virus (TuMV) is a potyvirus that is transmitted by aphids and infects a wide range of plant species. We investigated the evolution of this pathogen by collecting 32 isolates of TuMV, mostly from Brassicaceae plants, in Australia and New Zealand. We performed a variety of sequence-based phylogenetic and population genetic analyses of the complete genomic sequences and of three non-recombinogenic regions of those sequences. The substitution rates, divergence times and phylogeographical patterns of the virus populations were estimated. Six inter- and seven intralineage recombination-type patterns were found in the genomes of the Australian and New Zealand isolates, and all were novel. Only one recombination-type pattern has been found in both countries. The Australian and New Zealand populations were genetically different, and were different from the European and Asian populations. Our Bayesian coalescent analyses, based on a combination of novel and published sequence data from three non-recombinogenic protein-encoding regions, showed that TuMV probably started to migrate from Europe to Australia and New Zealand more than 80 years ago, and that distinct populations arose as a result of evolutionary drivers such as recombination. The basal-B2 subpopulation in Australia and New Zealand seems to be older than those of the world-B2 and -B3 populations. To our knowledge, our study presents the first population genetic analysis of TuMV in Australia and New Zealand. We have shown that the time of migration of TuMV correlates well with the establishment of agriculture and migration of Europeans to these countries.
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Affiliation(s)
- Ryosuke Yasaka
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Kagoshima 890-0065, Japan
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
| | - Kiho Ohba
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
| | - Mark W Schwinghamer
- New South Wales Department of Primary Industries, Tamworth Agricultural Institute, 4 Marsden Park Road, Tamworth, NSW 2340, Australia
| | - John Fletcher
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch, New Zealand
| | - Francisco M Ochoa-Corona
- Investigation & Diagnostic Centre (IDC), Plant Health & Environment Laboratory (PHEL), Biosecurity New Zealand, Ministry of Agriculture & Forestry, 231 Morrin Road, St Johns, Auckland 1140, New Zealand
| | - John E Thomas
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Adrian J Gibbs
- Emeritus Faculty, Australian National University, ACT 2601, Australia
| | - Kazusato Ohshima
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Kagoshima 890-0065, Japan
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
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Recombination analysis of Maize dwarf mosaic virus (MDMV) in the Sugarcane mosaic virus (SCMV) subgroup of potyviruses. Virus Genes 2014; 50:79-86. [PMID: 25392089 DOI: 10.1007/s11262-014-1142-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/01/2014] [Indexed: 10/24/2022]
Abstract
Recombination among RNA viruses is a natural phenomenon that appears to have played a significant role in the species development and the evolution of many strains. It also has particular significance for the risk assessment of plants which have been genetically modified for disease resistance by incorporating viral sequences into their genomes. However, the exact recombination events taking place in viral genomes are not investigated in detail for many virus groups. In this analysis, different single-stranded positive-sense RNA potyviruses were compared using various in silico recombination detection methods and new recombination events in the Sugarcane mosaic virus (SCMV) subgroup were detected. For an extended in silico recombination analysis, two of the analyzed Maize dwarf mosaic virus full-length genomes were sequenced additionally during this work. These results strengthen the evidence that recombination is a major driving force in virus evolution, and the emergence of new virus variants in the SCMV subgroup, paired with mutations, could generate viruses with altered biological properties. The intra- and interspecific homolog recombinations seem to be a general trait in this virus group, causing little or no changes to the amino acid of the progenies. However, we found a few breakpoints between the members of SCMV subgroup and the weed-infecting distant relatives, but only a few methods of the RDP3 package predicted these events with low significance level.
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Abstract
The Potyvirus is the largest genus of the largest family of plant RNA viruses, the Potyviridae. The potyviruses infect not only dicotyledonous but also monocotyledonous plants. The potyvirus phylogeny shows that the genus probably originated from a virus of monocotyledonous plants and that it first diverged approximately 7250 years ago in Southwest Eurasia or North Africa. Turnip mosaic virus (TuMV) belongs to the genus Potyvirus and infects a wide range of plant species, most from the family Brassicaceae. TuMV is most studied a potyvirus species for molecular evolution and the genetic structure of populations. The use of computer programs for better understanding of the evolution and the genetic structures of populations of potyviruses and TuMV are illustrated.
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26
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Seruga Musić M, Duc Nguyen H, Cerni S, Mamula Ð, Ohshima K, Skorić D. Multilocus sequence analysis of 'Candidatus Phytoplasma asteris' strain and the genome analysis of Turnip mosaic virus co-infecting oilseed rape. J Appl Microbiol 2014; 117:774-85. [PMID: 24916721 DOI: 10.1111/jam.12567] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/21/2014] [Accepted: 06/02/2014] [Indexed: 12/01/2022]
Abstract
AIM Molecular characterization of a pathogenic complex infecting winter oilseed rape (Brassica napus ssp. oleifera (DC.) Metzg.) plants showing typical rape phyllody symptoms along with some atypical changes. METHODS AND RESULTS Phytoplasma ('Candidatus Phytoplasma') presence was confirmed by PCR-RFLP and 16S rRNA gene sequencing. Phylogenetic analyses of phytoplasma amp, tufB, secY, groEL and ribosomal protein genes confirmed its affiliation to the 'Ca. P. asteris' species. However, in the amp gene encoding a specific protein crucial for insect transmission specificity, significant SNPs were found. Biological and serological tests revealed the co-infection with Turnip mosaic virus (TuMV). The phylogenetic analysis of full TuMV genome sequence, the first reported from the Balkans, classified it into the world-B phylogenetic lineage. CONCLUSIONS A pathogenic complex consisting of 'Ca. P. asteris' and TuMV found to co-infect oilseed rape plants for the first time was molecularly characterized. SIGNIFICANCE AND IMPACT OF THE STUDY Rape phyllody is a serious problem in rapeseed production. The molecular information from this first multi-gene analysis of 'Ca. P. asteris' strain associated with rape phyllody as well as the first report of the complete sequence of TuMV isolate from the Balkans is a starting point for understanding the disease complexity and management.
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Affiliation(s)
- M Seruga Musić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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27
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Sun BJ, Sun LY, Tugume AK, Adams MJ, Yang J, Xie LH, Chen JP. Selection pressure and founder effects constrain genetic variation in differentiated populations of soilborne bymovirus Wheat yellow mosaic virus (Potyviridae) in China. PHYTOPATHOLOGY 2013; 103:949-59. [PMID: 23550972 DOI: 10.1094/phyto-01-13-0013-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
To study the population genetic structure and forces driving the evolution of Wheat yellow mosaic virus (WYMV), the nucleotide sequences encoding the coat protein (CP) (297 sequences) or the genome-linked virion protein (VPg) (87 sequences) were determined from wheat plants growing at 11 different locations distributed in five provinces in China. There were close phylogenetic relationships between all sequences but clustering on the phylogenetic trees was congruent with their provenance, suggesting an origin-dependent population genetic structure. There were low levels of genetic diversity, ranging from 0.00035 ± 0.00019 to 0.01536 ± 0.00043 (CP), and 0.00086 ± 0.00039 to 0.00573 ± 0.00111 (VPg), indicating genetic stability or recent emergence of WYMV in China. The results may suggest that founder effects play a role in shaping the genetic structure of WYMV. Between-population diversity was consistently higher than within-population diversity, suggesting limited gene flow between subpopulations (average FST 0.6241 for the CP and 0.7981 for the VPg). Consistent amino acid substitutions correlated with the provenance of the sequences were observed at nine positions in the CP (but none in the VPg), indicating an advanced stage in population structuring. Strong negative (purifying) selection was implicated on both the CP and VPg but positive selection on a few codons in the CP, indicating an ongoing molecular adaptation.
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Affiliation(s)
- B-J Sun
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, MoA Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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28
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Zubareva IA, Vinogradova SV, Gribova TN, Monakhos SG, Skryabin KG, Ignatov AN. Genetic diversity of turnip mosaic virus and the mechanism of its transmission by Brassica seeds. DOKL BIOCHEM BIOPHYS 2013; 450:119-22. [DOI: 10.1134/s1607672913030034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Indexed: 11/23/2022]
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29
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Yin X, Zheng FQ, Tang W, Zhu QQ, Li XD, Zhang GM, Liu HT, Liu BS. Genetic structure of rice black-streaked dwarf virus populations in China. Arch Virol 2013; 158:2505-15. [DOI: 10.1007/s00705-013-1766-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/06/2013] [Indexed: 01/21/2023]
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30
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Nguyen HD, Tomitaka Y, Ho SYW, Duchêne S, Vetten HJ, Lesemann D, Walsh JA, Gibbs AJ, Ohshima K. Turnip mosaic potyvirus probably first spread to Eurasian brassica crops from wild orchids about 1000 years ago. PLoS One 2013; 8:e55336. [PMID: 23405136 PMCID: PMC3566190 DOI: 10.1371/journal.pone.0055336] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 12/20/2012] [Indexed: 11/19/2022] Open
Abstract
Turnip mosaic potyvirus (TuMV) is probably the most widespread and damaging virus that infects cultivated brassicas worldwide. Previous work has indicated that the virus originated in western Eurasia, with all of its closest relatives being viruses of monocotyledonous plants. Here we report that we have identified a sister lineage of TuMV-like potyviruses (TuMV-OM) from European orchids. The isolates of TuMV-OM form a monophyletic sister lineage to the brassica-infecting TuMVs (TuMV-BIs), and are nested within a clade of monocotyledon-infecting viruses. Extensive host-range tests showed that all of the TuMV-OMs are biologically similar to, but distinct from, TuMV-BIs and do not readily infect brassicas. We conclude that it is more likely that TuMV evolved from a TuMV-OM-like ancestor than the reverse. We did Bayesian coalescent analyses using a combination of novel and published sequence data from four TuMV genes [helper component-proteinase protein (HC-Pro), protein 3(P3), nuclear inclusion b protein (NIb), and coat protein (CP)]. Three genes (HC-Pro, P3, and NIb), but not the CP gene, gave results indicating that the TuMV-BI viruses diverged from TuMV-OMs around 1000 years ago. Only 150 years later, the four lineages of the present global population of TuMV-BIs diverged from one another. These dates are congruent with historical records of the spread of agriculture in Western Europe. From about 1200 years ago, there was a warming of the climate, and agriculture and the human population of the region greatly increased. Farming replaced woodlands, fostering viruses and aphid vectors that could invade the crops, which included several brassica cultivars and weeds. Later, starting 500 years ago, inter-continental maritime trade probably spread the TuMV-BIs to the remainder of the world.
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Affiliation(s)
- Huy D. Nguyen
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Yasuhiro Tomitaka
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Simon Y. W. Ho
- School of Biological Sciences, University of Sydney, Sydney, Australia
| | - Sebastián Duchêne
- School of Biological Sciences, University of Sydney, Sydney, Australia
| | - Heinrich-Josef Vetten
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Dietrich Lesemann
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - John A. Walsh
- Life Sciences, University of Warwick, Wellesbourne, Warwick, United Kingdom
| | - Adrian J. Gibbs
- Emeritus Faculty, Australian National University, Canberra, Australia
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
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31
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Nguyen HD, Tran HTN, Ohshima K. Genetic variation of the Turnip mosaic virus population of Vietnam: a case study of founder, regional and local influences. Virus Res 2012. [PMID: 23201192 DOI: 10.1016/j.virusres.2012.11.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Turnip mosaic virus (TuMV) is one of the most important viruses infecting a wide range of plant species, primarily from the family Brassicaceae. Thirty TuMV isolates were collected from Brassica and Raphanus plants in Vietnam during 2006-2008. Host reaction studies showed that many of the isolates belonged to Brassica/Raphanus (BR) host-infecting type. Sequence-based phylogenetic and population genetic analyses were made of the complete polyprotein gene sequences, and of four non-recombinogenic regions of those sequences (i.e. genes of the helper-component proteinase protein, protein 3, nuclear inclusion b protein and coat protein). These were used to assess the subpopulation differentiation and divergence between Vietnamese TuMV populations and those of nearby Asian countries. Nine inter- and intralineage recombination type patterns were identified in the genomes of the Vietnamese isolates, of which seven were novel. All the Vietnamese non-recombinant isolates fell into the world-B group of TuMV and clustered with Chinese isolates. The estimates of genetic differentiation and gene flow reveal that the TuMV populations of Vietnam, China and Japan are genetically linked but have clear local founder effects. This, the first population genetic study of a TuMV population in Southeast Asia, indicates the importance of such studies for providing the scientific basis of control strategies.
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Affiliation(s)
- Huy Duc Nguyen
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
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32
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Abstract
Lettuce is frequently attacked by several viruses causing disease epidemics and considerable yield losses along the Mediterranean basin. Aphids are key pests and the major vectors of plant viruses in lettuce fields. Lettuce mosaic virus (LMV) is probably the most important because it is seed-transmitted in addition to be transmissible by many aphid species that alight on the crop. Tomato spotted wilt virus (TSWV) is another virus that causes severe damage since the introduction of its major vector, the thrips Frankliniella occidentalis. In regions with heavy and humid soils, Lettuce Mirafiori big-vein virus (LMBVV) can also produce major yield losses.
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Affiliation(s)
- Aranzazu Moreno
- Department of Plant Protection, Instituto de Ciencias Agrarias, ICA-CSIC, Madrid, Spain
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33
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Zhang CL, Gao R, Wang J, Zhang GM, Li XD, Liu HT. Molecular variability of Tobacco vein banding mosaic virus populations. Virus Res 2011; 158:188-98. [PMID: 21497622 DOI: 10.1016/j.virusres.2011.03.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 03/28/2011] [Accepted: 03/31/2011] [Indexed: 10/18/2022]
Abstract
The incidence of Tobacco vein banding mosaic virus (TVBMV) on tobacco increases dramatically in China recently and it has caused great economic losses. To gain insights into the evolutionary mechanisms of TVBMV, a total of 40 TVBMV isolates were collected from different tobacco production regions in China and their genomic regions encoding helper component-proteinase (HC-Pro), the third protein (P3), the first 6K protein (6K1) and coat protein (CP) were sequenced. Phylogenetic analyses revealed that TVBMV isolates can be divided into two evolutionary divergent groups based on P3, the frame-shifting pipo and 6K1 genes, and three groups on HC-Pro and CP genes. The populations from most parts of mainland China (MC) showed frequent gene flow; those from Yunnan province in south western China always formed a separate group (YN) and also had frequent within-group gene flow. However, the gene flow between groups MC and YN was uncommon. Our results revealed that all the tested TVBMV genes were under negative selection and the HC-Pro gene was under the strongest constraints. Recombination events were identified in 13 of the 42 analyzed isolates. This study suggested that negative selection, gene flow and recombination were important evolutionary factors driving the genetic diversification of TVBMV.
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Affiliation(s)
- Cheng-Ling Zhang
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, No. 61, Daizong Street, Tai'an, Shandong 271018, People's Republic of China
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34
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Ohshima K, Akaishi S, Kajiyama H, Koga R, Gibbs AJ. Evolutionary trajectory of turnip mosaic virus populations adapting to a new host. J Gen Virol 2010; 91:788-801. [PMID: 19906944 DOI: 10.1099/vir.0.016055-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Little is known about how some plant viruses establish successful cross-species transmission whilst others do not; the genetic basis for adaptation is largely unknown. This study investigated the genetic changes that occurred using the progeny of an infectious clone, p35Tunos, derived from the turnip mosaic virus (TuMV) UK 1 isolate, which has a Brassica host type, but rarely infects Raphanus systemically and then only asymptomatically. The genetic trajectory leading to viral adaptation was studied in a TuMV isolate passaged in Nicotiana benthamiana (parental), Brassica rapa, the old (susceptible) host and Raphanus sativus, the new (almost insusceptible) host. Almost-complete consensus genomic sequences were obtained by RT-PCR of viral populations passaged up to 35 times together with 59 full sequences of 578,200 nt. There were significant differences in the nucleotide and encoded amino acid changes in the consensus genomes from the old and new hosts. Furthermore, a 3264 nt region corresponding to nt 3222-6485 of the UK 1 genome was cloned, and 269 clones from 23 populations were sequenced; this region covered 33 % of the genome and represented a total of 878,016 nt. The results showed that the nucleotide diversity and the non-synonymous/synonymous ratio of the populations from the new host were higher than those from the old host. An analysis of molecular variance showed significant differences among the populations from the old and new hosts. As far as is known, this is the first report comparing the evolutionary trajectory dynamics of plant virus populations in old and new hosts.
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Affiliation(s)
- Kazusato Ohshima
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan.
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35
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Abstract
The potyviruses are one of the two most speciose taxa of plant viruses. Our expanded knowledge of the breadth and depth of their diversity and its origins has depended greatly on the use of computing and the Internet in biological research and is reviewed here. We report a fully supported phylogeny based on gene sequence data for approximately half the named species. The phylogeny shows that the genus probably originated from a virus of monocotyledonous plants and that it first diverged approximately 7250 years ago in Southwest Eurasia or North Africa. The use of computer programs to better understand the structure and evolutionary trajectory of potyvirus populations is illustrated. The review concludes with recommendations for improving potyvirus nomenclature and the databasing of potyvirus information.
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Affiliation(s)
- Adrian Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 0200, Australia.
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36
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Seo JK, Ohshima K, Lee HG, Son M, Choi HS, Lee SH, Sohn SH, Kim KH. Molecular variability and genetic structure of the population of soybean mosaic virus based on the analysis of complete genome sequences. Virology 2009; 393:91-103. [PMID: 19716150 DOI: 10.1016/j.virol.2009.07.007] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 07/01/2009] [Accepted: 07/06/2009] [Indexed: 11/18/2022]
Abstract
The complete genomes of 30 Soybean mosaic virus (SMV) isolates and strains were sequenced in this study. Together with fourteen previously reported sequences, we analyzed the genetic structure of the SMV population. Analyses of genetic diversity showed that different genomic regions of SMV are under different evolutionary constraints and that there was no significant genetic differentiation between East Asian and North American populations of SMV. Phylogenetic analyses revealed a significant correlation between phylogeny of the cylindrical inclusion (CI) gene of SMV and SMV resistance gene 3 (Rsv3)-relating pathogenicity of SMV, suggesting CI might be a pathogenic determinant in Rsv3-mediated disease response. Interestingly, recombination analyses identified 19 'clear' recombination events in the SMV population. Furthermore, as several resistance-breaking strains were identified as recombinants, it appears that recombination might contribute to overcome host resistance in SMV-soybean pathosystem. Our finding suggests that recombination as well as mutation is an important evolutionary process in the genetic diversification of SMV population.
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Affiliation(s)
- Jang-Kyun Seo
- Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
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37
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Wang HY, Liu JL, Gao R, Chen J, Shao YH, Li XD. Complete genomic sequence analyses of Turnip mosaic virus basal-BR isolates from China. Virus Genes 2009; 38:421-8. [PMID: 19238532 DOI: 10.1007/s11262-009-0335-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2008] [Accepted: 02/04/2009] [Indexed: 11/28/2022]
Abstract
Isolates of Turnip mosaic virus (TuMV) are divided into four molecular lineages based on host range and geographical origins. Basal-BR is one of the four lineages and represented a new emergent lineage in East Asia. In one previous paper, we report the occurrence of basal-BR isolates in China. Here, we presented the first two complete genomic sequences of Chinese TuMV basal-BR isolates, WFLB06 and TANX2. The genomes of both isolates were 9833 nucleotides excluding the poly(A) tail, and had identical genomic structure. Most of their genes shared the highest identities with Japanese isolates. Recombination analysis showed that WFLB06 was an interlineage recombinant of basal-BR and Asian-BR parents, while TANX2 was an intralineage recombinant of basal-BR parents, and these two isolates represented two novel recombination patterns of TuMV. The ratio of nonsynonymous and synonymous substitution for the P1 gene of Chinese TuMV population was the highest and amounted to 12 times higher than that for the NIa-Pro gene, which implies that the selection pressure on the P1 gene was the highest among the genes present in the genome.
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Affiliation(s)
- Hong-Yan Wang
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
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38
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Ogawa T, Tomitaka Y, Nakagawa A, Ohshima K. Genetic structure of a population of Potato virus Y inducing potato tuber necrotic ringspot disease in Japan; comparison with North American and European populations. Virus Res 2007; 131:199-212. [PMID: 18029044 DOI: 10.1016/j.virusres.2007.09.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Revised: 09/03/2007] [Accepted: 09/03/2007] [Indexed: 10/22/2022]
Abstract
The structure of Potato virus Y (PVY) populations causing potato tuber necrotic ringspot disease (PTNRD) was analysed. The full-length sequences of the genomic RNAs of five geographically distinct isolates from Japan were determined. Recombination and phylogenetic analyses of European, North American and Japanese isolates of PVY showed that the world PVY population has three major lineages and two sublineages. Most recombinants were interlineage, and one isolate from Europe was identified as an intralineage recombinant. No recombinants were found among Japanese PTNRD isolates, which were most closely related to PTNRD isolates previously found in North America. Comparison of the within- and between population nucleotide diversities in the N lineage sequences from Japan, Europe and North America showed that Japanese population was distinct from the European and North American populations. The nucleotide sequences of the protein 1 and coat protein genes of a further 18 isolates were determined. One Japanese clade had radiated in a star burst as shown by its deviation from the neutral equilibrium model and its small nucleotide diversity. Our results suggest that PVY PTNRD was recently introduced into Japan more than once, and has expanded throughout Japan from founder populations.
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Affiliation(s)
- Tetsuji Ogawa
- Aino Potato Branch, Nagasaki Agriculture and Forestry Experiment Station, Nagasaki 854-0302, Japan
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39
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Kozubek E, Irzykowski W, Lehmann P. Genetic and molecular variability of a Turnip mosaic virus population from horseradish (Cochlearia armoracia L.). J Appl Genet 2007; 48:295-306. [PMID: 17666784 DOI: 10.1007/bf03195226] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Variability and genetic structure of a novel Turnip mosaic virus (TuMV) population from horseradish (Cochlearia armoracia L.) were examined. Over 60 horseradish plants were tested to identify a total of 28 TuMV isolates, constituting the Cochlearia ARmoracia (CAR) TuMV population. Two subgroups of the CAR TuMV isolates could be distinguished: subgroup N did not infect oilseed rape (Brassica napus var. oleifera) cv. Westar plants, while subgroup A infected these plants systemically. Two types of infection of oilseed rape plants were induced by inoculation with the CAR TuMV isolates: systemic mosaic infection and systemic necrotic lesions. The complete sequences of isolates CAR37 (subgroup N) and CAR37A (subgroup A) were determined and compared. The sequences of HC-Pro and CP genes of CAR37 and CAR37A and other isolates of TuMV from other countries were compared to provide some insight into their relatedness. CAR37A, initially regarded as a variant, proved to be very different from CAR37. Re-sequencing after repeated passages confirmed the genetic stability of both isolates.
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Affiliation(s)
- Edward Kozubek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznań, Poland
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40
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Pierrugues O, Guilbaud L, Fernandez-Delmond I, Fabre F, Tepfer M, Jacquemond M. Biological properties and relative fitness of inter-subgroup cucumber mosaic virus RNA 3 recombinants produced in vitro. J Gen Virol 2007; 88:2852-2861. [PMID: 17872540 DOI: 10.1099/vir.0.83077-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In vitro reverse transcription of a mixture of total RNA from plants infected with the I17F or R strains of cucumber mosaic virus (CMV), representative of subgroups IA and II, respectively, results in viral cDNA populations including rare recombinant RNA 3 molecules, some of which also have point mutations. The biological properties of 17 recombinants in the capsid gene or the 3' non-coding region of RNA 3 were evaluated when associated with I17F RNAs 1 and 2. Six viruses displayed deficiencies (non-viability, deficiencies for movement and/or replication, delayed infection, loss of aphid transmissibility). Nine induced symptoms close to those of I17F-CMV on tobacco and pepper plants. All recombinants bearing the movement protein (MP) of R-CMV and part or most of the capsid protein (CP) of I17F-CMV, as well as the recombinant created in vitro by exchanging the corresponding open reading frames, also induced filiformism on tobacco, but induced only faint symptoms on melon. Two recombinants induced atypically severe symptoms on both tobacco and pepper. Most of the recombinants generally accumulated to lower levels than the wild-type I17F strain in tobacco. Three recombinants, however, including one responsible for severe symptoms, accumulated to generally higher levels than I17F-CMV. When two of these were tested in co-infection experiments with I17F RNA 3, they proved to be poorly competitive, suggesting that they would be unlikely to emerge in the field.
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Affiliation(s)
- Olivier Pierrugues
- INRA, UR407, Station de Pathologie Végétale, BP 94, 84143 Montfavet cedex, France
| | - Laurent Guilbaud
- INRA, UR407, Station de Pathologie Végétale, BP 94, 84143 Montfavet cedex, France
| | | | - Frédéric Fabre
- INRA, UR407, Station de Pathologie Végétale, BP 94, 84143 Montfavet cedex, France
| | - Mark Tepfer
- Plant Virology Group, ICGEB Biosafety Outstation, Via Piovega 23, 31056 Ca' Tron di Roncade, Italy
- INRA, UR501, Laboratoire de Biologie Cellulaire, 78026 Versailles cedex, France
| | - Mireille Jacquemond
- INRA, UR407, Station de Pathologie Végétale, BP 94, 84143 Montfavet cedex, France
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41
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Zhang C, Gu H, Ghabrial SA. Molecular Characterization of Naturally Occurring RNA1 Recombinants of the Comovirus Bean pod mottle virus. PHYTOPATHOLOGY 2007; 97:1255-1262. [PMID: 18943683 DOI: 10.1094/phyto-97-10-1255] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT The Bean pod mottle virus, a member of the genus Comovirus, has a bipartite genome consisting of RNA1 and RNA2. We previously reported the occurrence in nature of two distinct subgroups of BPMV strains (subgroups I and II), as well as reassortants between the two subgroups. Here, we report on the isolation and molecular characterization of RNA1 recombinants from soybean plants infected with the partial diploid reassortant strain IL-Cb1, which induces very severe symptoms on soybean. cDNA cloning and sequencing of RNA1 from strain IL-Cb1 revealed the presence of chimeric and mosaic recombinant RNA1s. The full-length mosaic and chimeric recombinant RNA1s were infectious and induced mild symptoms on soybean. Although the recombinant RNA1 accumulated to high levels in the absence of wild-type RNA1, its accumulation level was low in mixed infections with wild-type RNA1. Recombinant RNA1 molecules with similar structures to the naturally occurring recombinant RNA1s were generated in soybean after four passages following inoculation with RNA1 transcripts derived from cDNAs of two distinct strains. This suggests that recombination events are frequent and that a recombination hot spot exists. Sequence analysis of the recombination region showed that it has AU-rich sequences characteristic of recombination hot spots.
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42
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Ha C, Revill P, Harding RM, Vu M, Dale JL. Identification and sequence analysis of potyviruses infecting crops in Vietnam. Arch Virol 2007; 153:45-60. [PMID: 17906829 DOI: 10.1007/s00705-007-1067-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Accepted: 08/27/2007] [Indexed: 10/22/2022]
Abstract
Fifty-two virus isolates from 13 distinct potyvirus species infecting crops in Vietnam were identified and the 3' region of each genome was sequenced. The viruses were: bean common mosaic virus (BCMV), potato virus Y (PVY), sugarcane mosaic virus (SCMV), sorghum mosaic virus (SrMV), chilli veinal mottle virus (ChiVMV), zucchini yellow mosaic virus (ZYMV), leek yellow stripe virus (LYMV), shallot yellow stripe virus (SYSV), onion yellow dwarf virus (OYDV), turnip mosaic virus (TuMV), dasheen mosaic virus (DsMV), sweet potato feathery mottle virus (SPFMV) and a novel potyvirus infecting chilli, tentatively named chilli ringspot virus (ChiRSV). With the exception of BCMV and PVY, this is first report of these viruses in Vietnam. Further, rabbit bell (Crotalaria anagyroides) and typhonia (Typhonium trilobatum) were identified as new natural hosts of the peanut stunt virus (PStV) strain of BCMV and of DsMV, respectively. Sequence and phylogenetic analyses of the entire CP-coding region revealed considerable variability in BCMV, SCMV, PVY, ZYMV and DsMV.
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Affiliation(s)
- C Ha
- Tropical Crops and Biocommodities Domain, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
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43
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Glasa M, Svoboda J, Nováková S. Analysis of the molecular and biological variability of zucchini yellow mosaic virus isolates from Slovakia and Czech Republic. Virus Genes 2007; 35:415-21. [PMID: 17497214 DOI: 10.1007/s11262-007-0101-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Accepted: 03/23/2007] [Indexed: 10/23/2022]
Abstract
The diversity of ZYMV isolates was analysed by the biological and molecular characterisation of 11 isolates sampled from cucumber, squash and zucchini between 2001 and 2006 in various localities of Slovakia and Czech Republic. Analysis of the molecular variability targeting three separate genomic regions of the ZYMV genome [P1, P3 and (Cter)NIb-(Nter)CP] revealed a remarkable low level of nucleotide variability between isolates, despite their temporal and spatial distinction. Phylogenetic analysis based on the 5'-terminal part of the CP gene highlighted the close relatedness of Slovak, Czech and other central European isolates. Low level of genetic diversity within central European ZYMV isolates is in contrast to the diversity observed for isolates from other geographical regions, in particular Asia. No evidence of recombination in the ZYMV genome was detected. Sequence comparison between aggressive and moderate ZYMV isolates revealed one amino acid difference in the N-terminal part of the P3 protein, potentially involved in the tolerance breaking.
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Affiliation(s)
- Miroslav Glasa
- Department of Plant Virology, Institute of Virology, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05, Bratislava, Slovakia.
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44
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Sánchez F, Rodríguez-Mateos M, Touriño A, Fresno J, Gómez-Campo C, Jenner CE, Walsh JA, Ponz F. Identification of new isolates of Turnip mosaic virus that cluster with less common viral strains. Arch Virol 2007; 152:1061-8. [PMID: 17347771 DOI: 10.1007/s00705-007-0943-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Accepted: 01/22/2007] [Indexed: 10/23/2022]
Abstract
Turnip mosaic virus (TuMV) was found infecting cultivated brassicas and wild and cultivated ornamental Brassicaceae plants in different regions of Spain. Five new TuMV isolates, originating from different host plant species (Brassica cretica, Brassica juncea, Brassica napus, Eruca vesicaria subsp. sativa and Sisymbrium orientale), have been identified. The nucleotide sequences of the coat protein (CP) genes of the five isolates were determined. Phylogenetic analysis of the CP sequences showed that the five isolates grouped into two different clusters. The three isolates from the central region of Spain clustered with a previously reported Pisum sativum isolate from southeastern Spain, whereas the other two isolates from the eastern region clustered with two Italian and two Greek isolates. Both clusters were genetically distinct and belonged to the multi-lineage group OBR. The OBR group contains mainly TuMV isolates from hosts other than Brassica spp. and Raphanus sativus and mostly originating from Mediterranean countries. These new sequences provide further phylogenetic resolution of the OBR group. Although new TuMV isolates have been found in Spain, they were not associated with any serious disease outbreaks.
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Affiliation(s)
- F Sánchez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Madrid, Spain
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45
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Ohshima K, Tomitaka Y, Wood JT, Minematsu Y, Kajiyama H, Tomimura K, Gibbs AJ. Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination. J Gen Virol 2007; 88:298-315. [PMID: 17170463 DOI: 10.1099/vir.0.82335-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Potyviruses have variable single-stranded RNA genomes and many show clear evidence of recombination. This report studied the distribution of recombination sites in the genomes of 92 isolates of the potyvirus Turnip mosaic virus (TuMV); 42 came from the international gene sequence databases and an additional 50 complete genomic sequences were generated from field samples collected in Europe and Asia. The sequences were examined for evidence of recombination using seven different sequence comparison methods and the exact position of each site was confirmed by sequence composition analysis. Recombination sites were found throughout the genomes, except in the small 6K1 protein gene, and only 24 of the genomes (26%) showed no evidence of recombination. Statistically significant clusters of recombination sites were found in the P1 gene and in the CI/6K2/VPg gene region. Most recombination sites were bordered by an upstream (5') region of GC-rich and downstream (3') region of AU-rich sequence of a similar length. Correlations between the presence and type of recombination site and provenance, host type and phylogenetic relationships are discussed, as is the role of recombination in TuMV evolution.
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Affiliation(s)
- Kazusato Ohshima
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Yasuhiro Tomitaka
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Jeffery T Wood
- Statistical Consulting Unit, Graduate School, Australian National University, Canberra, ACT 0200, Australia
| | - Yoshiteru Minematsu
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Hiromi Kajiyama
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Kenta Tomimura
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
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46
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Desbiez C, Costa C, Wipf-Scheibel C, Girard M, Lecoq H. Serological and molecular variability of watermelon mosaic virus (genus Potyvirus). Arch Virol 2007; 152:775-81. [PMID: 17219020 DOI: 10.1007/s00705-006-0899-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Accepted: 11/13/2006] [Indexed: 10/23/2022]
Abstract
Watermelon mosaic virus (WMV, genus Potyvirus) is very common in cucurbits worldwide, but its variability has been little studied. In France, where WMV has been known since 1974, unusually severe symptoms on zucchini squash have been found to be associated with WMV since 1999. We have developed serological and molecular tools to study WMV variability and the origin of severe strains. Eight monoclonal antibodies were obtained, characterized by epitope mapping, and used to assess the serological variability of 42 isolates from different countries. Sequence analysis based on the NIb-CP region revealed an important variability, with three distinct molecular groups. These analyses also suggested frequent intraspecific recombination in WMV.
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Affiliation(s)
- C Desbiez
- INRA, Station de Pathologie Végétale, Montfavet, France.
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47
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Tomitaka Y, Ohshima K. A phylogeographical study of the Turnip mosaic virus population in East Asia reveals an 'emergent' lineage in Japan. Mol Ecol 2007; 15:4437-57. [PMID: 17107475 PMCID: PMC7201873 DOI: 10.1111/j.1365-294x.2006.03094.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The genetic structure of populations of Turnip mosaic virus (TuMV) in East Asia was assessed by making host range and gene sequence comparisons of 118 isolates utilizing a population genetic approach. Most, but not all, isolates collected from Brassica plants in China infected only Brassica plants, whereas those from Japan infected both Brassica and Raphanus (BR) plants. Analyses of the positions of recombination sites in five regions of the genomes (one third of the full sequence) of the many recombinant isolates were fully congruent with the results of phylogenetic analysis, and at least one recombination type pattern was shared between Chinese and Japanese populations. One lineage of nonrecombinant isolates from the basal‐BR lineage was found in 2000 in Kyushu, Japan but none in China, and have since been found over the whole island. The sudden expansion of this basal‐BR population was strongly supported by calculations showing the deviations from the neutral equilibrium model for the individual geographical lineages with overall lack of nucleotide diversity, and by analysis of mismatch distribution. Our study shows that the recent Chinese and Japanese TuMV isolates are part of the same population but are discrete lineages.
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Affiliation(s)
- Yasuhiro Tomitaka
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
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48
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Moury B, Desbiez C, Jacquemond M, Lecoq H. Genetic diversity of plant virus populations: towards hypothesis testing in molecular epidemiology. Adv Virus Res 2006; 67:49-87. [PMID: 17027677 DOI: 10.1016/s0065-3527(06)67002-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- B Moury
- INRA Avignon, Station de Pathologie Végétale, Domaine St Maurice BP94 84143 Montfavet cedex, France
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49
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Hall G. Selective constraint and genetic differentiation in geographically distant barley yellow dwarf virus populations. J Gen Virol 2006; 87:3067-3075. [PMID: 16963766 DOI: 10.1099/vir.0.81834-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Numerous studies have documented molecular variability in plant virus populations, but few have assessed the relative contribution of natural selection and genetic drift in generating the observed pattern of diversity. To this end, gene function, environment and phylogenetic history were examined to observe the effect on genetic diversity and population structure of the PAV and PAS species of Barley yellow dwarf virus (family Luteoviridae). Three functional classes of gene were analysed: transcription-related (RdRp), structural (CP) and movement-related (MP). The results indicate that there were no inherent differences, in terms of total diversity or diversity at synonymous or non-synonymous nucleotide sites, between functional classes of genes or populations. Rather, selective constraints on a gene may be more or less relaxed depending on its function and the phylogenetic history of the population sampled. The CP of the PAS species, but not the PAV species, was differentiated genetically between regions. This is probably due to genetic drift, as there was no evidence that any gene deviated from a neutral model of evolution or is under positive selection. In general, the MP was under considerably less functional constraint than structural or replication-related proteins and four positively selected codon sites were identified. Mutations at these sites differentiate species and geographical subpopulations, so presumably they have aided the virus in adaptation to its host environment and contributed to intra- and interspecies diversification.
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Affiliation(s)
- Gerod Hall
- Cornell University, Department of Ecology and Evolutionary Biology, Corson Hall, Ithaca, NY 14853, USA
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50
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Niu QW, Lin SS, Reyes JL, Chen KC, Wu HW, Yeh SD, Chua NH. Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance. Nat Biotechnol 2006; 24:1420-8. [PMID: 17057702 DOI: 10.1038/nbt1255] [Citation(s) in RCA: 299] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Accepted: 09/25/2006] [Indexed: 12/31/2022]
Abstract
Plant microRNAs (miRNAs) regulate the abundance of target mRNAs by guiding their cleavage at the sequence complementary region. We have modified an Arabidopsis thaliana miR159 precursor to express artificial miRNAs (amiRNAs) targeting viral mRNA sequences encoding two gene silencing suppressors, P69 of turnip yellow mosaic virus (TYMV) and HC-Pro of turnip mosaic virus (TuMV). Production of these amiRNAs requires A. thaliana DICER-like protein 1. Transgenic A. thaliana plants expressing amiR-P69(159) and amiR-HC-Pro(159) are specifically resistant to TYMV and TuMV, respectively. Expression of amiR-TuCP(159) targeting TuMV coat protein sequences also confers specific TuMV resistance. However, transgenic plants that express both amiR-P69(159) and amiR-HC-Pro(159) from a dimeric pre-amiR-P69(159)/amiR-HC-Pro(159) transgene are resistant to both viruses. The virus resistance trait is displayed at the cell level and is hereditable. More important, the resistance trait is maintained at 15 degrees C, a temperature that compromises small interfering RNA-mediated gene silencing. The amiRNA-mediated approach should have broad applicability for engineering multiple virus resistance in crop plants.
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Affiliation(s)
- Qi-Wen Niu
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
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