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Song Z, Seo EY, Hu WX, Kim JK, Kang JS, Lee SE, Hammond J, Lim HS. Evaluation of a Series of Turnip Mosaic Virus Chimeric Clones Reveals Two Amino Acid Sites Critical for Systemic Infection in Chinese Cabbage. PHYTOPATHOLOGY 2023; 113:2006-2013. [PMID: 37260102 DOI: 10.1094/phyto-01-23-0013-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Two infectious clones of turnip mosaic virus (TuMV), pKBC-1 and pKBC-8, with differential infectivity in Chinese cabbage (Brassica rapa subsp. pekinensis), were obtained. Both infected Nicotiana benthamiana systemically, inducing similar symptoms, whereas only virus KBC-8 infected Chinese cabbage systemically. To identify the determinants affecting infectivity on Chinese cabbage, chimeric clones were constructed by restriction fragment exchange between the parental clones and tested on several Chinese cabbage cultivars. Chimeric clones p1N8C and p8N1C demonstrated that the C-terminal portion of the polyprotein determines systemic infection of Chinese cabbage despite only three amino acid differences in this region, in the cylindrical inclusion (CI), viral protein genome-linked (VPg), and coat protein (CP). A second pair of hybrid constructs, pHindIII-1N8C and pHindIII-8N1C, failed to infect cultivars CR Victory and Jinseonnorang systemically, yet pHindIII-1N8C caused hypersensitive response-like lesions on inoculated leaves of these cultivars, and could systemically infect cultivars CR Chusarang and Jeongsang; this suggests that R genes effective against TuMV may exist in the first two cultivars but not the latter two. Constructs with single amino acid changes in both VPg (K2045E) and CP (Y3095H) failed to infect Chinese cabbage, implying that at least one of these two amino acid substitutions is essential for successful infection on Chinese cabbage. Successful infection by mutant KBC-8-CP-H and delayed infection with mutant HJY1-VPg-E following mutation or reversion suggested that VPg (2045K) is the residue required for infection of Chinese cabbage and involved in the interaction between VPg and eukaryotic initiation factor eIF(iso)4E, confirmed by yeast two-hybrid assay.
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Affiliation(s)
- Zhengxing Song
- Department of Smart Agriculture Systems, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Eun-Young Seo
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Wen-Xing Hu
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Jung-Kyu Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jun-Seong Kang
- Department of Smart Agriculture Systems, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Seung-Eun Lee
- Department of Smart Agriculture Systems, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - John Hammond
- U.S. Department of Agriculture-Agricultural Research Service, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Beltsville, MD 20705
| | - Hyoun-Sub Lim
- Department of Smart Agriculture Systems, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
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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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Song ZX, Seo EY, Hu WX, Jeong JH, Moon JS, Kim KH, Eom WS, Cho IS, Hammond J, Lim HS. Construction of full-length infectious cDNA clones of two Korean isolates of turnip mosaic virus breaking resistance in Brassica napus. Arch Virol 2022; 167:1157-1162. [PMID: 35258648 DOI: 10.1007/s00705-022-05381-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/23/2021] [Indexed: 11/02/2022]
Abstract
In this work, two new turnip mosaic virus (TuMV) strains (Canola-12 and Canola-14) overcoming resistance in canola (Brassica napus) were isolated from a B. napus sample that showed typical TuMV-like symptoms and was collected in the city of Gimcheon, South Korea, in 2020. The complete genome sequence was determined and an infectious clone was made for each isolate. Phylogenetic analysis indicated that the strains isolated from canola belonged to the World-B group. Both infectious clones, which used 35S and T7 promoters to drive expression, induced systemic symptoms in Nicotiana benthamiana and B. napus. To our knowledge, this is the first report of TuMV infecting B. napus in South Korea.
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Affiliation(s)
- Zheng-Xing Song
- Department of Smart Agriculture Systems, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Eun-Young Seo
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Wen-Xing Hu
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jong-Hyeon Jeong
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jae Sun Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Kang-Hee Kim
- Department of Smart Agriculture Systems, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Won-Seob Eom
- Department of Smart Agriculture Systems, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - In-Sook Cho
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea.
| | - John Hammond
- United States Department of Agriculture-Agricultural Research Service, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Beltsville, MD, 20705, USA.
| | - Hyoun-Sub Lim
- Department of Smart Agriculture Systems, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea. .,Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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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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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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6
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Ágoston J, Almási A, Salánki K, Palkovics L. Genetic Diversity of Potyviruses Associated with Tulip Breaking Syndrome. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1807. [PMID: 33352796 PMCID: PMC7766433 DOI: 10.3390/plants9121807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/12/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022]
Abstract
Tulip breaking is economically the most important viral disease of modern-day tulip growing. It is characterized by irregular flame and feather-like patterns in the flowers and mosaic on the foliage. Thirty-two leaf samples were collected from cultivated tulip plants showing tulip breaking syndrome from Hungary in 2017 and 2018. Virus identification was performed by serological (ELISA) and molecular (RT-PCR) methods. All samples proved to be infected with a potyvirus and evidence was provided that three potyvirus species could be identified in the samples: Lily mottle virus (LMoV), Tulip breaking virus (TBV) and Rembrandt tulip-breaking virus (ReTBV). Recombination prediction accomplished with Recombination Detection Program (RDP) v4.98 revealed potential intraspecies recombination in the case of TBV and LMoV. Phylogenetic analyses of the coat protein (CP) regions proved the monophyletic origin of these viruses and verified them as three different species according to current International Committee on Taxonomy of Viruses (ICTV) species demarcation criteria. Based on these results, we analyzed taxonomic relations concerning potyviruses associated with tulip breaking syndrome. We propose the elevation of ReTBV to species level, and emergence of two new subgroups in ReTBV.
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Affiliation(s)
- János Ágoston
- Department of Plant Pathology, Faculty of Horticultural Science, Szent István University, 1118 Budapest, Hungary;
- Department of Agriculture, Faculty of Horticulture and Rural Development, John von Neumann University, 6000 Kecskemét, Hungary
| | - Asztéria Almási
- Plant Protection Institute, Centre for Agricultural Research, 1022 Budapest, Hungary; (A.A.); (K.S.)
| | - Katalin Salánki
- Plant Protection Institute, Centre for Agricultural Research, 1022 Budapest, Hungary; (A.A.); (K.S.)
| | - László Palkovics
- Department of Plant Pathology, Faculty of Horticultural Science, Szent István University, 1118 Budapest, Hungary;
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7
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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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9
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Pepper veinal mottle virus in Japan is closely related to isolates from other Asian countries, but more distantly to most of those from Africa. Virus Genes 2019; 55:347-355. [PMID: 30895438 DOI: 10.1007/s11262-019-01656-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/11/2019] [Indexed: 10/27/2022]
Abstract
Pepper veinal mottle virus (PVMV) is known to infect chilli pepper and belongs to the Chilli veinal mottle virus phylogroup of potyviruses. PVMV has recently appeared in Japan. In this study, we report six complete genomic sequences of PVMV isolates from chilli pepper (i.e. Capsicum annuum) in Okinawa Islands in Japan, and we determined the evolutionary relationships between Japanese isolates and the isolates reported earlier from African and Asian countries. Complete genomic sequences of the six Japanese PVMV isolates were 9760 nucleotides in length, excluding the nucleotide primer sequences used for amplifying 5' end of the genomes. The major findings of this study are as follows: (1) all the Japanese isolates of PVMV have similar biological and molecular characteristics, indicating the presence of only one population in Japan; (2) there are at least three major phylogenetic groups of PVMV worldwide; (3) PVMV probably originated in East Africa; and (4) all the Asian isolates are closely related to the Ghanaian isolate.
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10
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Adachi S, Honma T, Yasaka R, Ohshima K, Tokuda M. Effects of infection by Turnip mosaic virus on the population growth of generalist and specialist aphid vectors on turnip plants. PLoS One 2018; 13:e0200784. [PMID: 30016354 PMCID: PMC6049944 DOI: 10.1371/journal.pone.0200784] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 07/03/2018] [Indexed: 11/18/2022] Open
Abstract
Recent studies have revealed that relationships between plant pathogens and their vectors differ depending on species, strains and associated host plants. Turnip mosaic virus (TuMV) is one of the most important plant viruses worldwide and is transmitted by at least 89 aphid species in a non-persistent manner. TuMV is fundamentally divided into six phylogenetic groups; among which Asian-BR, basal-BR and world-B groups are known to occur in Japan. In Kyushu Japan, basal-BR has invaded approximately 2000 and immediately replaced the predominant world-B virus group. To clarify the relationships between TuMV and vector aphids, we examined the effects of the TuMV phylogenetic group on the population growth of aphid vectors in turnip plants. The population growth of a generalist aphid, Myzus persicae, was not significantly different between non-infected and TuMV-infected treatments. The population growth of a specialist aphid, Lipaphis erysimi, was higher in TuMV-infected plants than non-infected ones. Similar results were obtained in experiments using world-B and basal-BR groups of TuMV. Therefore, we conclude that L. erysimi is more mutualistic with TuMV than M. persicae, and differences in TuMV phylogenetic groups do not affect the growth of aphid vectors on turnip plants.
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Affiliation(s)
- Shuhei Adachi
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Laboratory of Systems Ecology, Faculty of Agriculture, Saga University, Saga, Japan
- * E-mail:
| | - Tomoki Honma
- Laboratory of Systems Ecology, Faculty of Agriculture, Saga University, Saga, Japan
| | - Ryosuke Yasaka
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga, Japan
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga, Japan
| | - Makoto Tokuda
- Laboratory of Systems Ecology, Faculty of Agriculture, Saga University, Saga, Japan
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Picard C, Dallot S, Brunker K, Berthier K, Roumagnac P, Soubeyrand S, Jacquot E, Thébaud G. Exploiting Genetic Information to Trace Plant Virus Dispersal in Landscapes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:139-160. [PMID: 28525307 DOI: 10.1146/annurev-phyto-080516-035616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.
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Affiliation(s)
- Coralie Picard
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Sylvie Dallot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | | | - Philippe Roumagnac
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | | | - Emmanuel Jacquot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Gaël Thébaud
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
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Yasaka R, Fukagawa H, Ikematsu M, Soda H, Korkmaz S, Golnaraghi A, Katis N, Ho SYW, Gibbs AJ, Ohshima K. The Timescale of Emergence and Spread of Turnip Mosaic Potyvirus. Sci Rep 2017; 7:4240. [PMID: 28652582 PMCID: PMC5484681 DOI: 10.1038/s41598-017-01934-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/05/2017] [Indexed: 11/16/2022] Open
Abstract
Plant viruses have important global impacts on crops, and identifying their centre and date of emergence is important for planning control measures. Turnip mosaic virus (TuMV) is a member of the genus Potyvirus in the family Potyviridae and is a major worldwide pathogen of brassica crops. For two decades, we have collected TuMV isolates, mostly from brassicas, in Turkey and neighbouring countries. This region is thought to be the centre of emergence of this virus. We determined the genomic sequences of 179 of these isolates and used these to estimate the timescale of the spread of this virus. Our Bayesian coalescent analyses used synonymous sites from a total of 417 novel and published whole-genome sequences. We conclude that TuMV probably originated from a virus of wild orchids in Germany and, while adapting to wild and domestic brassicas, spread via Southern Europe to Asia Minor no more than 700 years ago. The population of basal-B group TuMVs in Asia Minor is older than all other populations of this virus, including a newly discovered population in Iran. The timescale of the spread of TuMV correlates well with the establishment of agriculture in these countries.
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Affiliation(s)
- Ryosuke Yasaka
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga, 840-8502, Japan.,The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Kagoshima, 890-0065, Japan
| | - Hirofumi Fukagawa
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga, 840-8502, Japan
| | - Mutsumi Ikematsu
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga, 840-8502, Japan
| | - Hiroko Soda
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga, 840-8502, Japan
| | - Savas Korkmaz
- Department of Plant Protection, Faculty of Agriculture, University of Canakkale Onsekiz Mart, Canakkale, Turkey
| | - Alireza Golnaraghi
- Department of Plant Protection, College of Agriculture and Natural Resources, Science and Research Branch, Islamic Azad University, Tehran, P.O. Box 14515-775, Iran
| | - Nikolaos Katis
- Plant Pathology Laboratory, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, 540 06, Greece
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Adrian J Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga, 840-8502, Japan. .,The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Kagoshima, 890-0065, Japan.
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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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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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15
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Ohshima K, Matsumoto K, Yasaka R, Nishiyama M, Soejima K, Korkmaz S, Ho SY, Gibbs AJ, Takeshita M. Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: Extra clues from its segmented genome. Virology 2016; 487:188-97. [DOI: 10.1016/j.virol.2015.09.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 08/29/2015] [Accepted: 09/28/2015] [Indexed: 01/17/2023]
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First report of Turnip mosaic virus occurrence in cole crops (Brssica spp) from Arunachal Pradesh, India. Virusdisease 2015; 26:211-3. [PMID: 26396991 DOI: 10.1007/s13337-015-0272-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 08/03/2015] [Indexed: 10/23/2022] Open
Abstract
The occurrence of Turnip mosaic virus (TuMV) in cole crops (Brassica spp) grown in Basar, Arunachal Pradesh, India was confirmed by symptomatology, transmission electron microscopy, reverse transcription-polymerase chain reaction and partial characterization of cytoplasmic inclusion protein and coat protein (CP) domains. Phylogenetic analysis of the partial CP sequences of the new TuMV isolates from Indian mustard (AR-IndM), broad leaved mustard (AR-BrLM) and broccoli (AR-Broc) revealed their closest relationship with members of the World-B genogroup of TuMV. This is the first molecular evidence of TuMV infection in Brassica spp from India.
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17
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Molecular Genetic Analysis and Evolution of Segment 7 in Rice Black-Streaked Dwarf Virus in China. PLoS One 2015; 10:e0131410. [PMID: 26121638 PMCID: PMC4488072 DOI: 10.1371/journal.pone.0131410] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/01/2015] [Indexed: 12/03/2022] Open
Abstract
Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease or rice black-streaked dwarf disease and can lead to severe yield losses in maize and rice. To analyse RBSDV evolution, codon usage bias and genetic structure were investigated in 111 maize and rice RBSDV isolates from eight geographic locations in 2013 and 2014. The linear dsRNA S7 is A+U rich, with overall codon usage biased toward codons ending with A (A3s, S7-1: 32.64%, S7-2: 29.95%) or U (U3s, S7-1: 44.18%, S7-2: 46.06%). Effective number of codons (Nc) values of 45.63 in S7-1 (the first open reading frame of S7) and 39.96 in S7-2 (the second open reading frame of S7) indicate low degrees of RBSDV-S7 codon usage bias, likely driven by mutational bias regardless of year, host, or geographical origin. Twelve optimal codons were detected in S7. The nucleotide diversity (π) of S7 sequences in 2013 isolates (0.0307) was significantly higher than in 2014 isolates (0.0244, P = 0.0226). The nucleotide diversity (π) of S7 sequences in isolates from Jinan (0.0391) was higher than that from the other seven locations (P < 0.01). Only one S7 recombinant was detected in Baoding. RBSDV isolates could be phylogenetically classified into two groups according to S7 sequences, and further classified into two subgroups. S7-1 and S7-2 were under negative and purifying selection, with respective Ka/Ks ratios of 0.0179 and 0.0537. These RBSDV populations were expanding (P < 0.01) as indicated by negative values for Tajima's D, Fu and Li's D, and Fu and Li's F. Genetic differentiation was detected in six RBSDV subpopulations (P < 0.05). Absolute Fst (0.0790) and Nm (65.12) between 2013 and 2014, absolute Fst (0.1720) and Nm (38.49) between maize and rice, and absolute Fst values of 0.0085-0.3069 and Nm values of 0.56-29.61 among these eight geographic locations revealed frequent gene flow between subpopulations. Gene flow between 2013 and 2014 was the most frequent.
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18
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Marzano SYL, Hobbs HA, Nelson BD, Hartman GL, Eastburn DM, McCoppin NK, Domier LL. Transfection of Sclerotinia sclerotiorum with in vitro transcripts of a naturally occurring interspecific recombinant of Sclerotinia sclerotiorum hypovirus 2 significantly reduces virulence of the fungus. J Virol 2015; 89:5060-71. [PMID: 25694604 PMCID: PMC4403457 DOI: 10.1128/jvi.03199-14] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/16/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A recombinant strain of Sclerotinia sclerotiorum hypovirus 2 (SsHV2) was identified from a North American Sclerotinia sclerotiorum isolate (328) from lettuce (Lactuca sativa L.) by high-throughput sequencing of total RNA. The 5'- and 3'-terminal regions of the genome were determined by rapid amplification of cDNA ends. The assembled nucleotide sequence was up to 92% identical to two recently reported SsHV2 strains but contained a deletion near its 5' terminus of more than 1.2 kb relative to the other SsHV2 strains and an insertion of 524 nucleotides (nt) that was distantly related to Valsa ceratosperma hypovirus 1. This suggests that the new isolate is a heterologous recombinant of SsHV2 with a yet-uncharacterized hypovirus. We named the new strain Sclerotinia sclerotiorum hypovirus 2 Lactuca (SsHV2L) and deposited the sequence in GenBank with accession number KF898354. Sclerotinia sclerotiorum isolate 328 was coinfected with a strain of Sclerotinia sclerotiorum endornavirus 1 and was debilitated compared to cultures of the same isolate that had been cured of virus infection by cycloheximide treatment and hyphal tipping. To determine whether SsHV2L alone could induce hypovirulence in S. sclerotiorum, a full-length cDNA of the 14,538-nt viral genome was cloned. Transcripts corresponding to the viral RNA were synthesized in vitro and transfected into a virus-free isolate of S. sclerotiorum, DK3. Isolate DK3 transfected with SsHV2L was hypovirulent on soybean and lettuce and exhibited delayed maturation of sclerotia relative to virus-free DK3, completing Koch's postulates for the association of hypovirulence with SsHV2L. IMPORTANCE A cosmopolitan fungus, Sclerotinia sclerotiorum infects more than 400 plant species and causes a plant disease known as white mold that produces significant yield losses in major crops annually. Mycoviruses have been used successfully to reduce losses caused by fungal plant pathogens, but definitive relationships between hypovirus infections and hypovirulence in S. sclerotiorum were lacking. By establishing a cause-and-effect relationship between Sclerotinia sclerotiorum hypovirus Lactuca (SsHV2L) infection and the reduction in host virulence, we showed direct evidence that hypoviruses have the potential to reduce the severity of white mold disease. In addition to intraspecific recombination, this study showed that recent interspecific recombination is an important factor shaping viral genomes. The construction of an infectious clone of SsHV2L allows future exploration of the interactions between SsHV2L and S. sclerotiorum, a widespread fungal pathogen of plants.
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Affiliation(s)
| | - Houston A Hobbs
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Berlin D Nelson
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Glen L Hartman
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA United States Department of Agriculture/Agricultural Research Service, Urbana, Illinois, USA
| | - Darin M Eastburn
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Nancy K McCoppin
- United States Department of Agriculture/Agricultural Research Service, Urbana, Illinois, USA
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA United States Department of Agriculture/Agricultural Research Service, Urbana, Illinois, USA
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19
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Thekke-Veetil T, Polashock JJ, Marn MV, Plesko IM, Schilder AC, Keller KE, Martin RR, Tzanetakis IE. Population structure of blueberry mosaic associated virus: Evidence of reassortment in geographically distinct isolates. Virus Res 2015; 201:79-84. [PMID: 25733053 DOI: 10.1016/j.virusres.2015.02.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 02/19/2015] [Accepted: 02/22/2015] [Indexed: 10/23/2022]
Abstract
The population structure of blueberry mosaic associated virus (BlMaV), a putative member of the family Ophioviridae, was examined using 61 isolates collected from North America and Slovenia. The studied isolates displayed low diversity in the movement and nucleocapsid proteins and low ratios of non-synonymous to synonymous nucleotide substitutions, indicative of strong purifying selection. Phylogenetic analyses revealed grouping primarily based on geography with some isolates deviating from this rule. Phylogenetic incongruence in the two regions, coupled with detection of reassortment events, indicated the possible role of genetic exchange in the evolution of BlMaV.
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Affiliation(s)
- Thanuja Thekke-Veetil
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, United States
| | | | - Mojca V Marn
- Agricultural Institute of Slovenia, Hacquetova 17, Ljubljana, Slovenia
| | - Irena M Plesko
- Agricultural Institute of Slovenia, Hacquetova 17, Ljubljana, Slovenia
| | - Annemiek C Schilder
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | | | | | - Ioannis E Tzanetakis
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, United States.
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20
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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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21
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Zhou GC, Wu XY, Zhang YM, Wu P, Wu XZ, Liu LW, Wang Q, Hang YY, Yang JY, Shao ZQ, Wang B, Chen JQ. A genomic survey of thirty soybean-infecting bean common mosaic virus (BCMV) isolates from China pointed BCMV as a potential threat to soybean production. Virus Res 2014; 191:125-33. [PMID: 25107622 DOI: 10.1016/j.virusres.2014.07.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/23/2014] [Accepted: 07/26/2014] [Indexed: 10/24/2022]
Abstract
Widely known as a severe pathogen of bean plants, the bean common mosaic virus (BCMV) has been reported to infect soybeans only sporadically and the involved strains were all found in China regions. To explore variations among soybean-infecting BCMV strains, hundreds of soybean mosaic leave samples were collected throughout China, with a total of 30 BCMV isolates detected and their genomes sequenced. These newly obtained genomes, together with 16 other BCMV genomes available in GenBank were examined from multiple aspects to characterize BCMV evolutionary processes. Phylogenetic analysis showed that both soybean-infecting BCMVs (group I) and peanut-infecting BCMVs (group II) are distantly related to other BCMVs, suggesting ancestral differentiation and host adaptation. Genetic variation analysis showed that P1, P3 and 6K2 genes and the beginning portion of CP gene showed higher levels of variation relative to other genes. Moreover, selection analyses further confirmed that a number of sites within the P1 and P3 genes have suffered positive selection. These obtained BCMV sequences also exhibit high recombination frequencies, indicating a more dynamic evolutionary history. Finally, 12 different soybean cultivars were challenged with two BCMV isolates (DXH015 and HZZB011), with most of the cultivars successfully infected. These findings suggest that BCMV is indeed a potential threat to soybean production.
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Affiliation(s)
- Guang-Can Zhou
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Xiao-Yi Wu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yan-Mei Zhang
- Jiangsu Province & Chinese Academy of Science, Institute of Botany, Nanjing 210014, China
| | - Ping Wu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Xun-Zong Wu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Li-Wei Liu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Qiang Wang
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yue-Yu Hang
- Jiangsu Province & Chinese Academy of Science, Institute of Botany, Nanjing 210014, China
| | - Jia-Yin Yang
- Crop Research & Development Center, Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an 223001, China
| | - Zhu-Qing Shao
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China.
| | - Bin Wang
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China.
| | - Jian-Qun Chen
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China.
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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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Genetic variation in potato virus M isolates infecting pepino (Solanum muricatum) in China. Arch Virol 2014; 159:3197-210. [PMID: 25233939 DOI: 10.1007/s00705-014-2180-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 07/15/2014] [Indexed: 02/05/2023]
Abstract
Potato virus M (PVM, genus Carlavirus, family Betaflexviridae) is considered to be one of most economically important pathogens of pepino in China. However, the details and the mechanisms underlying PVM evolution are unknown. In this study, we determined and analyzed 40 TGB 1 gene sequences, 67 TGB 2 and TGB 3 gene sequences, and 88 CP and NABP gene sequences from viruses isolated from 19 samples of pepino (Solanum muricatum) and one sample of tomato (S. lycopersicum) collected from different areas of China. Recombination analysis identified only one clear recombinant in the TGB2-TGB3-CP region, but no recombinants were detected for each of the five individual genes. Phylogenetic analysis showed that all PVM isolates could be divided into at least two lineages in trees derived from the TGB 2, CP, and NABP gene sequences, and the lineages seemed to reflect geographical origin. The five PVM genes in this study were found to be under strong negative selection pressure. The PVM isolates examined showed frequent gene flow between the Chinese and European populations, and also within the Chinese population. Clear star phylogenies and the neutral equilibrium model test showed that pepino isolates of PVM appear to be experiencing a new expansion after a recent introduction into China, and these isolates display low levels of genetic diversity. To our knowledge, this study is the first report describing genetic structure, recombination, and gene flow in PVM populations, and it provides strong evolutionary evidence for the virus populations from different geographic regions of China.
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Feng X, Poplawsky AR, Nikolaeva OV, Myers JR, Karasev AV. Recombinants of bean common mosaic virus (BCMV) and genetic determinants of BCMV involved in overcoming resistance in common bean. PHYTOPATHOLOGY 2014; 104:786-793. [PMID: 24915430 DOI: 10.1094/phyto-08-13-0243-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Bean common mosaic virus (BCMV) exists as a complex of strains classified by reactions to resistance genes found in common bean (Phaseolus vulgaris); seven BCMV pathotypes have been distinguished thus far, numbered I to VII. Virus genetic determinants involved in pathogenicity interactions with resistance genes have not yet been identified. Here, we describe the characterization of two novel field isolates of BCMV that helped to narrow down these genetic determinants interacting with specific P. vulgaris resistance factors. Based on a biological characterization on common bean differentials, both isolates were classified as belonging to pathotype VII, similar to control isolate US10, and both isolates exhibited the B serotype. The whole genome was sequenced for both isolates and found to be 98 to 99% identical to the BCMV isolate RU1 (pathotype VI), and a single name was retained: BCMV RU1-OR. To identify a genetic determinant of BCMV linked to the BCMV pathotype VII, the whole genome was also sequenced for two control isolates, US10 and RU1-P. Inspection of the nucleotide sequences for BCMV RU1-OR and US10 (both pathotype VII) and three closely related sequences of BCMV (RU1-P, RU1-D, and RU1-W, all pathotype VI) revealed that RU1-OR originated through a series of recombination events between US10 and an as-yet-unidentified BCMV parental genome, resulting in changes in virus pathology. The data obtained suggest that a fragment of the RU1-OR genome between positions 723 and 1,961 nucleotides that is common to US10 and RU1-OR in the P1-HC-Pro region of the BCMV genome may be responsible for the ability to overcome resistance in bean conferred by the bc-2(2) gene. This is the first report of a virus genetic determinant responsible for overcoming a specific BCMV resistance gene in common bean.
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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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The temporal evolution and global spread of Cauliflower mosaic virus, a plant pararetrovirus. PLoS One 2014; 9:e85641. [PMID: 24465629 PMCID: PMC3897471 DOI: 10.1371/journal.pone.0085641] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 12/02/2013] [Indexed: 11/29/2022] Open
Abstract
Cauliflower mosaic virus (CaMV) is a plant pararetrovirus with a double-stranded DNA genome. It is the type member of the genus Caulimovirus in the family Caulimoviridae. CaMV is transmitted by sap inoculation and in nature by aphids in a semi-persistent manner. To investigate the patterns and timescale of CaMV migration and evolution, we sequenced and analyzed the genomes of 67 isolates of CaMV collected mostly in Greece, Iran, Turkey, and Japan together with nine published sequences. We identified the open-reading frames (ORFs) in the genomes and inferred their phylogeny. After removing recombinant sequences, we estimated the substitution rates, divergence times, and phylogeographic patterns of the virus populations. We found that recombination has been a common feature of CaMV evolution, and that ORFs I–V have a different evolutionary history from ORF VI. The ORFs have evolved at rates between 1.71 and 5.81×10−4 substitutions/site/year, similar to those of viruses with RNA or ssDNA genomes. We found four geographically confined lineages. CaMV probably spread from a single population to other parts of the world around 400–500 years ago, and is now widely distributed among Eurasian countries. Our results revealed evidence of frequent gene flow between populations in Turkey and those of its neighboring countries, with similar patterns observed for Japan and the USA. Our study represents the first report on the spatial and temporal spread of a plant pararetrovirus.
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Ahangaran A, Habibi MK, Mohammadi GHM, Winter S, García-Arenal F. Analysis of Soybean mosaic virus genetic diversity in Iran allows the characterization of a new mutation resulting in overcoming Rsv4-resistance. J Gen Virol 2013; 94:2557-2568. [PMID: 23939982 DOI: 10.1099/vir.0.055434-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The genetic variation and population structure of Soybean mosaic virus (SMV) in Iran was analysed through the characterization of a set of isolates collected in the soybean-growing provinces of Iran. The partial nucleotide sequence of these isolates showed a single, undifferentiated population with low genetic diversity, highly differentiated from other SMV world populations. These traits are compatible with a population bottleneck associated with the recent introduction of SMV in Iran. Phylogenetic analyses suggest that SMV was introduced into Iran from East Asia, with at least three introduction events. The limited genetic diversification of SMV in Iran may be explained by strong negative selection in most viral genes eliminating the majority of mutations, together with recombination purging deleterious mutations. The pathogenicity of Iranian SMV isolates was typified on a set of soybean differential lines either susceptible or carrying different resistance genes or alleles to SMV. Two pathotypes were distinguished according to the ability to overcome Rsv4 resistance in line V94-5152. Amino acid sequence comparisons of virulent and avirulent isolates on V94-5152 (Rsv4), plus site-directed mutagenesis in a biologically active cDNA clone, identified mutation S1053N in the P3 protein as the determinant for virulence on V94-5152. Codon 1053 was shown to be under positive selection, and S1053N-determined Rsv4-virulence occurred in isolates with different genealogies. The V94-5152 (Rsv4)-virulence determinant in Iranian isolates maps into a different amino acid position in the P3 protein than those previously reported, indicating different evolutionary pathways towards resistance breaking that might be conditioned by sequence context.
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Affiliation(s)
- Akbar Ahangaran
- Department of Plant Protection, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Mina Koohi Habibi
- Department of Plant Protection, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | | | - Stephan Winter
- German Collection of Microorganisms and Cell Cultures, DSMZ, Braunschweig, Germany
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Campus Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
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Molecular variability of sugarcane streak mosaic virus in China based on an analysis of the P1 and CP protein coding regions. Arch Virol 2013; 159:1149-54. [PMID: 24178307 DOI: 10.1007/s00705-013-1854-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 08/14/2013] [Indexed: 10/26/2022]
Abstract
Sequences of the protein 1 (P1) and coat protein (CP) coding regions of 22 sugarcane streak mosaic virus (SCSMV) isolates were determined. Phylogenetic analysis showed that SCSMV had at least three major lineages, and the lineages seemed to reflect geographical origin. The sudden expansions of the Chinese and Indian subpopulations were supported by calculations showing deviations from the neutral equilibrium model for the individual lineages with an overall lack of nucleotide diversity. Our study shows that Chinese and Indian SCSMV isolates are part of a distinct population, and the subpopulations probably reflect founder effects.
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29
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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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30
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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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Achon MA, Larrañaga A, Alonso-Dueñas N. The population genetics of maize dwarf mosaic virus in Spain. Arch Virol 2012; 157:2377-82. [PMID: 22855126 DOI: 10.1007/s00705-012-1427-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 06/14/2012] [Indexed: 11/30/2022]
Abstract
The population genetics of maize dwarf mosaic virus (MDMV) in Spain was assessed by analysis of the P1-HC region. Restriction fragment length polymorphism analysis of 363 isolates revealed that the MDMV population consisted of 69 haplotypes. Sequence analysis of 112 isolates confirmed a high degree of nucleotide sequence diversity (0.143), which was higher for P1 than for the HC. Twelve sequences showed a single different recombination event. Selection pressure analysis revealed that the P1-HC region was under strong negative selection. The MDMV population was spatially structured but not structured temporally or by host. Phylogenetic analysis split the sequences into five major groups.
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Affiliation(s)
- M A Achon
- Departamento de Producción Vegetal y Ciencia Forestal, Universidad de Lleida, Rovira Roure 191, 25198 Lleida, Spain.
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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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Acosta-Leal R, Duffy S, Xiong Z, Hammond RW, Elena SF. Advances in plant virus evolution: translating evolutionary insights into better disease management. PHYTOPATHOLOGY 2011; 101:1136-48. [PMID: 21554186 DOI: 10.1094/phyto-01-11-0017] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recent studies in plant virus evolution are revealing that genetic structure and behavior of virus and viroid populations can explain important pathogenic properties of these agents, such as host resistance breakdown, disease severity, and host shifting, among others. Genetic variation is essential for the survival of organisms. The exploration of how these subcellular parasites generate and maintain a certain frequency of mutations at the intra- and inter-host levels is revealing novel molecular virus-plant interactions. They emphasize the role of host environment in the dynamic genetic composition of virus populations. Functional genomics has identified host factors that are transcriptionally altered after virus infections. The analyses of these data by means of systems biology approaches are uncovering critical plant genes specifically targeted by viruses during host adaptation. Also, a next-generation resequencing approach of a whole virus genome is opening new avenues to study virus recombination and the relationships between intra-host virus composition and pathogenesis. Altogether, the analyzed data indicate that systematic disruption of some specific parameters of evolving virus populations could lead to more efficient ways of disease prevention, eradication, or tolerable virus-plant coexistence.
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Abstract
Recombination occurs in many RNA viruses and can be of major evolutionary significance. However, rates of recombination vary dramatically among RNA viruses, which can range from clonal to highly recombinogenic. Here, we review the factors that might explain this variation in recombination frequency and show that there is little evidence that recombination is favoured by natural selection to create advantageous genotypes or purge deleterious mutations, as predicted if recombination functions as a form of sexual reproduction. Rather, recombination rates seemingly reflect larger-scale patterns of viral genome organization, such that recombination may be a mechanistic by-product of the evolutionary pressures acting on other aspects of virus biology.
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Affiliation(s)
- Etienne Simon-Loriere
- Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, USA.
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35
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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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36
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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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37
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Visser JC, Bellstedt DU. An assessment of molecular variability and recombination patterns in South African isolates of Potato virus Y. Arch Virol 2009; 154:1891-900. [PMID: 19862472 DOI: 10.1007/s00705-009-0525-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 10/11/2009] [Indexed: 11/30/2022]
Abstract
The coat protein (CP) gene of 75 South African Potato virus Y (PVY) isolates was amplified using reverse-transcriptase polymerase chain reaction (RT-PCR). The resulting cDNA products were cloned and sequenced. These sequences were used to identify the strains to which the isolates belonged. Some, when compared to reference sequences, belonged to the PVY(N) and PVY(O) strains. A number of isolates were found to demonstrate significant homology to PVY(N) strains from China. A large number of South African isolates possessed CP sequences showing evidence of recombination between PVY(N) and PVY(O) strains, similar to those of PVY(NTN) isolates. Multiplex RT-PCR analysis allowed further differentiation of PVY(O) isolates and revealed that the majority were of the PVY(N)-Wilga strain. It was deduced that the most likely way in which these isolates reached South Africa was via the importation of infected material.
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Affiliation(s)
- Johan Christiaan Visser
- Department of Biochemistry, The University of Stellenbosch, Private Bag X1, Stellenbosch, South Africa
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38
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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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YAMASAKI S, SAKAI J, KAMISOYAMA S, HANADA K. Characterization of an isolate of the common strain group of Sweet potato feathery mottle virus from sweet potato in Japan. ACTA ACUST UNITED AC 2009. [DOI: 10.3186/jjphytopath.75.156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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40
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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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41
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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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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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García-Andrés S, Accotto GP, Navas-Castillo J, Moriones E. Founder effect, plant host, and recombination shape the emergent population of begomoviruses that cause the tomato yellow leaf curl disease in the Mediterranean basin. Virology 2007; 359:302-12. [PMID: 17070885 DOI: 10.1016/j.virol.2006.09.030] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2006] [Revised: 08/10/2006] [Accepted: 09/19/2006] [Indexed: 11/28/2022]
Abstract
Tomato yellow leaf curl disease (TYLCD)-associated viruses present a highly structured population in the western Mediterranean basin, depending on host, geographical region and time. About 1,900 tomato and common bean samples were analyzed from which 111 isolates were characterized genetically based on a genome sequence that comprises coding and non-coding regions. Isolates of three distinct begomoviruses previously described were found (Tomato yellow leaf curl virus, TYLCV, Tomato yellow leaf curl Sardinia virus, TYLCSV, and Tomato yellow leaf curl Málaga virus, TYLCMalV), together with a novel recombinant virus. Mixed infections were detected in single plants, rationalizing the occurrence of recombinants. Except for TYLCV-type strain, single, undifferentiated subpopulations were present for each virus type, probably the result of founder effects. Limited genetic variation was observed in genomic regions, with selection against amino acid change in coding regions.
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Affiliation(s)
- Susana García-Andrés
- Estación Experimental "La Mayora", Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Málaga, Spain
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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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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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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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47
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Inoue-Nagata AK, Franco CDM, Martin DP, Rezende JAM, Ferreira GB, Dutra LS, Nagata T. Genome analysis of a severe and a mild isolate of Papaya ringspot virus-type W found in Brazil. Virus Genes 2006; 35:119-27. [PMID: 17024323 DOI: 10.1007/s11262-006-0032-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2006] [Accepted: 08/11/2006] [Indexed: 11/29/2022]
Abstract
Papaya ringspot virus-type W (PRSV-W) is one of the most economically threatening viruses of cucurbits in Brazil. Premunization is one of the most effective PRSV control measures currently applied in squash and zucchini crops. PRSV-W-1, a mild and premunizing strain of PRSV has been successfully used to protect cucurbits against both the severe PRSV-W-C strain and other Brazilian PRSVs. To aid in understanding the mechanism by which PRSV-W-1 premunization operates, the complete genome sequences of PRSV-W-1 and PRSV-W-C were determined. PRSV-W-1 had a genome size of 10,332 nucleotides, whereas indels within the coat protein encoding gene meant that the genome size of PRSV-W-C was six nucleotides shorter than that of the mild strain. The genomes of the two strains shared 94.63% nucleotide sequence identity, with the 5' UTR and P1 being the most variable regions, and the coat protein and 3' UTR being the most conserved. Rigorous recombination analysis revealed that neither PRSV-W-1 nor PRSV-W-C was obviously recombinant, there was significant evidence that many other fully sequenced PRSV genomes were recombinant.
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Rebenstorf K, Candresse T, Dulucq MJ, Büttner C, Obermeier C. Host species-dependent population structure of a pollen-borne plant virus, Cherry leaf roll virus. J Virol 2006; 80:2453-62. [PMID: 16474152 PMCID: PMC1395386 DOI: 10.1128/jvi.80.5.2453-2462.2006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cherry leaf roll virus (CLRV) belongs to the Nepovirus genus within the family Comoviridae. It has a host range which includes a number of wild tree and shrub species. The serological and molecular diversity of CLRV was assessed using a collection of isolates and samples recovered from woody and herbaceous host plants from different geographical origins. Molecular diversity was assessed by sequencing a short (375-bp) region of the 3' noncoding region (NCR) of the genomic RNAs while serological diversity was assessed using a panel of seven monoclonal antibodies raised initially against a walnut isolate of CLRV. The genomic region analyzed was shown to exhibit a significant degree of molecular variability with an average pairwise divergence of 8.5% (nucleotide identity). Similarly, serological variability proved to be high, with no single monoclonal antibody being able to recognize all isolates analyzed. Serological and molecular phylogenetic reconstructions showed a strong correlation. Remarkably, the diversity of CLRV populations is to a large extent defined by the host plant from which the viral samples are originally obtained. There are relatively few reports of plant viruses for which the genetic diversity is structured by the host plant. In the case of CLRV, we hypothesize that this situation may reflect the exclusive mode of transmission in natural plant populations by pollen and by seeds. These modes of transmission are likely to impose barriers to host change by the virus, leading to rapid biological and genetic separation of CLRV variants coevolving with different plant host species.
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Affiliation(s)
- Kathrin Rebenstorf
- Section Phytomedicine, Institute for Horticultural Sciences, Humboldt-Universität zu Berlin, Germany
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49
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Tan Z, Gibbs AJ, Tomitaka Y, Sánchez F, Ponz F, Ohshima K. Mutations in Turnip mosaic virus genomes that have adapted to Raphanus sativus. J Gen Virol 2005; 86:501-510. [PMID: 15659771 DOI: 10.1099/vir.0.80540-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic basis for virulence in potyviruses is largely unknown. Earlier studies showed that there are two host types of Turnip mosaic virus (TuMV); the Brassica/Raphanus (BR)-host type infects both Brassica and Raphanus systemically, whereas the Brassica (B)-host type infects Brassica fully and systemically, but not Raphanus. The genetic basis of this difference has been explored by using the progeny of an infectious clone, p35Tunos; this clone is derived from the UK1 isolate, which is of the B-host type, but rarely infects Raphanus systemically and then only asymptomatically. Two inocula from one such infection were adapted to Raphanus by passaging, during which the infectivity and concentration of the virions of successive infections increased. The variant genomes in the samples, 16 in total, were sequenced fully. Four of the 39 nucleotide substitutions that were detected among the Raphanus sativus-adapted variant genomes were probably crucial for adaptation, as they were found in several variants with independent passage histories. These four were found in the protein 1 (P1), protein 3 (P3), cylindrical inclusion protein (CI) and genome-liked viral protein (VPg) genes. One of four 'parallel evolution' substitutions, 3430G-->A, resulted in a 1100Met-->Ile amino acid change in the C terminus of P3. It seems likely that this site is important in the initial stages of adaptation to R. sativus. Other independent substitutions were mostly found in the P3, CI and VPg genes.
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Affiliation(s)
- Zhongyang Tan
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Adrian J Gibbs
- School of Botany and Zoology, Australian National University, Canberra, ACT 0200, Australia
| | - Yasuhiro Tomitaka
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Flora Sánchez
- Departamento de Biotecnologia, INIA, Autopista A-6 km 7, 28040 Madrid, Spain
| | - Fernando Ponz
- Departamento de Biotecnologia, INIA, Autopista A-6 km 7, 28040 Madrid, Spain
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
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