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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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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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Komorowska B, Hasiów-Jaroszewska B, Elena SF. Evolving by deleting: patterns of molecular evolution of Apple stem pitting virus isolates from Poland. J Gen Virol 2019; 100:1442-1456. [PMID: 31424379 DOI: 10.1099/jgv.0.001290] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, 267 coat protein gene (CP) sequences from 48 Polish isolates of Apple stem pitting virus (ASPV) were determined. The genetic structure of the virus population was analysed and possible mechanisms of molecular evolution explored. We found evidence of recombination within the ASPV population and the presence of 17 ASPV molecular variants that differ in the length, number and arrangement of deletions in the CP. Population genetic analyses showed significant variation among isolates from pear and apple trees, between isolates from the same host species and, more interestingly, within isolates, supporting the existence of significant levels of variability within individual hosts, as expected by a quasispecies population structure. In addition, different tests support that selection might have been an important force driving diversification within isolates: positive selection was found acting upon certain amino acids. Phylogenetic analyses also showed that isolates did not classify according to the host species (pear or apple trees) but according to the pattern of deletions, suggesting a possible role for deletions during clade diversification.
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Affiliation(s)
- Beata Komorowska
- Research Institute of Horticulture, Department of Phytopathology, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - Beata Hasiów-Jaroszewska
- Department of Virology and Bacteriology, Institute of Plant Protection - National Research Institute, Wł. Węgorka 20, 60-318 Poznań, Poland
| | - Santiago F Elena
- The Santa Fe Institute, Santa Fe, NM 87501, USA.,Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, 46980 Paterna, València, Spain
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Parmar N, Thakur AK, Kumar P, Thakur PD, Bhardwaj SV. Molecular characterization of Turnip mosaic potyvirus ( TuMV)-infecting radish ( Raphanus sativus L.) crop in India. 3 Biotech 2017; 7:382. [PMID: 29134159 DOI: 10.1007/s13205-017-1016-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/24/2017] [Indexed: 11/30/2022] Open
Abstract
Nine isolates of Turnip mosaic potyvirus (TuMV)-infecting radish collected from different regions of Northern India were characterized. All isolates except for New Delhi and Rajasthan isolates resulted positive for TuMV in double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA). RNA was isolated from leaves of infected plants and used in reverse transcriptase-polymerase chain reaction (RT-PCR) with TuMV coat protein (CP) gene-specific primers. Viral amplicons of expected 1000 bp size were obtained, which were further subjected to cloning and sequencing. CP gene of all the seven isolates was 867 bp long, encoding 288 amino acid residues. Percent homology of CP gene of all the Indian isolates among themselves and with other TuMV isolates retrieved from NCBI was in the range of 87-99 and 92-100% at nucleotide and amino acid levels, respectively. Phylogenetic analysis based upon CP gene nucleotide and amino acid sequences with other TuMV isolates reported from across the globe using unweighted pair group method with arithmetic mean (UPGMA) inferred classification of test isolates into basal-BR group due to their occurrence nearest to the TuMV isolates belonging to the basal-BR group. Information generated about the characteristic features of TuMV and geographical distribution of particular virus genotype-infecting radish crop will provide a platform for formulating disease resistance strategies.
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Affiliation(s)
- Nehanjali Parmar
- Dr. Y.S. Parmar University of Horticulture and Forestry, Nauni, Solan, HP 173 230 India
| | - Ajay Kumar Thakur
- ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur, Rajasthan 321 303 India
| | - Pardeep Kumar
- Dr. Y.S. Parmar University of Horticulture and Forestry, Nauni, Solan, HP 173 230 India
| | - P D Thakur
- Dr. Y.S. Parmar University of Horticulture and Forestry, Nauni, Solan, HP 173 230 India
| | - Sat Vrat Bhardwaj
- Dr. Y.S. Parmar University of Horticulture and Forestry, Nauni, Solan, HP 173 230 India
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