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Ghafari M, Sõmera M, Sarmiento C, Niehl A, Hébrard E, Tsoleridis T, Ball J, Moury B, Lemey P, Katzourakis A, Fargette D. Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses. PLoS Pathog 2024; 20:e1011911. [PMID: 38206964 PMCID: PMC10807823 DOI: 10.1371/journal.ppat.1011911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/24/2024] [Accepted: 12/18/2023] [Indexed: 01/13/2024] Open
Abstract
The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. The TDRP reveals a decline in evolutionary rate estimates with the measurement timescale, explained empirically by a power-law rate decay, notably observed in animal and human viruses. A mechanistic evolutionary model, the Prisoner of War (PoW) model, has been proposed to address TDRP in viruses. Although TDRP has been studied in animal viruses, its impact on plant virus evolutionary history remains largely unexplored. Here, we investigated the consequences of TDRP in plant viruses by applying the PoW model to reconstruct the evolutionary history of sobemoviruses, plant pathogens with significant importance due to their impact on agriculture and plant health. Our analysis showed that the Sobemovirus genus dates back over four million years, indicating an ancient origin. We found evidence that supports deep host jumps to Poaceae, Fabaceae, and Solanaceae occurring between tens to hundreds of thousand years ago, followed by specialization. Remarkably, the TDRP-corrected evolutionary history of sobemoviruses was extended far beyond previous estimates that had suggested their emergence nearly 9,000 years ago, a time coinciding with the Neolithic period in the Near East. By incorporating sequences collected through metagenomic analyses, the resulting phylogenetic tree showcases increased genetic diversity, reflecting a deep history of sobemovirus species. We identified major radiation events beginning between 4,600 to 2,000 years ago, which aligns with the Neolithic period in various regions, suggesting a period of rapid diversification from then to the present. Our findings make a case for the possibility of deep evolutionary origins of plant viruses.
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Affiliation(s)
- Mahan Ghafari
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Annette Niehl
- Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Eugénie Hébrard
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Theocharis Tsoleridis
- The Wolfson Centre for Global Virus Research and School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Jonathan Ball
- The Wolfson Centre for Global Virus Research and School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Aris Katzourakis
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Denis Fargette
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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2
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Billard E, Barro M, Sérémé D, Bangratz M, Wonni I, Koala M, Kassankogno AI, Hébrard E, Thébaud G, Brugidou C, Poulicard N, Tollenaere C. Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot. Virus Evol 2023; 9:vead049. [PMID: 37649958 PMCID: PMC10465090 DOI: 10.1093/ve/vead049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/04/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023] Open
Abstract
The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at a local scale remains scarce, in spite of potential implications for crop protection. Here, we describe a 5-year (2015-9) monitoring of RYMV prevalence in six sites from western Burkina Faso (geographic areas of Bama, Banzon, and Karfiguela). It confirmed one irrigated site as a disease hotspot and also found one rainfed lowland (RL) site with occasional high prevalence levels. Within the studied fields, a pattern of disease aggregation was evidenced at a 5-m distance, as expected for a mechanically transmitted virus. Next, we monitored RYMV genetic diversity in the irrigated disease hotspot site, revealing a high viral diversity, with the current coexistence of various distinct genetic groups at the site scale (ca. 520 ha) and also within various specific fields (25 m side). One genetic lineage, named S1bzn, is the most recently emerged group and increased in frequency over the studied period (from 20 per cent or less in 2015-6 to more than 65 per cent in 2019). Its genome results from a recombination between two other lineages (S1wa and S1ca). Finally, experimental work revealed that three rice varieties commonly cultivated in Burkina Faso were not different in terms of resistance level, and we also found no significant effect of RYMV genetic groups on symptom expression and viral load. We found, however, that infection outcome depended on the specific RYMV isolate, with two isolates from the lineage S1bzn accumulating at the highest level at early infections. Overall, this study documents a case of high viral prevalence, high viral diversity, and co-occurrence of divergent genetic lineages at a small geographic scale. A recently emerged lineage, which comprises viral isolates inducing severe symptoms and high accumulation under controlled conditions, could be recently rising through natural selection. Following up the monitoring of RYMV diversity is required to confirm this trend and further understand the factors driving the local maintenance of viral diversity.
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Affiliation(s)
- Estelle Billard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Mariam Barro
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Drissa Sérémé
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Virologie et de Biologie Végétale, Kamboinsé, Burkina Faso
| | - Martine Bangratz
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Issa Wonni
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Moustapha Koala
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Virologie et de Biologie Végétale, Kamboinsé, Burkina Faso
| | - Abalo Itolou Kassankogno
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Eugénie Hébrard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Gaël Thébaud
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Christophe Brugidou
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Nils Poulicard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Charlotte Tollenaere
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
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3
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Dossou L, Pinel-Galzi A, Aribi J, Poulicard N, Albar L, Fatogoma S, Ndjiondjop MN, Koné D, Hébrard E. Molecular Tools to Infer Resistance-Breaking Abilities of Rice Yellow Mottle Virus Isolates. Viruses 2023; 15:v15040959. [PMID: 37112939 PMCID: PMC10144094 DOI: 10.3390/v15040959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Rice yellow mottle virus (RYMV) is a major biotic constraint to rice cultivation in Africa. RYMV shows a high genetic diversity. Viral lineages were defined according to the coat protein (CP) phylogeny. Varietal selection is considered as the most efficient way to manage RYMV. Sources of high resistance were identified mostly in accessions of the African rice species, Oryza glaberrima. Emergence of resistance-breaking (RB) genotypes was observed in controlled conditions. The RB ability was highly contrasted, depending on the resistance sources and on the RYMV lineages. A molecular marker linked to the adaptation to susceptible and resistant O. glaberrima was identified in the viral protein genome-linked (VPg). By contrast, as no molecular method was available to identify the hypervirulent lineage able to overcome all known resistance sources, plant inoculation assays were still required. Here, we designed specific RT-PCR primers to infer the RB abilities of RYMV isolates without greenhouse experiments or sequencing steps. These primers were tested and validated on 52 isolates, representative of RYMV genetic diversity. The molecular tools described in this study will contribute to optimizing the deployment strategy of resistant lines, considering the RYMV lineages identified in fields and their potential adaptability.
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Affiliation(s)
- Laurence Dossou
- AfricaRice Center, M'bé Research Station, Bouaké 01 BP 2551, Côte d'Ivoire
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | - Agnès Pinel-Galzi
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Jamel Aribi
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Nils Poulicard
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Laurence Albar
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Sorho Fatogoma
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | | | - Daouda Koné
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | - Eugénie Hébrard
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
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4
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Omiat EG, Asante MD, Traoré VSE, Oppong A, Ifie BE, Ofosu KA, Aribi J, Pinel-Galzi A, Comte A, Fargette D, Hébrard E, Traoré O, Offei SK, Danquah EY, Poulicard N. Genetic diversity and epidemic histories of rice yellow mottle virus in Ghana. Virus Res 2023; 329:199106. [PMID: 36990396 DOI: 10.1016/j.virusres.2023.199106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023]
Abstract
Rice yellow mottle virus (RYMV) has persisted as a major biotic constraint to rice production in Africa. However, no data on RYMV epidemics were available in Ghana, although it is an intensive rice-producing country. Surveys were performed from 2010 to 2020 in eleven rice-growing regions of Ghana. Symptom observations and serological detections confirmed that RYMV is circulating in most of these regions. Coat protein gene and complete genome sequencings revealed that RYMV in Ghana almost exclusively belongs to the strain S2, one of the strains covering the largest area in West Africa. We also detected the presence of the S1ca strain which is being reported for the first time outside its area of origin. These results suggested a complex epidemiological history of RYMV in Ghana and a recent expansion of S1ca to West Africa. Phylogeographic analyses reconstructed at least five independent RYMV introductions in Ghana for the last 40 years, probably due to rice cultivation intensification in West Africa leading to a better circulation of RYMV. In addition to identifying some routes of RYMV dispersion in Ghana, this study contributes to the epidemiological surveillance of RYMV and helps to design disease management strategies, especially through breeding for rice disease resistance.
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Affiliation(s)
- Emmanuel Gilbert Omiat
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, PMB 30, Legon, Accra, Ghana; National Agricultural Research Organisation (NARO), Buginyanya Zonal Agricultural Research and Development Institute, P. O. Box 1356, Mbale, Uganda
| | - Maxwell Darko Asante
- Council for Scientific and Industrial Research - Crops Research Institute (CSIR- CRI), Fumesua, P. O. Box 3785, Kumasi, Ghana; Department of Plant Resources Development, CSIR College of Science and Technology, Fumesua, Kumasi, Ghana
| | | | - Allen Oppong
- Council for Scientific and Industrial Research - Crops Research Institute (CSIR- CRI), Fumesua, P. O. Box 3785, Kumasi, Ghana
| | - Beatrice Elohor Ifie
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, PMB 30, Legon, Accra, Ghana
| | - Kirpal Agyemang Ofosu
- Council for Scientific and Industrial Research - Crops Research Institute (CSIR- CRI), Fumesua, P. O. Box 3785, Kumasi, Ghana
| | - Jamel Aribi
- PHIM, Université Montpellier, IRD, INRAE, Cirad, Institut Agro, Montpellier, France
| | - Agnès Pinel-Galzi
- PHIM, Université Montpellier, IRD, INRAE, Cirad, Institut Agro, Montpellier, France
| | - Aurore Comte
- PHIM, Université Montpellier, IRD, INRAE, Cirad, Institut Agro, Montpellier, France
| | - Denis Fargette
- PHIM, Université Montpellier, IRD, INRAE, Cirad, Institut Agro, Montpellier, France
| | - Eugénie Hébrard
- PHIM, Université Montpellier, IRD, INRAE, Cirad, Institut Agro, Montpellier, France
| | | | - Samuel Kwame Offei
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, PMB 30, Legon, Accra, Ghana
| | - Eric Yirenkyi Danquah
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, PMB 30, Legon, Accra, Ghana
| | - Nils Poulicard
- PHIM, Université Montpellier, IRD, INRAE, Cirad, Institut Agro, Montpellier, France.
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5
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Bonnamy M, Pinel-Galzi A, Gorgues L, Chalvon V, Hébrard E, Chéron S, Nguyen TH, Poulicard N, Sabot F, Pidon H, Champion A, Césari S, Kroj T, Albar L. Rapid evolution of an RNA virus to escape recognition by a rice nucleotide-binding and leucine-rich repeat domain immune receptor. New Phytol 2023; 237:900-913. [PMID: 36229931 DOI: 10.1111/nph.18532] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Viral diseases are a major limitation for crop production, and their control is crucial for sustainable food supply. We investigated by a combination of functional genetics and experimental evolution the resistance of rice to the rice yellow mottle virus (RYMV), which is among the most devastating rice pathogens in Africa, and the mechanisms underlying the extremely fast adaptation of the virus to its host. We found that the RYMV3 gene that protects rice against the virus codes for a nucleotide-binding and leucine-rich repeat domain immune receptor (NLRs) from the Mla-like clade of NLRs. RYMV3 detects the virus by forming a recognition complex with the viral coat protein (CP). The virus escapes efficiently from detection by mutations in its CP, some of which interfere with the formation of the recognition complex. This study establishes that NLRs also confer in monocotyledonous plants immunity to viruses, and reveals an unexpected functional diversity for NLRs of the Mla clade that were previously only known as fungal disease resistance proteins. In addition, it provides precise insight into the mechanisms by which viruses adapt to plant immunity and gives important knowledge for the development of sustainable resistance against viral diseases of cereals.
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Affiliation(s)
- Mélia Bonnamy
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Agnès Pinel-Galzi
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Lucille Gorgues
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Véronique Chalvon
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Eugénie Hébrard
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Sophie Chéron
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | | | - Nils Poulicard
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - François Sabot
- DIADE, Univ Montpellier, IRD, 34394, Montpellier, France
| | - Hélène Pidon
- DIADE, Univ Montpellier, IRD, 34394, Montpellier, France
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, 06484, Quedlinburg, Germany
| | | | - Stella Césari
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Laurence Albar
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
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Abstract
The family Solemoviridae includes viruses with icosahedral particles (26–34 nm in diameter) assembled on T=3 symmetry with a 4–6 kb positive-sense, monopartite, polycistronic RNA genome. Transmission of members of the genera Sobemovirus and Polemovirus occurs via mechanical wounding, vegetative propagation, insect vectors or abiotically through soil; members of the genera Polerovirus and Enamovirus are transmitted by specific aphids. Most solemoviruses have a narrow host range. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Solemoviridae, which is available at ictv.global/report/solemoviridae.
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Affiliation(s)
- Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia
| | - Denis Fargette
- IRD, Cirad, Université Montpellier, IPME, Montpellier 34394, France
| | - Eugénie Hébrard
- IRD, Cirad, Université Montpellier, IPME, Montpellier 34394, France
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia
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7
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Issaka S, Traoré O, Longué RDS, Pinel-Galzi A, Gill MS, Dellicour S, Bastide P, Guindon S, Hébrard E, Dugué MJ, Séré Y, Semballa S, Aké S, Lemey P, Fargette D. Rivers and landscape ecology of a plant virus, Rice yellow mottle virus along the Niger Valley. Virus Evol 2021; 7:veab072. [PMID: 36819970 PMCID: PMC9927878 DOI: 10.1093/ve/veab072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/08/2021] [Accepted: 08/16/2021] [Indexed: 11/14/2022] Open
Abstract
To investigate the spread of Rice yellow mottle virus (RYMV) along the Niger River, regular sampling of virus isolates was conducted along 500 km of the Niger Valley in the Republic of Niger and was complemented by additional sampling in neighbouring countries in West Africa and Central Africa. The spread of RYMV into and within the Republic of Niger was inferred as a continuous process using a Bayesian statistical framework applied previously to reconstruct its dispersal history in West Africa, East Africa, and Madagascar. The spatial resolution along this section of the Niger River was the highest implemented for RYMV and possibly for any plant virus. We benefited from the results of early field surveys of the disease for the validation of the phylogeographic reconstruction and from the well-documented history of rice cultivation changes along the Niger River for their interpretation. As a prerequisite, the temporal signal of the RYMV data sets was revisited in the light of recent methodological advances. The role of the hydrographic network of the Niger Basin in RYMV spread was examined, and the link between virus population dynamics and the extent of irrigated rice was assessed. RYMV was introduced along the Niger River in the Republic of Niger in the early 1980s from areas to the southwest of the country where rice was increasingly grown. Viral spread was triggered by a major irrigation scheme made of a set of rice perimeters along the river valley. The subsequent spatial and temporal host continuity and the inoculum build-up allowed for a rapid spread of RYMV along the Niger River, upstream and downstream, over hundreds of kilometres, and led to the development of severe epidemics. There was no evidence of long-distance dissemination of the virus through natural water. Floating rice in the main meanders of the Middle Niger did not contribute to virus dispersal from West Africa to Central Africa. RYMV along the Niger River is an insightful example of how agricultural intensification favours pathogen emergence and spread.
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Affiliation(s)
| | - Oumar Traoré
- Laboratoire de Virologie et de Biotechnologie Végétale (LVBV), Laboratoire National de Biosécurité, Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou 01 BP 476, Burkina Faso
| | - Régis Dimitri Skopé Longué
- Laboratoire des Sciences Biologiques et Agronomiques pour le Développement (LaSBAD), Département des Sciences de la Vie, Université de Bangui, Bangui BP 908, République Centrafricaine
| | - Agnès Pinel-Galzi
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro., Montpellier cedex 5 BP 64501 34394, France
| | - Mandev S Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, Leuven 3000, Belgium,Spatial Epidemiology Lab. (SpELL), Université Libre de Bruxelles, CP160/12, 50, av. FD Roosevelt, Bruxelles 1050, Belgium
| | - Paul Bastide
- IMAG – UMR 5149, Université de Montpellier, Case courrier 051, Place Eugène Bataillon, Montpellier 34090, France
| | - Stéphane Guindon
- Department of Computer Science, LIRMM, CNRS and Université de Montpellier, Montpellier, France
| | - Eugénie Hébrard
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro., Montpellier cedex 5 BP 64501 34394, France
| | - Marie-Jo Dugué
- Agronomy and Farming Systems, 3 avenue des Cistes, Saint Mathieu de Tréviers 34270, France
| | - Yacouba Séré
- Agricultural Research and Development, Bobo-Dioulasso BP 1324, Burkina Faso
| | - Silla Semballa
- Laboratoire des Sciences Biologiques et Agronomiques pour le Développement (LaSBAD), Département des Sciences de la Vie, Université de Bangui, Bangui BP 908, République Centrafricaine
| | - Séverin Aké
- UFR Biosciences, Laboratoire de Physiologie Végétale, Université Félix Houphouët-Boigny, Abidjan 22 BP 582, Côte d’Ivoire
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8
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Bagayoko I, Celli MG, Romay G, Poulicard N, Pinel-Galzi A, Julian C, Filloux D, Roumagnac P, Sérémé D, Bragard C, Hébrard E. Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus. Viruses 2021; 13:v13050737. [PMID: 33922593 PMCID: PMC8145960 DOI: 10.3390/v13050737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/12/2021] [Accepted: 04/21/2021] [Indexed: 01/02/2023] Open
Abstract
The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.
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Affiliation(s)
- Issiaka Bagayoko
- Earth and Life Institute, Applied Microbiology-Phytopathology, Université Catholique de Louvain (UCLouvain), Croix du Sud 2 Bte L07.05.03, 1348 Louvain-la-Neuve, Belgium; (I.B.); (G.R.); (C.B.)
| | - Marcos Giovanni Celli
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1425, Argentina;
- Instituto de Patología Vegetal (IPAVE, CIAP, INTA), Camino 60 cuadras Km 5, Cordoba 5119, Argentina
| | - Gustavo Romay
- Earth and Life Institute, Applied Microbiology-Phytopathology, Université Catholique de Louvain (UCLouvain), Croix du Sud 2 Bte L07.05.03, 1348 Louvain-la-Neuve, Belgium; (I.B.); (G.R.); (C.B.)
| | - Nils Poulicard
- PHIM, Plant Health Institute, Université de Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France; (N.P.); (A.P.-G.); (C.J.); (D.F.); (P.R.)
| | - Agnès Pinel-Galzi
- PHIM, Plant Health Institute, Université de Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France; (N.P.); (A.P.-G.); (C.J.); (D.F.); (P.R.)
| | - Charlotte Julian
- PHIM, Plant Health Institute, Université de Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France; (N.P.); (A.P.-G.); (C.J.); (D.F.); (P.R.)
- CIRAD, UMR PHIM, Campus International de Montferrier-Baillarguet, 34398 Montpellier, France
| | - Denis Filloux
- PHIM, Plant Health Institute, Université de Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France; (N.P.); (A.P.-G.); (C.J.); (D.F.); (P.R.)
- CIRAD, UMR PHIM, Campus International de Montferrier-Baillarguet, 34398 Montpellier, France
| | - Philippe Roumagnac
- PHIM, Plant Health Institute, Université de Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France; (N.P.); (A.P.-G.); (C.J.); (D.F.); (P.R.)
- CIRAD, UMR PHIM, Campus International de Montferrier-Baillarguet, 34398 Montpellier, France
| | - Drissa Sérémé
- Laboratoire de Laboratoire de Virologie et de Biotechnologies Végétales, INERA—Institut de l’Environnement et de Recherches Agricoles, LMI Patho-Bios, Ouagadougou 01 BP 476, Burkina Faso;
| | - Claude Bragard
- Earth and Life Institute, Applied Microbiology-Phytopathology, Université Catholique de Louvain (UCLouvain), Croix du Sud 2 Bte L07.05.03, 1348 Louvain-la-Neuve, Belgium; (I.B.); (G.R.); (C.B.)
| | - Eugénie Hébrard
- PHIM, Plant Health Institute, Université de Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France; (N.P.); (A.P.-G.); (C.J.); (D.F.); (P.R.)
- Correspondence:
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9
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Affiliation(s)
| | - M.G. Celli
- IPAVE‐CIAP‐INTAkm 5 1/2, Camino 60 CuadrasCórdobaArgentina
- IRD, CiradUniversity of Montpellier, IPME911 Avenue Agropolis34394MontpellierFrance
| | | | | | - E. Hébrard
- IRD, CiradUniversity of Montpellier, IPME911 Avenue Agropolis34394MontpellierFrance
| | - N. Poulicard
- IRD, CiradUniversity of Montpellier, IPME911 Avenue Agropolis34394MontpellierFrance
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10
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Rakotomalala M, Vrancken B, Pinel-Galzi A, Ramavovololona P, Hébrard E, Randrianangaly JS, Dellicour S, Lemey P, Fargette D. Comparing patterns and scales of plant virus phylogeography: Rice yellow mottle virus in Madagascar and in continental Africa. Virus Evol 2019; 5:vez023. [PMID: 31384483 PMCID: PMC6671560 DOI: 10.1093/ve/vez023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Rice yellow mottle virus (RYMV) in Madagascar Island provides an opportunity to study the spread of a plant virus disease after a relatively recent introduction in a large and isolated country with a heterogeneous host landscape ecology. Here, we take advantage of field survey data on the occurrence of RYMV disease throughout Madagascar dating back to the 1970s, and of virus genetic data from ninety-four isolates collected since 1989 in most regions of the country to reconstruct the epidemic history. We find that the Malagasy isolates belong to a unique recombinant strain that most likely entered Madagascar through a long-distance introduction from the most eastern part of mainland Africa. We infer the spread of RYMV as a continuous process using a Bayesian statistical framework. In order to calibrate the time scale in calendar time units in this analysis, we pool the information about the RYMV evolutionary rate from several geographical partitions. Whereas the field surveys and the phylogeographic reconstructions both point to a rapid southward invasion across hundreds of kilometers throughout Madagascar within three to four decades, they differ on the inferred origin location and time of the epidemic. The phylogeographic reconstructions suggest a lineage displacement and unveil a re-invasion of the northern regions that may have remained unnoticed otherwise. Despite ecological differences that could affect the transmission potential of RYMV in Madagascar and in mainland Africa, we estimate similar invasion and dispersal rates. We could not identify environmental factors that have a relevant impact on the lineage dispersal velocity of RYMV in Madagascar. This study highlights the value and complementarity of (historical) nongenetic and (more contemporaneous) genetic surveillance data for reconstructing the history of spread of plant viruses.
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Affiliation(s)
- Mbolarinosy Rakotomalala
- Centre Régional de Recherche du Nord-Ouest du FOFIFA, BP 289, Mahavoky Avaratra, Mahajanga 401, Madagascar
| | - Bram Vrancken
- Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Herestraat 49 box 1040, 3000 Leuven, Belgium
| | - Agnès Pinel-Galzi
- IRD, Cirad, Université Montpellier, IPME, 911 avenue Agropolis, BP 64501 34934 Montpellier cedex 5, France
| | - Perle Ramavovololona
- Département de Biologie et d'Ecologie Végétales, Faculté des Sciences, Université d'Antananarivo, BP 906
| | - Eugénie Hébrard
- IRD, Cirad, Université Montpellier, IPME, 911 avenue Agropolis, BP 64501 34934 Montpellier cedex 5, France
| | | | - Simon Dellicour
- Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Herestraat 49 box 1040, 3000 Leuven, Belgium.,Spatial Epidemiology Lab, Université Libre de Bruxelles, CP 264 / 3,50 av FD Roosevelt, B-1050 Brussels, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Herestraat 49 box 1040, 3000 Leuven, Belgium
| | - Denis Fargette
- IRD, Cirad, Université Montpellier, IPME, 911 avenue Agropolis, BP 64501 34934 Montpellier cedex 5, France
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11
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Charon J, Barra A, Walter J, Millot P, Hébrard E, Moury B, Michon T. First Experimental Assessment of Protein Intrinsic Disorder Involvement in an RNA Virus Natural Adaptive Process. Mol Biol Evol 2019; 35:38-49. [PMID: 29029259 PMCID: PMC5850501 DOI: 10.1093/molbev/msx249] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Intrinsic disorder (ID) in proteins is defined as a lack of stable structure in physiological conditions. Intrinsically disordered regions (IDRs) are highly abundant in some RNA virus proteomes. Low topological constraints exerted on IDRs are expected to buffer the effect of numerous deleterious mutations and could be related to the remarkable adaptive potential of RNA viruses to overcome resistance of their host. To experimentally test this hypothesis in a natural pathosystem, a set of four variants of Potato virus Y (PVY; Potyvirus genus) containing various ID degrees in the Viral genome-linked (VPg) protein, a key determinant of potyvirus adaptation, was designed. To estimate the ID contribution to the VPg-based PVY adaptation, the adaptive ability of the four PVY variants was monitored in the pepper host (Capsicum annuum) carrying a recessive resistance gene. Intriguingly, the two mutants with the highest ID content displayed a significantly higher ability to restore infection in the resistant host, whereas the less intrinsically disordered mutant was unable to restore infection. The role of ID on virus adaptation may be due either to a larger exploration of evolutionary pathways or the minimization of fitness penalty caused by resistance-breaking mutations. This pioneering study strongly suggests the positive impact of ID in an RNA virus adaptive capacity.
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Affiliation(s)
- Justine Charon
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d'Ornon, France.,CNRS 5320, INSERM U1212, Pessac, France
| | - Amandine Barra
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d'Ornon, France
| | - Jocelyne Walter
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d'Ornon, France
| | | | - Eugénie Hébrard
- UMR Interactions Plantes-Microorganismes-Environnement, IRD, CIRAD, Université de Montpellier, Montpellier, France
| | | | - Thierry Michon
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d'Ornon, France
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12
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Pinel-Galzi A, Hébrard E, Traoré O, Silué D, Albar L. Protocol for RYMV Inoculation and Resistance Evaluation in Rice Seedlings. Bio Protoc 2018; 8:e2863. [PMID: 34285979 DOI: 10.21769/bioprotoc.2863] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/08/2018] [Accepted: 05/13/2018] [Indexed: 11/02/2022] Open
Abstract
Rice yellow mottle virus (RYMV), a mechanically transmitted virus that causes serious damage to cultivated rice plants, is endemic to Africa. Varietal selection for resistance is considered to be the most effective and sustainable management strategy. Standardized resistance evaluation procedures are required for the identification and characterization of resistance sources. This paper describes a protocol for mechanical inoculation of rice seedlings with RYMV and two methods of resistance evaluation - one based on a symptom severity index and the other on virus detection through double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA).
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13
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Hébrard E, Pinel-Galzi A, Oludare A, Poulicard N, Aribi J, Fabre S, Issaka S, Mariac C, Dereeper A, Albar L, Silué D, Fargette D. Identification of a Hypervirulent Pathotype of Rice yellow mottle virus: A Threat to Genetic Resistance Deployment in West-Central Africa. Phytopathology 2018; 108:299-307. [PMID: 28990483 DOI: 10.1094/phyto-05-17-0190-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Rice yellow mottle virus (RYMV) causes high losses to rice production in Africa. Several sources of varietal high resistance are available but the emergence of virulent pathotypes that are able to overcome one or two resistance alleles can sometimes occur. Both resistance spectra and viral adaptability have to be taken into account to develop sustainable rice breeding strategies against RYMV. In this study, we extended previous resistance spectrum analyses by testing the rymv1-4 and rymv1-5 alleles that are carried by the rice accessions Tog5438 and Tog5674, respectively, against isolates that are representative of RYMV genetic and pathogenic diversity. Our study revealed a hypervirulent pathotype, named thereafter pathotype T', that is able to overcome all known sources of high resistance. This pathotype, which is spatially localized in West-Central Africa, appears to be more abundant than previously suspected. To better understand the adaptive processes of pathotype T', molecular determinants of resistance breakdown were identified via Sanger sequencing and validated through directed mutagenesis of an infectious clone. These analyses confirmed the key role of convergent nonsynonymous substitutions in the central part of the viral genome-linked protein to overcome RYMV1-mediated resistance. In addition, deep-sequencing analyses revealed that resistance breakdown does not always coincide with fixed mutations. Actually, virulence mutations that are present in a small proportion of the virus population can be sufficient for resistance breakdown. Considering the spatial distribution of RYMV strains in Africa and their ability to overcome the RYMV resistance genes and alleles, we established a resistance-breaking risk map to optimize strategies for the deployment of sustainable and resistant rice lines in Africa.
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Affiliation(s)
- Eugénie Hébrard
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Agnès Pinel-Galzi
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Aderonke Oludare
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Nils Poulicard
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Jamel Aribi
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Sandrine Fabre
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Souley Issaka
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Cédric Mariac
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Alexis Dereeper
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Laurence Albar
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Drissa Silué
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Denis Fargette
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
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14
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Ndikumana I, Pinel-Galzi A, Fargette D, Hébrard E. Complete Genome Sequence of a New Strain of Rice yellow mottle virus from Malawi, Characterized by a Recombinant VPg Protein. Genome Announc 2017; 5:e01198-17. [PMID: 29097464 PMCID: PMC5668540 DOI: 10.1128/genomea.01198-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/09/2017] [Indexed: 12/02/2022]
Abstract
The complete sequence of the isolate Mw10 of Rice yellow mottle virus was determined. Sequence comparisons revealed 8.4% to 10.7% nucleotide divergence from the published sequences, resulting in the definition of the strain S7. Importantly, a putative recombination event was identified encompassing the viral genome-linked protein involved in host adaptation.
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Affiliation(s)
| | - Agnès Pinel-Galzi
- Interactions Plantes Microorganismes Environnement, Institut de Recherche Pour le Développement, Cirad, Université Montpellier, Montpellier, France
| | - Denis Fargette
- Interactions Plantes Microorganismes Environnement, Institut de Recherche Pour le Développement, Cirad, Université Montpellier, Montpellier, France
| | - Eugénie Hébrard
- Interactions Plantes Microorganismes Environnement, Institut de Recherche Pour le Développement, Cirad, Université Montpellier, Montpellier, France
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15
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Abstract
Prediction of pathogen emergence is an important field of research, both in human health and in agronomy. Most studies of pathogen emergence have focused on the ecological or anthropic factors involved rather than on the role of intrinsic pathogen properties. The capacity of pathogens to infect a large set of host species, i.e. to possess a large host range breadth (HRB), is tightly linked to their emergence propensity. Using an extensive plant virus database, we found that four traits related to virus genome or transmission properties were strongly and robustly linked to virus HRB. Broader host ranges were observed for viruses with single-stranded genomes, those with three genome segments and nematode-transmitted viruses. Also, two contrasted groups of seed-transmitted viruses were evidenced. Those with a single-stranded genome had larger HRB than non-seed-transmitted viruses, whereas those with a double-stranded genome (almost exclusively RNA) had an extremely small HRB. From the plant side, the family taxonomic rank appeared as a critical threshold for virus host range, with a highly significant increase in barriers to infection between plant families. Accordingly, the plant-virus infectivity matrix shows a dual structure pattern: a modular pattern mainly due to viruses specialized to infect plants of a given family and a nested pattern due to generalist viruses. These results contribute to a better prediction of virus host jumps and emergence risks.
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Affiliation(s)
- Benoît Moury
- Pathologie Végétale, INRA, 84140 Montfavet, France
| | - Frédéric Fabre
- UMR 1065, Santé et Agroécologie du Vignoble, INRA, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, F-33883 Villenave d'Ornon, France
| | - Eugénie Hébrard
- UMR186, IRD-Cirad-UM, Laboratory 'Interactions Plantes Microorganismes Environnement', Montpellier, France
| | - Rémy Froissart
- UMR5290, CNRS-IRD-UM1-UM2, Laboratory 'Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle', Montpellier, France.,UMR385, INRA-Cirad-SupAgro, Laboratory 'Biologie des Interactions Plantes-Parasites', Campus International de Baillarguet, F-34398 Montpellier, France
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16
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Pidon H, Ghesquière A, Chéron S, Issaka S, Hébrard E, Sabot F, Kolade O, Silué D, Albar L. Fine mapping of RYMV3: a new resistance gene to Rice yellow mottle virus from Oryza glaberrima. Theor Appl Genet 2017; 130:807-818. [PMID: 28144699 DOI: 10.1007/s00122-017-2853-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/04/2017] [Indexed: 05/24/2023]
Abstract
A new resistance gene against Rice yellow mottle virus was identified and mapped in a 15-kb interval. The best candidate is a CC-NBS-LRR gene. Rice yellow mottle virus (RYMV) disease is a serious constraint to the cultivation of rice in Africa and selection for resistance is considered to be the most effective management strategy. The aim of this study was to characterize the resistance of Tog5307, a highly resistant accession belonging to the African cultivated rice species (Oryza glaberrima), that has none of the previously identified resistance genes to RYMV. The specificity of Tog5307 resistance was analyzed using 18 RYMV isolates. While three of them were able to infect Tog5307 very rapidly, resistance against the others was effective despite infection events attributed to resistance-breakdown or incomplete penetrance of the resistance. Segregation of resistance in an interspecific backcross population derived from a cross between Tog5307 and the susceptible Oryza sativa variety IR64 showed that resistance is dominant and is controlled by a single gene, named RYMV3. RYMV3 was mapped in an approximately 15-kb interval in which two candidate genes, coding for a putative transmembrane protein and a CC-NBS-LRR domain-containing protein, were annotated. Sequencing revealed non-synonymous polymorphisms between Tog5307 and the O. glaberrima susceptible accession CG14 in both candidate genes. An additional resistant O. glaberrima accession, Tog5672, was found to have the Tog5307 genotype for the CC-NBS-LRR gene but not for the putative transmembrane protein gene. Analysis of the cosegregation of Tog5672 resistance with the RYMV3 locus suggests that RYMV3 is also involved in Tog5672 resistance, thereby supporting the CC-NBS-LRR gene as the best candidate for RYMV3.
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Affiliation(s)
- Hélène Pidon
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Alain Ghesquière
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Sophie Chéron
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Souley Issaka
- Africa Rice Center, Cotonou, Benin
- FSAE, Université de Tillabéri, Tillabéri, Niger
| | - Eugénie Hébrard
- Interactions Plantes Microorganismes Environnement, Institut de Recherche pour le Développement - Centre de Coopération Internationale en Recherche Agronomique pour le Développement - Université de Montpellier, Montpellier, France
| | - François Sabot
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Olufisayo Kolade
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
- Africa Rice Center, Cotonou, Benin
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Laurence Albar
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France.
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17
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Pinel-Galzi A, Dubreuil-Tranchant C, Hébrard E, Mariac C, Ghesquière A, Albar L. Mutations in Rice yellow mottle virus Polyprotein P2a Involved in RYMV2 Gene Resistance Breakdown. Front Plant Sci 2016; 7:1779. [PMID: 27965688 PMCID: PMC5125353 DOI: 10.3389/fpls.2016.01779] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/11/2016] [Indexed: 05/09/2023]
Abstract
Rice yellow mottle virus (RYMV) is one of the major diseases of rice in Africa. The high resistance of the Oryza glaberrima Tog7291 accession involves a null allele of the RYMV2 gene, whose ortholog in Arabidopsis, CPR5, is a transmembrane nucleoporin involved in effector-triggered immunity. To optimize field deployment of the RYMV2 gene and improve its durability, which is often a weak point in varietal resistance, we analyzed its efficiency toward RYMV isolates representing the genetic diversity of the virus and the molecular basis of resistance breakdown. Tog7291 resistance efficiency was highly variable depending on the isolate used, with infection rates ranging from 0 to 98% of plants. Back-inoculation experiments indicated that infection cases were not due to an incomplete resistance phenotype but to the emergence of resistance-breaking (RB) variants. Interestingly, the capacity of the virus to overcome Tog7291 resistance is associated with a polymorphism at amino-acid 49 of the VPg protein which also affects capacity to overcome the previously studied RYMV1 resistance gene. This polymorphism appeared to be a main determinant of the emergence of RB variants. It acts independently of the resistance gene and rather reflects inter-species adaptation with potential consequences for the durability of resistance. RB mutations were identified by full-length or partial sequencing of the RYMV genome in infected Tog7291 plants and were validated by directed mutagenesis of an infectious viral clone. We found that Tog7291 resistance breakdown involved mutations in the putative membrane anchor domain of the polyprotein P2a. Although the precise effect of these mutations on rice/RYMV interaction is still unknown, our results offer a new perspective for the understanding of RYMV2 mediated resistance mechanisms. Interestingly, in the susceptible IR64 variety, RB variants showed low infectivity and frequent reversion to the wild-type genotype, suggesting that Tog7291 resistance breakdown is associated with a major loss of viral fitness in normally susceptible O. sativa varieties. Despite the high frequency of resistance breakdown in controlled conditions, this loss of fitness is an encouraging element with regards to RYMV2 resistance durability.
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Affiliation(s)
- Agnès Pinel-Galzi
- Interactions Plantes Microorganismes Environnement, Institut de Recherche pour le Développement – Centre de Coopération Internationale en Recherche Agronomique pour le Développement – Université de MontpellierMontpellier, France
| | - Christine Dubreuil-Tranchant
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement – Université de MontpellierMontpellier, France
| | - Eugénie Hébrard
- Interactions Plantes Microorganismes Environnement, Institut de Recherche pour le Développement – Centre de Coopération Internationale en Recherche Agronomique pour le Développement – Université de MontpellierMontpellier, France
| | - Cédric Mariac
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement – Université de MontpellierMontpellier, France
| | - Alain Ghesquière
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement – Université de MontpellierMontpellier, France
| | - Laurence Albar
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement – Université de MontpellierMontpellier, France
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Pinel-Galzi A, Traoré O, Séré Y, Hébrard E, Fargette D. The biogeography of viral emergence: rice yellow mottle virus as a case study. Curr Opin Virol 2015; 10:7-13. [DOI: 10.1016/j.coviro.2014.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 11/28/2014] [Accepted: 12/03/2014] [Indexed: 12/23/2022]
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Hubert JG, Pinel-Galzi A, Dibwe D, Cinyabuguma E, Kaboré A, Fargette D, Silué D, Hébrard E, Séré Y. First Report of Rice yellow mottle virus on Rice in the Democratic Republic of Congo. Plant Dis 2013; 97:1664. [PMID: 30716857 DOI: 10.1094/pdis-06-13-0650-pdn] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rice yellow mottle virus (RYMV), genus Sobemovirus, is a widespread rice pathogen reported in nearly all rice-growing countries of Africa. Although the virus was detected in Cameroon, Chad, Tanzania, Rwanda, Burundi, and Uganda (2,3), RYMV has never been described in the Democratic Republic of Congo (DRC). In July 2012, plants with leaf yellowing and mottling symptoms were observed in large irrigated rice production schemes 30 km south of Bukavu, in eastern DRC, and in lowland subsistence fields in the surroundings of Bukavu. Several dozen hectares affected by the disease were abandoned by the farmers. Symptomatic leaf samples were collected in different farmer fields. Back-inoculations to susceptible rice variety IR64 resulted in the same yellowing and mottling symptoms 7 to 9 days post-inoculation. Infected leaves gave positive results using double antibody sandwich (DAS)-ELISA tests with polyclonal antisera (as described in [1]), indicating for the first time the presence of RYMV in DRC. Triple antibody sandwich (TAS)-ELISA tests with discriminant monoclonal antibodies (1) revealed that they all belong to serotype 4 found in the neighboring region in Rwanda. Total RNA of three samples from South Kivu was extracted with the RNeasy Plant Mini kit (Qiagen, Germany). The 720 nucleotide coat protein (CP) gene was amplified by reverse transcription (RT)-PCR with primers 5'CTCCCCCACCCATCCCGAGAATT3' and 5'CAAAGATGGCCAGGAA3' (1). The sequences were deposited in GenBank (Accessions KC788208, KC788209, and KC788210). A set of CP sequences of 45 isolates representative of the RYMV diversity in Africa, including the sequences of the DRC samples, were used for phylogenetic reconstruction by maximum-likelihood method. The isolates from South Kivu belonged to strain S4-lv, mainly found around Lake Victoria. Specifically, within the S4-lv strain, the South Kivu isolates clustered with isolates from eastern and southern provinces of Rwanda and Burundi, respectively (2), suggesting a recent spread from these countries. Recently, efforts have been directed to shift from the traditional upland system to lowland and irrigated systems in which water availability allows sequential planting and maintenance of higher crop intensity. This agricultural change may increase insect vectors and alternate host plant populations which may result in higher RYMV incidence in DRC (3). Similar yellowing and mottling symptoms have been observed in Bas-Congo and Equateur provinces of the country, which would justify further surveys and characterisation of RYMV in the DRC. References: (1) D. Fargette et al. Arch. Virol. 147:583, 2002. (2) I. Ndikumana et al. Plant Dis. 96:1230, 2012. (3) O. Traoré et al. Mol. Ecol. 14:2097, 2005.
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Affiliation(s)
- J G Hubert
- Africa Rice Center (AfricaRice), P.O. Box 33581, Dar es Salaam, Tanzania
| | - A Pinel-Galzi
- UMR RPB, Institut de Recherche Pour le Développement (IRD), BP 64501, 34394 Montpellier cedex 5, France
| | - D Dibwe
- Institut National pour l'Etude et la Recherche Agronomiques (INERA), Kinshasa, Democratic Republic of Congo
| | | | | | | | | | | | - Y Séré
- AfricaRice, Dar es Salaam, Tanzania
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Poulicard N, Pinel-Galzi A, Fargette D, Hébrard E. Alternative mutational pathways, outside the VPg, of rice yellow mottle virus to overcome eIF(iso)4G-mediated rice resistance under strong genetic constraints. J Gen Virol 2013; 95:219-224. [PMID: 24141250 DOI: 10.1099/vir.0.057810-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The adaptation of rice yellow mottle virus (RYMV) to rymv1-mediated resistance has been reported to involve mutations in the viral genome-linked protein (VPg). In this study, we analysed several cases of rymv1-2 resistance breakdown by an isolate with low adaptability. Surprisingly, in these rarely occurring resistance-breaking (RB) genotypes, mutations were detected outside the VPg, in the ORF2a/ORF2b overlapping region. The causal role of three mutations associated with rymv1-2 resistance breakdown was validated via directed mutagenesis of an infectious clone. In resistant plants, these mutations increased viral accumulation as efficiently as suboptimal RB mutations in the VPg. Interestingly, these mutations are located in a highly conserved, but unfolded, domain. Altogether, our results indicate that under strong genetic constraints, a priori unfit genotypes can follow alternative mutational pathways, i.e. outside the VPg, to overcome rymv1-2 resistance.
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Affiliation(s)
- Nils Poulicard
- Institut de Recherche pour le Développement (IRD), UMR RPB, Montpellier, France
| | - Agnès Pinel-Galzi
- Institut de Recherche pour le Développement (IRD), UMR RPB, Montpellier, France
| | - Denis Fargette
- Institut de Recherche pour le Développement (IRD), UMR RPB, Montpellier, France
| | - Eugénie Hébrard
- Institut de Recherche pour le Développement (IRD), UMR RPB, Montpellier, France
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21
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Ndikumana I, Pinel-Galzi A, Negussie Z, Msolla SN, Njau P, Singh RK, Choi IR, Bigirimana J, Fargette D, Hébrard E. First Report of Rice yellow mottle virus on Rice in Burundi. Plant Dis 2012; 96:1230. [PMID: 30727071 DOI: 10.1094/pdis-03-12-0293-pdn] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Since the mid-1980s, rice cultivation has expanded rapidly in Burundi to reach approximately 50,000 ha in 2011. In 2007, leaf mottling, reduced tillering, and stunting symptoms were observed on rice at Gatumba near Bujumbura, causing small patches in less than 10% of the fields. Rice yellow mottle virus (RYMV, genus Sobemovirus), which has seriously threatened rice cultivation in Africa (1) and was recently described in the neighboring Rwanda (3), was suspected to be involved because of similar symptoms. To identify the pathogen that caused the disease in Burundi, a survey was performed in the major rice-producing regions of Burundi and Rwanda. Six locations in Burundi and four in Rwanda were investigated in April and October 2011. Disease incidence in the fields was estimated to be 15 ± 5%. Symptomatic leaves of 24 cultivated rice plants were collected and tested by double antibody sandwich-ELISA with polyclonal antibodies raised against the RYMV isolate Mg1 (2). All tested samples reacted positively. Four isolates were inoculated on susceptible Oryza sativa cultivar IR64 (2). The typical symptoms of RYMV were reproduced 7 days after inoculation, whereas the noninoculated controls remained healthy. Total RNA was extracted by the RNeasy Plant Mini kit (QIAGEN, Hilden, Germany) from 12 samples. The RYMV coat protein gene was amplified by RT-PCR with primers 5'CGCTCAACATCCTTTTCAGGGTAG3' and 5'CAAAGATGGCCAGGAA3' (3). The sequences were deposited in GenBank (Accession Nos. HE654712 to HE654723). To characterize the isolates, the sequences of the tested samples were compared in a phylogenic tree including a set of 45 sequences of isolates from Rwanda, Uganda, western Kenya, and northern Tanzania (2,3). Six isolates from western Burundi, namely Bu1, Bu2, Bu4, Bu7, Bu10, and Bu13 (Accession Nos. HE654712 to HE654716 and HE654718), and the isolate Rw208 (HE654720) from southwestern Rwanda, belonged to strain S4-lm previously reported near Lakes Malawi and Tanganyika. They fell within the group gathering isolates from the western Bugarama plain of Rwanda (3). The isolates Bu16 (HE654719) and Bu17 (HE654717) from Mishiha in eastern Burundi belonged to strain S4-lv previously reported around Lake Victoria. However, they did not cluster with isolates from the eastern and southern provinces of Rwanda. They were genetically more closely related to isolates of strain S4-lv from northern Tanzania. Overall, the phylogeography of RYMV in Burundi and Rwanda region was similar. In the western plain of the two countries, the isolates belonged to the S4-lm lineage, whereas at the east of the two countries at midland altitude, they belonged to the S4-lv lineage. The presence of RYMV in Burundi should be considered in the future integrative pest management strategies for rice cultivation in the country. References: (1) D. Fargette et al. Annu. Rev. Phytopathol. 44:235, 2006. (2) Z. L. Kanyeka et al. Afr. Crop Sci. J. 15:201, 2007. (3) I. Ndikumana et al. New Dis. Rep. 23:18, 2011.
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Affiliation(s)
- I Ndikumana
- Crop Production Unit, Rwanda Agriculture Board, P. O. Box 5016, Kigali, Rwanda
| | - A Pinel-Galzi
- UMR RPB, Institut de Recherche pour le Developpment (IRD), BP 64501, 34394 Montpellier Cedex 5, France
| | - Z Negussie
- Africa Rice Center (AfricaRice), P. O. Box 33581, Dar es Salaam, Tanzania
| | - S N'chimbi Msolla
- Sokoine University of Agriculture, P. O. Box 3000 Morogoro, Tanzania
| | - P Njau
- Sokoine University of Agriculture, P. O. Box 3000 Morogoro, Tanzania
| | - R K Singh
- International Rice Research Institute (IRRI), P. O. Box 33581, Dar es Salaam, Tanzania
| | - I R Choi
- IRRI, DAPO Box 7777, Metro Manila, Philippines
| | - J Bigirimana
- University of Burundi, P. O. Box 5132 Bujumbura, Burundi
| | - D Fargette
- UMR RPB, IRD, BP 64501, 34394 Montpellier Cedex 5, France
| | - E Hébrard
- UMR RPB, IRD, BP 64501, 34394 Montpellier Cedex 5, France
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Poulicard N, Pinel-Galzi A, Traoré O, Vignols F, Ghesquière A, Konaté G, Hébrard E, Fargette D. Historical contingencies modulate the adaptability of Rice yellow mottle virus. PLoS Pathog 2012; 8:e1002482. [PMID: 22291591 PMCID: PMC3266926 DOI: 10.1371/journal.ppat.1002482] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 11/29/2011] [Indexed: 12/28/2022] Open
Abstract
The rymv1-2 and rymv1-3 alleles of the RYMV1 resistance to Rice yellow mottle virus (RYMV), coded by an eIF(iso)4G1 gene, occur in a few cultivars of the Asiatic (Oryza sativa) and African (O. glaberrima) rice species, respectively. The most salient feature of the resistance breaking (RB) process is the converse genetic barrier to rymv1-2 and rymv1-3 resistance breakdown. This specificity is modulated by the amino acid (glutamic acid vs. threonine) at codon 49 of the Viral Protein genome-linked (VPg), a position which is adjacent to the virulence codons 48 and 52. Isolates with a glutamic acid (E) do not overcome rymv1-3 whereas those with a threonine (T) rarely overcome rymv1-2. We found that isolates with T49 had a strong selective advantage over isolates with E49 in O. glaberrima susceptible cultivars. This explains the fixation of the mutation T49 during RYMV evolution and accounts for the diversifying selection estimated at codon 49. Better adapted to O. glaberrima, isolates with T49 are also more prone than isolates with E49 to fix rymv1-3 RB mutations at codon 52 in resistant O. glaberrima cultivars. However, subsequent genetic constraints impaired the ability of isolates with T49 to fix rymv1-2 RB mutations at codons 48 and 52 in resistant O. sativa cultivars. The origin and role of the amino acid at codon 49 of the VPg exemplifies the importance of historical contingencies in the ability of RYMV to overcome RYMV1 resistance.
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Affiliation(s)
- Nils Poulicard
- Institut de Recherche pour le Développement (IRD), UMR RPB (IRD, CIRAD, Université Montpellier 2), Montpellier, France
| | - Agnès Pinel-Galzi
- Institut de Recherche pour le Développement (IRD), UMR RPB (IRD, CIRAD, Université Montpellier 2), Montpellier, France
| | - Oumar Traoré
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina-Faso
| | - Florence Vignols
- Institut de Recherche pour le Développement (IRD), UMR RPB (IRD, CIRAD, Université Montpellier 2), Montpellier, France
| | - Alain Ghesquière
- Institut de Recherche pour la Développement (IRD), UMR DIADE (IRD, CIRAD, Université Montpellier 2), Montpellier, France
| | - Gnissa Konaté
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina-Faso
| | - Eugénie Hébrard
- Institut de Recherche pour le Développement (IRD), UMR RPB (IRD, CIRAD, Université Montpellier 2), Montpellier, France
| | - Denis Fargette
- Institut de Recherche pour le Développement (IRD), UMR RPB (IRD, CIRAD, Université Montpellier 2), Montpellier, France
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Hoang AT, Zhang HM, Yang J, Chen JP, Hébrard E, Zhou GH, Vinh VN, Cheng JA. Identification, Characterization, and Distribution of Southern rice black-streaked dwarf virus in Vietnam. Plant Dis 2011; 95:1063-1069. [PMID: 30732067 DOI: 10.1094/pdis-07-10-0535] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A novel dwarf and twisting syndrome first observed on rice in Nghe An Province, Vietnam, in 2009 has spread rapidly to the other 19 provinces of North and Central Vietnam. Infected rice plants showed stunting, darkening of leaves, twisting of leaf tips, and splitting of leaf margins. At a later stage, white waxy enations that eventually turned black were observed on the underside of leaf blades, leaf sheaths, and culms. The disease also infected maize after rice was harvested. Infected maize plants were stunted and dark green with small enations along the minor veins on the back of leaves. The disease agent has now been identified as Southern rice black-streaked dwarf virus (SRBSDV) recently reported from Southern China. Typical fijivirus viroplasms containing crystalline arrayed spherical virions approximately 70 to 75 nm in diameter were observed under the electron microscope in ultrathin sections of infected rice leaves. The virus was transmitted to rice and maize seedlings by the white-backed planthopper (Sogatella furcimera). A one-step reverse transcription-polymerase chain reaction (RT-PCR) protocol was used to confirm the presence of SRBSDV in 477 samples of rice or maize from 29 provinces among 5 agroecological regions in North and Central Vietnam. Rice black-streaked dwarf virus was not detected in these samples. Partial sequences of RNA segments 4 and 10 from several isolates showed very low genetic divergences between isolates from Vietnam and China, suggesting a common origin, and phylogenetic analysis confirmed the placement of SRBSDV as a distinct virus within subgroup 2 of the genus Fijivirus.
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Affiliation(s)
- Anh Ta Hoang
- Plant Protection Research Institute, Hanoi, Vietnam
| | - Heng-Mu Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences (ZAAS), Hangzhou 310021, China
| | - Jian Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences (ZAAS), Hangzhou 310021, China
| | - Jian-Ping Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences (ZAAS), Hangzhou 310021, China
| | - Eugénie Hébrard
- UMR 186 Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement (IRD), 34394 Montpellier, Cedex 05, France
| | - Guo-Hui Zhou
- Laboratory of Plant Virology, South China Agricultural University, Guangzhou 510642, China
| | | | - Jia-An Cheng
- Institute of Entomology, Zhejiang University, Hangzhou 310029, China
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Hébrard E, Poulicard N, Gérard C, Traoré O, Wu HC, Albar L, Fargette D, Bessin Y, Vignols F. Direct interaction between the Rice yellow mottle virus (RYMV) VPg and the central domain of the rice eIF(iso)4G1 factor correlates with rice susceptibility and RYMV virulence. Mol Plant Microbe Interact 2010; 23:1506-13. [PMID: 20653414 DOI: 10.1094/mpmi-03-10-0073] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The adaptation of Rice yellow mottle virus (RYMV) to recessive resistance mediated by the rymv1-2 allele has been reported as a model to study the emergence and evolution of virulent variants. The resistance and virulence factors have been identified as eukaryotic translation initiation factor eIF(iso)4G1 and viral genome-linked protein (VPg), respectively, but the molecular mechanisms involved in their interaction are still unknown. In this study, we demonstrated a direct interaction between RYMV VPg and the central domain of rice eIF(iso)4G1 both in vitro, using recombinant proteins, and in vivo, using a yeast two-hybrid assay. Insertion of the E309K mutation in eIF(iso)4G1, conferring resistance in planta, strongly diminished the interaction with avirulent VPg. The efficiency of the major virulence mutations at restoring the interaction with the resistance protein was assessed. Our results explain the prevalence of virulence mutations fixed during experimental evolution studies and are consistent with the respective viral RNA accumulation levels of avirulent and virulent isolates. Our results also explain the origin of the residual multiplication of wild-type isolates in rymv1-2-resistant plants and the role of genetic context in the poor adaptability of the S2/S3 strain. Finally, the strategies of RYMV and members of family Potyviridae to overcome recessive resistance were compared.
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Affiliation(s)
- Eugénie Hébrard
- UMR186 Résistance des Plantes aux Bio-agresseurs, Institut de Recherche pour le Développement BP 64501, 34394 Montpellier cedex 5, France.
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25
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Hébrard E, Dobrijevic M, Pernot P, Carrasco N, Bergeat A, Hickson KM, Canosa A, Le Picard SD, Sims IR. How Measurements of Rate Coefficients at Low Temperature Increase the Predictivity of Photochemical Models of Titan’s Atmosphere. J Phys Chem A 2009; 113:11227-37. [DOI: 10.1021/jp905524e] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - P. Pernot
- Laboratoire de Chimie Physique, UMR 8000, CNRS-Université Paris-Sud 11, Bât. 349, Orsay, F-91405, France
| | - N. Carrasco
- Laboratoire Atmosphères, Milieux, Observations Spatiales, UMR 8190, CNRS-IPSL-Université de Versailles Saint Quentin, BP 3, Verrières le Buisson, F-91371, France
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Hébrard E, Bessin Y, Michon T, Longhi S, Uversky VN, Delalande F, Van Dorsselaer A, Romero P, Walter J, Declerk N, Fargette D. Intrinsic disorder in Viral Proteins Genome-Linked: experimental and predictive analyses. Virol J 2009; 6:23. [PMID: 19220875 PMCID: PMC2649914 DOI: 10.1186/1743-422x-6-23] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Accepted: 02/16/2009] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND VPgs are viral proteins linked to the 5' end of some viral genomes. Interactions between several VPgs and eukaryotic translation initiation factors eIF4Es are critical for plant infection. However, VPgs are not restricted to phytoviruses, being also involved in genome replication and protein translation of several animal viruses. To date, structural data are still limited to small picornaviral VPgs. Recently three phytoviral VPgs were shown to be natively unfolded proteins. RESULTS In this paper, we report the bacterial expression, purification and biochemical characterization of two phytoviral VPgs, namely the VPgs of Rice yellow mottle virus (RYMV, genus Sobemovirus) and Lettuce mosaic virus (LMV, genus Potyvirus). Using far-UV circular dichroism and size exclusion chromatography, we show that RYMV and LMV VPgs are predominantly or partly unstructured in solution, respectively. Using several disorder predictors, we show that both proteins are predicted to possess disordered regions. We next extend theses results to 14 VPgs representative of the viral diversity. Disordered regions were predicted in all VPg sequences whatever the genus and the family. CONCLUSION Based on these results, we propose that intrinsic disorder is a common feature of VPgs. The functional role of intrinsic disorder is discussed in light of the biological roles of VPgs.
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Affiliation(s)
- Eugénie Hébrard
- UMR 1097 Résistance des Plantes aux Bio-agresseurs, IRD, CIRAD, Université de Montpellier II, BP 64501, 34394 Montpellier cedex 5, France
| | - Yannick Bessin
- Centre de Biochimie Structurale, UMR 5048, 29 rue de Navacelles, 34090 Montpellier, France
| | - Thierry Michon
- UMR1090 Génomique Diversité Pouvoir Pathogène, INRA, Université de Bordeaux 2, F-33883 Villenave D'Ornon, France
| | - Sonia Longhi
- UMR 6098 Architecture et Fonction des Macromolécules Biologiques, CNRS, Universités Aix-Marseille I et II, Campus de Luminy, 13288 Marseille Cedex 09, France
| | - Vladimir N Uversky
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - François Delalande
- Laboratoire de Spectrométrie de Masse Bio-Organique, ECPM, 67087 Strasbourg, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-Organique, ECPM, 67087 Strasbourg, France
| | - Pedro Romero
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jocelyne Walter
- UMR1090 Génomique Diversité Pouvoir Pathogène, INRA, Université de Bordeaux 2, F-33883 Villenave D'Ornon, France
| | - Nathalie Declerk
- Centre de Biochimie Structurale, UMR 5048, 29 rue de Navacelles, 34090 Montpellier, France
| | - Denis Fargette
- UMR 1097 Résistance des Plantes aux Bio-agresseurs, IRD, CIRAD, Université de Montpellier II, BP 64501, 34394 Montpellier cedex 5, France
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Fargette D, Pinel-Galzi A, Sérémé D, Lacombe S, Hébrard E, Traoré O, Konaté G. Diversification of rice yellow mottle virus and related viruses spans the history of agriculture from the neolithic to the present. PLoS Pathog 2008; 4:e1000125. [PMID: 18704169 PMCID: PMC2495034 DOI: 10.1371/journal.ppat.1000125] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Accepted: 07/14/2008] [Indexed: 11/18/2022] Open
Abstract
The mechanisms of evolution of plant viruses are being unraveled, yet the timescale of their evolution remains an enigma. To address this critical issue, the divergence time of plant viruses at the intra- and inter-specific levels was assessed. The time of the most recent common ancestor (TMRCA) of Rice yellow mottle virus (RYMV; genus Sobemovirus) was calculated by a Bayesian coalescent analysis of the coat protein sequences of 253 isolates collected between 1966 and 2006 from all over Africa. It is inferred that RYMV diversified approximately 200 years ago in Africa, i.e., centuries after rice was domesticated or introduced, and decades before epidemics were reported. The divergence time of sobemoviruses and viruses of related genera was subsequently assessed using the age of RYMV under a relaxed molecular clock for calibration. The divergence time between sobemoviruses and related viruses was estimated to be approximately 9,000 years, that between sobemoviruses and poleroviruses approximately 5,000 years, and that among sobemoviruses approximately 3,000 years. The TMRCA of closely related pairs of sobemoviruses, poleroviruses, and luteoviruses was approximately 500 years, which is a measure of the time associated with plant virus speciation. It is concluded that the diversification of RYMV and related viruses has spanned the history of agriculture, from the Neolithic age to the present.
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Affiliation(s)
- Denis Fargette
- Institut de Recherche pour le Développement, UMR RPB, Montpellier, France.
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Fargette D, Pinel A, Rakotomalala M, Sangu E, Traoré O, Sérémé D, Sorho F, Issaka S, Hébrard E, Séré Y, Kanyeka Z, Konaté G. Rice yellow mottle virus, an RNA plant virus, evolves as rapidly as most RNA animal viruses. J Virol 2008; 82:3584-9. [PMID: 18199644 PMCID: PMC2268501 DOI: 10.1128/jvi.02506-07] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Accepted: 01/04/2008] [Indexed: 11/20/2022] Open
Abstract
The rate of evolution of an RNA plant virus has never been estimated using temporally spaced sequence data, by contrast to the information available on an increasing range of animal viruses. Accordingly, the evolution rate of Rice yellow mottle virus (RYMV) was calculated from sequences of the coat protein gene of isolates collected from rice over a 40-year period in different parts of Africa. The evolution rate of RYMV was estimated by pairwise distance linear regression on five phylogeographically defined groups comprising a total of 135 isolates. It was further assessed from 253 isolates collected all over Africa by Bayesian coalescent methods under strict and relaxed molecular clock models and under constant size and skyline population genetic models. Consistent estimates of the evolution rate between 4 x 10(-4) and 8 x 10(-4) nucleotides (nt)/site/year were obtained whatever method and model were applied. The synonymous evolution rate was between 8 x 10(-4) and 11 x 10(-4) nt/site/year. The overall and synonymous evolution rates of RYMV were within the range of the rates of 50 RNA animal viruses, below the average but above the distribution median. Experimentally, in host change studies, substitutions accumulated at an even higher rate. The results show that an RNA plant virus such as RYMV evolves as rapidly as most RNA animal viruses. Knowledge of the molecular clock of plant viruses provides methods for testing a wide range of biological hypotheses.
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Affiliation(s)
- D Fargette
- Institut de Recherche pour le Développement (IRD), UMR RPB, BP 64501, 34394 Montpellier cedex 5, France.
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Blanc M, Uzest M, Candresse T, Drucker M, Fereres A, Gargani D, Garzo E, Hébrard E. [A key protein for transmission of plant viruses at the tip of the insect vector stylet]. Virologie (Montrouge) 2008; 12:70-72. [PMID: 36131435 DOI: 10.1684/12-1.2011.10009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- M Blanc
- UMR BGPI, Inra-Cirad-AgroM, TA A54/K, Campus international de Baillarguet, 34398 Montpellier Cedex 05
| | - M Uzest
- UMR BGPI, Inra-Cirad-AgroM, TA A54/K, Campus international de Baillarguet, 34398 Montpellier Cedex 05
| | | | - M Drucker
- UMR BGPI, Inra-Cirad-AgroM, TA A54/K, Campus international de Baillarguet, 34398 Montpellier Cedex 05
| | | | - D Gargani
- UMR BGPI, Inra-Cirad-AgroM, TA A54/K, Campus international de Baillarguet, 34398 Montpellier Cedex 05
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Pinel-Galzi A, Rakotomalala M, Sangu E, Sorho F, Kanyeka Z, Traoré O, Sérémé D, Poulicard N, Rabenantoandro Y, Séré Y, Konaté G, Ghesquière A, Hébrard E, Fargette D. Theme and variations in the evolutionary pathways to virulence of an RNA plant virus species. PLoS Pathog 2007; 3:e180. [PMID: 18039030 PMCID: PMC2094307 DOI: 10.1371/journal.ppat.0030180] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 10/12/2007] [Indexed: 11/19/2022] Open
Abstract
The diversity of a highly variable RNA plant virus was considered to determine the range of virulence substitutions, the evolutionary pathways to virulence, and whether intraspecific diversity modulates virulence pathways and propensity. In all, 114 isolates representative of the genetic and geographic diversity of Rice yellow mottle virus (RYMV) in Africa were inoculated to several cultivars with eIF(iso)4G-mediated Rymv1-2 resistance. Altogether, 41 virulent variants generated from ten wild isolates were analyzed. Nonconservative amino acid replacements at five positions located within a stretch of 15 codons in the central region of the 79-aa-long protein VPg were associated with virulence. Virulence substitutions were fixed predominantly at codon 48 in most strains, whatever the host genetic background or the experimental conditions. There were one major and two isolate-specific mutational pathways conferring virulence at codon 48. In the prevalent mutational pathway I, arginine (AGA) was successively displaced by glycine (GGA) and glutamic acid (GAA). Substitutions in the other virulence codons were displaced when E48 was fixed. In the isolate-specific mutational pathway II, isoleucine (ATA) emerged and often later coexisted with valine (GTA). In mutational pathway III, arginine, with the specific S2/S3 strain codon usage AGG, was displaced by tryptophane (TGG). Mutational pathway I never arose in the widely spread West African S2/S3 strain because G48 was not infectious in the S2/S3 genetic context. Strain S2/S3 least frequently overcame resistance, whereas two geographically localized variants of the strain S4 had a high propensity to virulence. Codons 49 and 26 of the VPg, under diversifying selection, are candidate positions in modulating the genetic barriers to virulence. The theme and variations in the evolutionary pathways to virulence of RYMV illustrates the extent of parallel evolution within a highly variable RNA plant virus species.
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Affiliation(s)
- Agnès Pinel-Galzi
- Institut de Recherche pour le Développement (IRD), UMR RPB, Montpellier, France
| | - Mbolarinosy Rakotomalala
- Centre National de la Recherche Appliquée au Développement Rural (FOFIFA), Mahajanga, Madagascar
| | - Emmanuel Sangu
- Botany Department, Dar es Salaam University, Dar es Salaam, Tanzania
| | | | - Zakaria Kanyeka
- Botany Department, Dar es Salaam University, Dar es Salaam, Tanzania
| | - Oumar Traoré
- Institut de l'Environnement et de Recherches Agricoles (INERA), Laboratoire de Biotechnologie et de Virologie Végétale, Kamboinsé, Ouagadougou, Burkina Faso
| | - Drissa Sérémé
- Institut de l'Environnement et de Recherches Agricoles (INERA), Laboratoire de Biotechnologie et de Virologie Végétale, Kamboinsé, Ouagadougou, Burkina Faso
| | - Nils Poulicard
- Institut de Recherche pour le Développement (IRD), UMR RPB, Montpellier, France
| | - Yvonne Rabenantoandro
- Centre National de la Recherche Appliquée au Développement Rural (FOFIFA), Antananarivo, Madagascar
| | | | - Gnissa Konaté
- Institut de l'Environnement et de Recherches Agricoles (INERA), Laboratoire de Biotechnologie et de Virologie Végétale, Kamboinsé, Ouagadougou, Burkina Faso
| | - Alain Ghesquière
- Institut de Recherche pour le Développement (IRD), UMR GDP, Montpellier, France
| | - Eugénie Hébrard
- Institut de Recherche pour le Développement (IRD), UMR RPB, Montpellier, France
| | - Denis Fargette
- Institut de Recherche pour le Développement (IRD), UMR RPB, Montpellier, France
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Hébrard E, Dobrijevic M, Bénilan Y, Raulin F. Photochemical kinetics uncertainties in modeling Titan’s atmosphere: A review. Journal of Photochemistry and Photobiology C: Photochemistry Reviews 2006. [DOI: 10.1016/j.jphotochemrev.2006.12.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Albar L, Bangratz-Reyser M, Hébrard E, Ndjiondjop MN, Jones M, Ghesquière A. Mutations in the eIF(iso)4G translation initiation factor confer high resistance of rice to Rice yellow mottle virus. Plant J 2006; 47:417-26. [PMID: 16774645 DOI: 10.1111/j.1365-313x.2006.02792.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We report here evidence of the role that the isoform of the eukaryotic translation initiation factor 4G (eIF(iso)4G) plays in naturally occurring resistance in plant/virus interactions. A genetic and physical mapping approach was developed to isolate the Rymv1 locus controlling the high recessive resistance to Rice yellow mottle virus (RYMV) in the rice (Oryza sativa) variety Gigante. The locus was mapped to a 160-kb interval containing a gene from the eIF(iso)4G family. The stable transformation of a resistant line with the cDNA of this gene, derived from a susceptible variety, resulted in the loss of resistance in transgenic plants. The allelic variability of this gene was analysed in three resistant and 17 susceptible varieties from different cultivated rice species or subspecies. Compared with susceptible varieties, resistant varieties present specific alleles, characterized by either amino acid substitutions or short amino-acid deletions in the middle domain of the protein. The structure of this domain was modelled and showed that the substitutions were clustered on a small surface patch. This suggests that this domain may be involved in an interaction with the virus.
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Affiliation(s)
- Laurence Albar
- UMR 5096, IRD/CNRS/Université de Perpignan, BP 64501, 34394 Montpellier CEDEX 5, France.
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Hébrard E, Pinel-Galzi A, Bersoult A, Siré C, Fargette D. Emergence of a resistance-breaking isolate of Rice yellow mottle virus during serial inoculations is due to a single substitution in the genome-linked viral protein VPg. J Gen Virol 2006; 87:1369-1373. [PMID: 16603540 DOI: 10.1099/vir.0.81659-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recessive gene rymv-1, responsible for the high resistance of Oryza sativa 'Gigante' to Rice yellow mottle virus (genus Sobemovirus), was overcome by the variant CI4*, which emerged after serial inoculations of the non-resistance-breaking (nRB) isolate CI4. By comparison of the full-length sequences of CI4 and CI4*, a non-synonymous mutation was identified at position 1729, localized in the putative VPg domain, and an assay was developed based on this single-nucleotide polymorphism. The mutation G1729T was detected as early as the first passage in resistant plants and was found in all subsequent passages. Neither reversion nor any additional mutation was observed. The substitution G1729T, introduced by mutagenesis into the VPg of an nRB infectious clone, was sufficient to induce symptoms in uninoculated leaves of O. sativa 'Gigante'. This is the first evidence that VPg is a virulence factor in plants with recessive resistance against viruses outside the family Potyviridae.
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Affiliation(s)
- Eugénie Hébrard
- UR 141, Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier cedex 5, France
| | - Agnès Pinel-Galzi
- UR 141, Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier cedex 5, France
| | - Anne Bersoult
- UR 141, Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier cedex 5, France
| | - Christelle Siré
- UR 121, Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier cedex 5, France
| | - Denis Fargette
- UR 141, Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier cedex 5, France
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Traoré O, Pinel A, Hébrard E, Dieudonné Gumedzoé MY, Fargette D, Traoré AS, Konaté G. Occurrence of Resistance-Breaking Isolates of Rice yellow mottle virus in West and Central Africa. Plant Dis 2006; 90:259-263. [PMID: 30786546 DOI: 10.1094/pd-90-0259] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rice yellow mottle virus (RYMV) is the most important rice-infecting virus in Africa. Highly resistant rice (Oryza spp.) cultivars Gigante and Tog5681 were challenged with virus isolates from five countries of the west and central African Sudano-savannah zone in order to investigate the occurrence and prevalence of resistance-breaking (RB) isolates. High resistance was overcome by 38.6% of the isolates. RB isolates could be divided into three main pathogenic groups. Isolates of the first group (17.5%) and of the second group (16.4%) were able to break down the resistance of Gigante only and of Tog5681 only, respectively. Resistance in both cultivars was overcome simultaneously by isolates of the third group (4.7%). In each group, some isolates induced symptoms, whereas plant infection by others was evidenced only by serological tests. RB isolates occurred in all five countries with varying frequencies (19 to 57%). The wide geographical distribution and high frequencies of RB isolates represent a high risk for the durability of resistance to RYMV in the Sudano-savannah zone.
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Affiliation(s)
- Oumar Traoré
- Institut de l' Environnement et de Recherches Agricoles (INERA) 01 BP 476 Ouagadougou 01, Burkina Faso
| | - Agnès Pinel
- Institut de Recherche pour le Développement, IRD, 64501, 34394 Montpellier cedex 5, France
| | - Eugénie Hébrard
- Institut de Recherche pour le Développement, IRD, 64501, 34394 Montpellier cedex 5, France
| | | | - Denis Fargette
- Institut de Recherche pour le Développement, IRD, 64501, 34394 Montpellier cedex 5, France
| | - Alfred S Traoré
- UFR/SVT, Département de Biochimie-Microbiologie, BP 7021 Oua-gadougou, Burkina Faso
| | - Gnissa Konaté
- Institut de l' Environnement et de Recherches Agricoles (INERA) 01 BP 476 Ouagadougou 01, Burkina Faso
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Moreno A, Hébrard E, Uzest M, Blanc S, Fereres A. A single amino acid position in the helper component of cauliflower mosaic virus can change the spectrum of transmitting vector species. J Virol 2005; 79:13587-93. [PMID: 16227279 PMCID: PMC1262581 DOI: 10.1128/jvi.79.21.13587-13593.2005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses frequently use insect vectors to effect rapid spread through host populations. In plant viruses, vector transmission is the major mode of transmission, used by nearly 80% of species described to date. Despite the importance of this phenomenon in epidemiology, the specificity of the virus-vector relationship is poorly understood at both the molecular and the evolutionary level, and very limited data are available on the precise viral protein motifs that control specificity. Here, using the aphid-transmitted Cauliflower mosaic virus (CaMV) as a biological model, we confirm that the "noncirculative" mode of transmission dominant in plant viruses (designated "mechanical vector transmission" in animal viruses) involves extremely specific virus-vector recognition, and we identify an amino acid position in the "helper component" (HC) protein of CaMV involved in such recognition. Site-directed mutagenesis revealed that changing the residue at this position can differentially affect transmission rates obtained with various aphid species, thus modifying the spectrum of vector species for CaMV. Most interestingly, in a virus line transmitted by a single vector species, we observed the rapid appearance of a spontaneous mutant specifically losing its transmissibility by another aphid species. Hence, in addition to the first identification of an HC motif directly involved in specific vector recognition, we demonstrate that change of a virus to a different vector species requires only a single mutation and can occur rapidly and spontaneously.
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Affiliation(s)
- Aranzazu Moreno
- UMR Biologie et Génétique des Interactions Plantes-Parasites, CIRAD-INRA-ENSAM, TA 41/K, Campus International de Baillarguet, 34398 Montpellier cedex 05, France
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36
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Hébrard E, Pinel-Galzi A, Catherinot V, Labesse G, Brugidou C, Fargette D. Internal point mutations of the capsid modify the serotype of Rice yellow mottle virus. J Virol 2005; 79:4407-14. [PMID: 15767440 PMCID: PMC1061534 DOI: 10.1128/jvi.79.7.4407-4414.2005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rice yellow mottle virus is classified in five major serotypes; the molecular diversity of the coat protein (CP) is well established, but the amino acids involved in the recognition by discriminant monoclonal antibodies (MAbs) remain unknown. Reconstruction of a phylogenetic tree and sequence alignment of the CP gene of a sample representative of the continental-large diversity were used to identify 10 serospecific amino acids (i.e., conserved in all isolates belonging to the same serotype and distinct in other serotypes). Positions occupied by serospecific residues were localized on the crystal structure of the CP monomer and on modeled capsomers. Structural, molecular, and serological properties of each serotype were analyzed, and subsequently, hypotheses on the potential role of amino acids in discriminating reactions with antibodies were formulated. The residues 114 and 115 (serospecific of Sr1) and 190 (serospecific of Sr2) were localized on the outer surface of the capsid and might be directly involved in the immunoreactivity with MAb D and MAb A, respectively. In contrast, residues 180 (Sr3) and 178 (Sr5) lay within the inner surface of the capsid. To understand the role of these internal positions in the recognition with the antibodies, two substitutions (T180K and G178D) were introduced in the CP of an infectious clone. These mutations modified the antigenicity with MAb G and MAb E discriminating Sr3 and Sr5, respectively, while the reaction with MAb D remained unaffected. This result suggests an indirect effect of these two internal mutations on local immunostructure while the global structure was maintained.
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Affiliation(s)
- Eugénie Hébrard
- Institut de Recherche pour le Dévelopment, Montpellier, France.
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Froissart R, Uzest M, Ruiz-Ferrer V, Drucker M, Hébrard E, Hohn T, Blanc S. Splicing of Cauliflower mosaic virus 35S RNA serves to downregulate a toxic gene product. J Gen Virol 2004; 85:2719-2726. [PMID: 15302965 DOI: 10.1099/vir.0.80029-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Alternative splicing usually leads to an increase in the number of gene products that can be derived from a single transcript. Here, a different and novel use of alternative splicing – as a means to control the amount of a potentially toxic gene product in the plant pararetrovirus Cauliflower mosaic virus (CaMV) – is reported. About 70 % of the CaMV 35S RNA, which serves as a substrate for both reverse transcription and polycistronic mRNA, is spliced into four additional RNA species. Splicing occurs between four donor sites – one in the 5′ untranslated region and three within open reading frame (ORF) I – and one unique acceptor site at position 1508 in ORF II. A previous study revealed that the acceptor site is vital for CaMV infectivity and expression of ORFs III and IV from one of the spliced RNA species suggested that splicing may facilitate expression of downstream CaMV ORFs. However, it is shown here that deleting the splice acceptor site and replacing ORF II with a cargo ORF that lacks splice acceptor sites does not interfere with virus proliferation. Furthermore, it is demonstrated that whenever P2 cannot accumulate in infected tissues, the splice acceptor site at position 1508 is no longer vital and has little effect on virus replication. This suggests that the vital role of splicing in CaMV is regulation of P2 expression and that P2 exhibits biological properties that, whilst indispensable for virus–vector interactions, can block in planta virus infection if this regulation is abolished.
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Affiliation(s)
- Rémy Froissart
- UMR BGPI, CIRAD-INRA-ENSAM, TA 41/K, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Maryline Uzest
- UMR BGPI, CIRAD-INRA-ENSAM, TA 41/K, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Virginia Ruiz-Ferrer
- UMR BGPI, CIRAD-INRA-ENSAM, TA 41/K, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Martin Drucker
- UMR BGPI, CIRAD-INRA-ENSAM, TA 41/K, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Eugénie Hébrard
- UMR BGPI, CIRAD-INRA-ENSAM, TA 41/K, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Thomas Hohn
- Friedrich Miescher Institut, PO Box 2543, CH-4002 Basel, Switzerland
| | - Stéphane Blanc
- UMR BGPI, CIRAD-INRA-ENSAM, TA 41/K, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
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Fargette D, Pinel A, Abubakar Z, Traoré O, Brugidou C, Fatogoma S, Hébrard E, Choisy M, Séré Y, Fauquet C, Konaté G. Inferring the evolutionary history of rice yellow mottle virus from genomic, phylogenetic, and phylogeographic studies. J Virol 2004; 78:3252-61. [PMID: 15016846 PMCID: PMC371063 DOI: 10.1128/jvi.78.7.3252-3261.2004] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2003] [Accepted: 12/09/2003] [Indexed: 11/20/2022] Open
Abstract
Fourteen isolates of Rice yellow mottle virus (RYMV) were selected as representative of the genetic variability of the virus in Africa from a total set of 320 isolates serologically typed or partially sequenced. The 14 isolates were fully sequenced and analyzed together with two previously reported sequences. RYMV had a genomic organization similar to that of Cocksfoot mottle sobemovirus. The average nucleotide diversity among the 16 isolates of RYMV was 7%, and the maximum diversity between any two isolates was 10%. A strong conservative selection was apparent on both synonymous and nonsynonymous substitutions, through the amino acid replacement pattern, on the genome size, and through the limited number of indel events. Furthermore, there was a lack of positive selection on single amino acid sites and no evidence of recombination events. RYMV diversity had a pronounced and characteristic geographic structure. The branching order of the clades correlated with the geographic origin of the isolates along an east-to-west transect across Africa, and there was a marked decrease in nucleotide diversity moving westward across the continent. The insertion-deletion polymorphism was related to virus phylogeny. There was a partial phylogenetic incongruence between the coat protein gene and the rest of the genome. Overall, our results support the hypothesis that RYMV originated in East Africa and then dispersed and differentiated gradually from the east to the west of the continent.
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Drucker M, Froissart R, Hébrard E, Uzest M, Ravallec M, Espérandieu P, Mani JC, Pugnière M, Roquet F, Fereres A, Blanc S. Intracellular distribution of viral gene products regulates a complex mechanism of cauliflower mosaic virus acquisition by its aphid vector. Proc Natl Acad Sci U S A 2002; 99:2422-7. [PMID: 11842201 PMCID: PMC122380 DOI: 10.1073/pnas.042587799] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Interactions between Cauliflower mosaic virus (CaMV) and its aphid vector are regulated by the viral protein P2, which binds to the aphid stylets, and protein P3, which bridges P2 and virions. By using baculovirus expression of P2 and P3, electron microscopy, surface plasmon resonance, affinity chromatography, and transmission assays, we demonstrate that P3 must be previously bound to virions in order that attachment to P2 will allow aphid transmission of CaMV. We also show that a P2:P3 complex exists in the absence of virions but is nonfunctional in transmission. Hence, unlike P2, P3 and virions cannot be sequentially acquired by the vector. Immunogold labeling revealed the predominance of spatially separated P2:P3 and P3:virion complexes in infected plant cells. This specific distribution indicates that the transmissible complex, P2:P3:virion, does not form primarily in infected plants but in aphids. A model, describing the regulating role of P3 in the formation of the transmissible CaMV complex in planta and during acquisition by aphids, is presented, and its consequences are discussed.
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Affiliation(s)
- Martin Drucker
- Station de Recherches de Pathologie Comparée, Unité Mixte de Recherche 5087 Institut National de la Recherche Agronomique-Centre National de la Recherche Scientifique-Université Montpellier II, 30380 Saint-Christol-lez-Alès, France
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