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Diouf MB, Guyader S, Nopoly MM, Gaspard O, Filloux D, Candresse T, Marais A, Teycheney PY, Umber M. Molecular diversity of yam virus Y and identification of banana mild mosaic virus isolates infecting yam (Dioscorea spp.). Arch Virol 2023; 168:180. [PMID: 37311875 DOI: 10.1007/s00705-023-05809-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 06/15/2023]
Abstract
Two members of the family Betaflexiviridae associated with yam (Dioscorea spp.) have been described so far: yam latent virus (YLV) and yam virus Y (YVY). However, their geographical distribution and molecular diversity remain poorly documented. Using a nested RT-PCR assay, we detected YVY in D. alata, D. bulbifera, D. cayenensis, D. rotundata, and D. trifida in Guadeloupe, and in D. rotundata in Côte d'Ivoire, thus extending the known host range of this virus and geographical distribution. Using amplicon sequencing, we determined that the molecular diversity of YVY in the yam samples analyzed in this work ranged between 0.0 and 29.1% and that this diversity is partially geographically structured. We also identified three isolates of banana mild mosaic virus (BanMMV) infecting D. alata in Guadeloupe, providing the first evidence for BanMMV infection in yam.
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Affiliation(s)
- Mame Boucar Diouf
- INRAE, UR ASTRO, 97170, Petit‑Bourg, Guadeloupe, France
- CIRAD, UMR AGAP Institut, 97130, Capesterre Belle Eau, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 97130, Capesterre Belle Eau, France
| | | | | | | | - Denis Filloux
- CIRAD, UMR PHIM, 34090, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | - Thierry Candresse
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Pierre-Yves Teycheney
- CIRAD, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France
- UMR PVBMT, Université de la Réunion, 97410, Saint-Pierre, La Réunion, France
| | - Marie Umber
- INRAE, UR ASTRO, 97170, Petit‑Bourg, Guadeloupe, France.
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Epidemiology of Yam Viruses in Guadeloupe: Role of Cropping Practices and Seed-Tuber Supply. Viruses 2022; 14:v14112366. [PMID: 36366464 PMCID: PMC9692558 DOI: 10.3390/v14112366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 01/31/2023] Open
Abstract
The epidemiology of yam viruses remains largely unexplored. We present a large-scale epidemiological study of yam viruses in Guadeloupe based on the analysis of 1124 leaf samples collected from yams and weeds. We addressed the prevalence of cucumber mosaic virus (CMV), Cordyline virus 1 (CoV1), Dioscorea mosaic associated virus (DMaV), yam asymptomatic virus 1 (YaV1), yam mosaic virus (YMV), yam mild mosaic virus (YMMV), badnaviruses, macluraviruses and potexviruses, and the key epidemiological drivers of these viruses. We provide evidence that several weeds are reservoirs of YMMV and that YMMV isolates infecting weeds cluster together with those infecting yams, pointing to the role of weeds in the epidemiology of YMMV. We report the occurrence of yam chlorotic necrosis virus (YCNV) in Guadeloupe, the introduction of YMMV isolates through the importation of yam tubers, and the absence of vertical transmission of YaV1. We identified specific effects on some cropping practices, such as weed management and the use of chemical pesticides, on the occurrence of a few viruses, but no crop-related factor had a strong or general effect on the overall epidemiology of the targeted viruses. Overall, our work provides insights into the epidemiology of yam viruses that will help design more efficient control strategies.
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Diouf MB, Festus R, Silva G, Guyader S, Umber M, Seal S, Teycheney PY. Viruses of Yams (Dioscorea spp.): Current Gaps in Knowledge and Future Research Directions to Improve Disease Management. Viruses 2022; 14:v14091884. [PMID: 36146691 PMCID: PMC9501508 DOI: 10.3390/v14091884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 12/24/2022] Open
Abstract
Viruses are a major constraint for yam production worldwide. They hamper the conservation, movement, and exchange of yam germplasm and are a threat to food security in tropical and subtropical areas of Africa and the Pacific where yam is a staple food and a source of income. However, the biology and impact of yam viruses remains largely unknown. This review summarizes current knowledge on yam viruses and emphasizes gaps that exist in the knowledge of the biology of these viruses, their diagnosis, and their impact on production. It provides essential information to inform the implementation of more effective virus control strategies.
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Affiliation(s)
- Mame Boucar Diouf
- INRAE, UR ASTRO, F-97170 Petit-Bourg, France
- CIRAD, UMR AGAP Institut, F-97130 Capesterre-Belle-Eau, France
- UMR AGAP Institut, University Montpellier, CIRAD, INRAE, Institut Agro, F-97130 Capesterre-Belle-Eau, France
| | - Ruth Festus
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | | | - Marie Umber
- INRAE, UR ASTRO, F-97170 Petit-Bourg, France
| | - Susan Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | - Pierre Yves Teycheney
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, France
- UMR PVBMT, Université de la Réunion, F-97410 Saint-Pierre, France
- Correspondence: ; Tel.: +33-262-492-819
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Mendoza AR, Margaria P, Nagata T, Winter S, Blawid R. Characterization of yam mosaic viruses from Brazil reveals a new phylogenetic group and possible incursion from the African continent. Virus Genes 2022; 58:294-307. [PMID: 35538384 DOI: 10.1007/s11262-022-01903-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/31/2022] [Indexed: 11/29/2022]
Abstract
Yam (Dioscorea spp.) is an important crop for smallholder farmers in the Northeast region of Brazil. Wherever yam is grown, diseases caused by yam mosaic virus (YMV) are prevalent. In the present study, the diversity of YMV infecting Dioscorea cayennensis-rotundata was analyzed. In addition, five species of Dioscorea (D. alata, D. altissima, D. bulbifera, D. subhastata, and D. trifida) commonly found in Brazil were analyzed using ELISA and high-throughput sequencing (HTS). YMV was detected only in D. cayennensis-rotundata, of which 66.7% of the samples tested positive in ELISA. Three YMV genome sequences were assembled from HTS and one by Sanger sequencing to group the sequences in a clade phylogenetically distinct from YMV from other origins. Temporal phylogenetic analyses estimated the mean evolutionary rate for the CP gene of YMV as 1.76 × 10-3 substitutions per site per year, and the time to the most recent common ancestor as 168.68 years (95% Highest Posterior Density, HPD: 48.56-363.28 years), with a most likely geographic origin in the African continent. The data presented in this study contribute to reveal key aspects of the probable epidemiological history of YMV in Brazil.
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Affiliation(s)
- Alejandro Risco Mendoza
- Department of Agronomy, Fitossanidade, Laboratory of Phytovirology, Federal Rural University of Pernambuco, Recife, Brazil. .,Department of Plant Pathology, Agronomy Faculty, Universidad Nacional Agraria La Molina, Lima, Peru.
| | - Paolo Margaria
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Brunswick, Germany
| | - Tatsuya Nagata
- Department of Cell Biology, Laboratory of Electron Microscopy and Virology, University of Brasília, Distrito Federal, Brasília, Brazil
| | - Stephan Winter
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Brunswick, Germany
| | - Rosana Blawid
- Department of Agronomy, Fitossanidade, Laboratory of Phytovirology, Federal Rural University of Pernambuco, Recife, Brazil
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A Review of Viruses Infecting Yam ( Dioscorea spp.). Viruses 2022; 14:v14040662. [PMID: 35458392 PMCID: PMC9033002 DOI: 10.3390/v14040662] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Yam is an important food staple for millions of people globally, particularly those in the developing countries of West Africa and the Pacific Islands. To sustain the growing population, yam production must be increased amidst the many biotic and abiotic stresses. Plant viruses are among the most detrimental of plant pathogens and have caused great losses of crop yield and quality, including those of yam. Knowledge and understanding of virus biology and ecology are important for the development of diagnostic tools and disease management strategies to combat the spread of yam-infecting viruses. This review aims to highlight current knowledge on key yam-infecting viruses by examining their characteristics, genetic diversity, disease symptoms, diagnostics, and elimination to provide a synopsis for consideration in developing diagnostic strategy and disease management for yam.
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Entezari A, Mehrvar M, Zakiaghl M. Identification of garlic-infecting leek yellow stripe virus through deep-sequencing analyses from Iran. Virusdisease 2021; 32:595-600. [PMID: 34631984 DOI: 10.1007/s13337-021-00733-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/23/2021] [Indexed: 11/28/2022] Open
Abstract
In the study presented here, the first complete genome sequence of Leek yellow stripe virus (LYSV) designated as isolate LYSV-AE65 from Southwest of Iran, was reported. The small RNA deep sequencing analysis showed that, the Iranian isolate has a full RNA genome of 10,142 nucleotide in length (Except for poly (A) tail) and it was shared 77.91-92.16% nucleotide (nt) and 83.62-96.35% amino acid (aa) sequences identities with other known LYSV isolates. The coat protein (CP) region showed 80.21-95.24% nucleotide identity to those of other isolates, while high degrees of nucleotide sequence identity with G77-LYSV isolate (MN059504) from China. Phylogenetic analysis based on full genome sequence of LYSV-AE65, showed the closest relationship with LYSV isolates from China, Australia, Spain and Mexico. Also, phylogenetic analysis of the 5´-untranslated region (UTR)-P1 gene sequences of 44 isolates, confirmed the formation of two main groups, N-type and S-type, in agreement with the previous studies. Isolate LYSV-AE65 was similar to the members of clade S and has two large deletions in P1 gene. Recombination analysis demonstrated that LYSV-AE65 was a recombinant with most part of its genome was derived from already reported LYSV isolates infecting allium species. To the best of our knowledge, this is the first report of complete genome sequencing of LYSV isolate infecting garlic through small RNA deep sequencing method in Iran. Supplementary Information The online version contains supplementary material available at (10.1007/s13337-021-00733-z).
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Affiliation(s)
- Azadeh Entezari
- Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohsen Mehrvar
- Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Zakiaghl
- Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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Bakayoko Y, Kouakou AM, Kouassi AB, Gomez R, Dibi KEB, Essis BS, N’Zué B, Adebola P, N’Guetta AS, Umber M. Detection and diversity of viruses infecting African yam ( Dioscorea rotundata) in a collection and F 1 progenies in Côte d'Ivoire shed light to plant-to-plant viral transmission. PLANT PATHOLOGY 2021; 70:1486-1495. [PMID: 34413548 PMCID: PMC8360134 DOI: 10.1111/ppa.13393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/02/2021] [Accepted: 04/15/2021] [Indexed: 05/03/2023]
Abstract
Yam (Dioscorea spp.) is a major staple food whose production is hampered by viral diseases. However, the prevalence, diversity, transmission, and impact of yam-infecting viruses remain poorly documented. This study reports on the symptomatology, prevalence, and molecular diversity of eight viruses in 38 D. rotundata accessions from a germplasm collection and 206 F1 hybrid progenies maintained in Côte d'Ivoire. Mean severity scores as assessed from leaf symptoms ranged from 2 to 4 in the germplasm collection and from 1 to 3 in F1 hybrids, respectively. Dioscorea mosaic-associated virus (DMaV), potexviruses, and yam mosaic virus (YMV) were detected by PCR-based diagnosis tools in single and mixed infections in both the D. rotundata collection and F1 progenies, whereas badnaviruses were detected only in the germplasm collection. In contrast, cucumber mosaic virus (CMV), yam macluraviruses, yam asymptomatic virus 1 (YaV1), and yam mild mosaic virus (YMMV) could not be detected. No correlation could be established between severity scores and indexing results. Phylogenetic analysis performed on partial viral sequences amplified from infected samples unveiled the presence of two putative novel viral species belonging to genera Badnavirus and Potexvirus and provided evidence for plant-to-plant transmission of YMV, DMaV, and yam potexviruses.
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Affiliation(s)
- Yacouba Bakayoko
- Laboratoire de BiotechnologieAgriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët BoignyAbidjanCôte d'Ivoire
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Amani M. Kouakou
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Abou B. Kouassi
- Laboratoire de BiotechnologieAgriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët BoignyAbidjanCôte d'Ivoire
| | - Rose‐Marie Gomez
- Unité de Recherche Agrosystèmes TropicauxInstitut National de Recherche pour l’Agriculture, l’Alimentation et l’EnvironnementPetit‐BourgGuadeloupeFrance
| | - Konan E. B. Dibi
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Brice S. Essis
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Boni N’Zué
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Patrick Adebola
- International Institut of Tropical AgricultureIITA‐Abuja StationAbujaNigeria
| | - Assanvon S.‐P. N’Guetta
- Laboratoire de BiotechnologieAgriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët BoignyAbidjanCôte d'Ivoire
| | - Marie Umber
- Unité de Recherche Agrosystèmes TropicauxInstitut National de Recherche pour l’Agriculture, l’Alimentation et l’EnvironnementPetit‐BourgGuadeloupeFrance
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8
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Umber M, Filloux D, Gélabale S, Gomez RM, Marais A, Gallet S, Gamiette F, Pavis C, Teycheney PY. Molecular Viral Diagnosis and Sanitation of Yam Genetic Resources: Implications for Safe Yam Germplasm Exchange. Viruses 2020; 12:v12101101. [PMID: 33003342 PMCID: PMC7650539 DOI: 10.3390/v12101101] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 01/25/2023] Open
Abstract
Yam (Dioscorea spp.) is an important crop in tropical and subtropical regions. Many viruses have been recently identified in yam, hampering genetic conservation and safe international exchanges of yam germplasm. We report on the implementation of reliable and cost-effective PCR-based detection tools targeting eight different yam-infecting viruses. Viral indexing of the in vitro yam collection maintained by the Biological Resources Center for Tropical Plants (BRC-TP) in Guadeloupe (French West Indies) unveiled a high prevalence of potyviruses, badnaviruses, Dioscorea mosaic associated virus (DMaV) and yam asymptomatic virus 1 (YaV1) and a high level of coinfections. Infected yam accessions were subjected to a combination of thermotherapy and meristem culture. Sanitation levels were monitored using PCR-based and high-throughput sequencing-based diagnosis, confirming the efficacy and reliability of PCR-based detection tools. Sanitation rates were highly variable depending on viruses. Sixteen accessions were successfully sanitized, paving the way to safe yam germplasm exchanges and the implementation of clean seed production programs worldwide.
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Affiliation(s)
- Marie Umber
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
- Correspondence: ; Tel.: +590-590-25-59-29
| | - Denis Filloux
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche—Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France;
- Biologie et Génétique des Interactions Plante-Parasite, Univ. Montpellier, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Institut National de Recherche pour l’Agriculture, Montpellier SupAgro, F-34060 Montpellier, France
| | - Suzia Gélabale
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Rose-Marie Gomez
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Armelle Marais
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Université de Bordeaux, Unité Mixte de Recherche Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France;
| | - Séverine Gallet
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Franciane Gamiette
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Claudie Pavis
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Pierre-Yves Teycheney
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-97130 Capesterre Belle-Eau, France;
- Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Univ. Montpellier, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Institut Agro, F-97130 Capesterre Belle-Eau, France
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Chicken Astrovirus (CAstV) Molecular Studies Reveal Evidence of Multiple Past Recombination Events in Sequences Originated from Clinical Samples of White Chick Syndrome (WCS) in Western Canada. Viruses 2020; 12:v12101096. [PMID: 32998356 PMCID: PMC7600043 DOI: 10.3390/v12101096] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 02/04/2023] Open
Abstract
In this study, we aimed to molecularly characterize 14 whole genome sequences of chicken astrovirus (CAstV) isolated from samples obtained from white chick syndrome (WCS) outbreaks in Western Canada during the period of 2014–2019. Genome sequence comparisons showed all these sequences correspond to the novel Biv group from which no confirmed representatives were published in GenBank. Molecular recombination analyses using recombination detection software (i.e., RDP5 and SimPlot) and phylogenetic analyses suggest multiple past recombination events in open reading frame (ORF)1a, ORF1b, and ORF2. Our findings suggest that recombination events and the accumulation of point mutations may have contributed to the substantial genetic variation observed in CAstV and evidenced by the current seven antigenic sub-clusters hitherto described. This is the first paper that describes recombination events in CAstV following analysis of complete CAstV sequences originated in Canada.
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10
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Extensive recombination challenges the utility of Sugarcane mosaic virus phylogeny and strain typing. Sci Rep 2019; 9:20067. [PMID: 31882631 PMCID: PMC6934591 DOI: 10.1038/s41598-019-56227-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/28/2019] [Indexed: 11/30/2022] Open
Abstract
Sugarcane mosaic virus (SCMV) is distributed worldwide and infects three major crops: sugarcane, maize, and sorghum. The impact of SCMV is increased by its interaction with Maize chlorotic mottle virus which causes the synergistic maize disease maize lethal necrosis. Here, we characterised maize lethal necrosis-infected maize from multiple sites in East Africa, and found that SCMV was present in all thirty samples. This distribution pattern indicates that SCMV is a major partner virus in the East African maize lethal necrosis outbreak. Consistent with previous studies, our SCMV isolates were highly variable with several statistically supported recombination hot- and cold-spots across the SCMV genome. The recombination events generate conflicting phylogenetic signals from different fragments of the SCMV genome, so it is not appropriate to group SCMV genomes by simple similarity.
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11
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Distribution and diversity of viruses infecting yams ( Dioscorea spp.) in Cameroon. Virusdisease 2019; 30:526-537. [PMID: 31890752 DOI: 10.1007/s13337-019-00552-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022] Open
Abstract
Yam (Dioscorea spp.) is an important food crop cultivated for its edible tubers in Cameroon. Surveys were conducted in Cameroon to determine the incidence and severity of yam mosaic disease and associated viruses in 124 yam farms in four agro-ecological zones in 2014 and 2016. Dioscorea rotundata, D. cayenensis, D. alata, D. Dumetorum and D. bulbifera were most frequently detected yam species in the fields. Symptoms of virus disease were observed on 81.5% of the farms surveyed and the disease incidence ranged from 0 to 96.7%, with an overall mean of 26.5%. Mean symptom severity estimated using a numerical rating scale of 1-5, ranged from 2 to 4.1, with an overall mean of 2.6. Representative set of leaf samples collected from farmers' fields were tested for three viruses known to cause yam mosaic disease in West Africa, viz., Yam mosaic virus (YMV), Yam mild mosaic virus (YMMV) and Cucumber mosaic virus (CMV), using multiplex RT-PCR. YMV and YMMV were detected in 220 (37.2%) of the 591 samples tested and 75% of the farms surveyed. None of the samples tested positive to CMV. Phylogenetic analysis based on the coat protein sequencing of 27 YMV isolates clustered these isolates into three phylogenetic groups. This study demonstrated high prevalence of mosaic disease in yam fields and YMV as main causal agent. Knowledge generated in this study will be useful to augment diagnostic tools and yam mosaic disease control with a view to improve on yam production in Cameroon.
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12
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Silva G, Bömer M, Rathnayake AI, Sewe SO, Visendi P, Oyekanmi JO, Quain MD, Akomeah B, Kumar PL, Seal SE. Molecular Characterization of a New Virus Species Identified in Yam ( Dioscorea spp.) by High-Throughput Sequencing. PLANTS (BASEL, SWITZERLAND) 2019; 8:E167. [PMID: 31212654 PMCID: PMC6630666 DOI: 10.3390/plants8060167] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/06/2019] [Accepted: 06/09/2019] [Indexed: 01/28/2023]
Abstract
To date, several viruses of different genera have been reported to infect yam (Dioscorea spp.). The full diversity of viruses infecting yam, however, remains to be explored. High-throughput sequencing (HTS) methods are increasingly being used in the discovery of new plant viral genomes. In this study, we employed HTS on yam to determine whether any undiscovered viruses were present that would restrict the international distribution of yam germplasm. We discovered a new virus sequence present in 31 yam samples tested and have tentatively named this virus "yam virus Y" (YVY). Twenty-three of the samples in which YVY was detected showed mosaic and chlorotic leaf symptoms, but Yam mosaic virus was also detected in these samples. Complete genome sequences of two YVY viral isolates were assembled and found to contain five open reading frames (ORFs). ORF1 encodes a large replication-associated protein, ORF2, ORF3 and ORF4 constitute the putative triple gene block proteins, and ORF5 encodes a putative coat protein. Considering the species demarcation criteria of the family Betaflexiviridae, YVY should be considered as a novel virus species in the family Betaflexiviridae. Further work is needed to understand the association of this new virus with any symptoms and yield loss and its implication on virus-free seed yam production.
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Affiliation(s)
- Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK.
| | - Moritz Bömer
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK.
| | - Ajith I Rathnayake
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK.
| | - Steven O Sewe
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK.
| | - Paul Visendi
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK.
| | - Joshua O Oyekanmi
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria.
| | - Marian D Quain
- Council for Scientific and Industrial Research-Crops Research Institute (CSIR-CRI), Fumesua, P. O. BOX 3785, Kumasi, Ghana.
| | - Belinda Akomeah
- Council for Scientific and Industrial Research-Crops Research Institute (CSIR-CRI), Fumesua, P. O. BOX 3785, Kumasi, Ghana.
| | - P Lava Kumar
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria.
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK.
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13
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Bömer M, Rathnayake AI, Visendi P, Sewe SO, Sicat JPA, Silva G, Kumar PL, Seal SE. Tissue culture and next-generation sequencing: A combined approach for detecting yam ( Dioscorea spp.) viruses. PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY 2019; 105:54-66. [PMID: 31007374 PMCID: PMC6472605 DOI: 10.1016/j.pmpp.2018.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/04/2018] [Accepted: 06/16/2018] [Indexed: 06/09/2023]
Abstract
In vitro culture offers many advantages for yam germplasm conservation, propagation and international distribution. However, low virus titres in the generated tissues pose a challenge for reliable virus detection, which makes it difficult to ensure that planting material is virus-free. In this study, we evaluated next-generation sequencing (NGS) for virus detection following yam propagation using a robust tissue culture methodology. We detected and assembled the genomes of novel isolates of already characterised viral species of the genera Badnavirus and Potyvirus, confirming the utility of NGS in diagnosing yam viruses and contributing towards the safe distribution of germplasm.
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Affiliation(s)
- Moritz Bömer
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Ajith I. Rathnayake
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Visendi
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Steven O. Sewe
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Juan Paolo A. Sicat
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - P. Lava Kumar
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria
| | - Susan E. Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
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14
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Ruiz L, Simón A, García C, Velasco L, Janssen D. First natural crossover recombination between two distinct species of the family Closteroviridae leads to the emergence of a new disease. PLoS One 2018; 13:e0198228. [PMID: 30212464 PMCID: PMC6136708 DOI: 10.1371/journal.pone.0198228] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 09/01/2018] [Indexed: 11/21/2022] Open
Abstract
Lettuce chlorosis virus-SP (LCV-SP) (family Closteroviridae, genus Crinivirus), is a new strain of LCV which is able to infect green bean plants but not lettuce. In the present study, high-throughput and Sanger sequencing of RNA was used to obtain the LCV-SP full-length sequence. The LCV-SP genome comprises 8825 nt and 8672 nt long RNA1 and RNA2 respectively. RNA1 of LCV-SP contains four ORFs, the proteins encoded by the ORF1a and ORF1b are closely related to LCV RNA1 from California (FJ380118) whereas the 3´ end encodes proteins which share high amino acid sequence identity with RNA1 of Bean yellow disorder virus (BnYDV; EU191904). The genomic sequence of RNA2 consists of 8 ORFs, instead of 10 ORFs contained in LCV-California isolate. The distribution of vsiRNA (virus-derived small interfering RNA) along the LCV-SP genome suggested the presence of subgenomic RNAs corresponding with HSP70, P6.4 and P60. Results of the analysis using RDP4 and Simplot programs are the proof of the evidence that LCV-SP is the first recombinant of the family Closteroviridae by crossover recombination of intact ORFs, being the LCV RNA1 (FJ380118) and BnYDV RNA1 (EU191904) the origin of the new LCV strain. Genetic diversity values of virus isolates in the recombinant region obtained after sampling LCV-SP infected green bean between 2011 and 2017 might suggest that the recombinant virus event occurred in the area before this period. The presence of LCV-SP shows the role of recombination as a driving force of evolution within the genus Crinivirus, a globally distributed, emergent genus.
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Affiliation(s)
- Leticia Ruiz
- IFAPA Centro La Mojonera, IFAPA, La Mojonera, Almería, Spain
| | - Almudena Simón
- IFAPA Centro La Mojonera, IFAPA, La Mojonera, Almería, Spain
| | - Carmen García
- IFAPA Centro La Mojonera, IFAPA, La Mojonera, Almería, Spain
| | | | - Dirk Janssen
- IFAPA Centro La Mojonera, IFAPA, La Mojonera, Almería, Spain
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15
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Plant Virus Diversity and Evolution. CURRENT RESEARCH TOPICS IN PLANT VIROLOGY 2016. [PMCID: PMC7123681 DOI: 10.1007/978-3-319-32919-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Historically, the majority of plant virology focused on agricultural systems. Recent efforts have expanded our knowledge of the true diversity of plant viruses by studying those viruses that infect wild, undomesticated plants. Those efforts have provided answers to basic ecological questions regarding viruses in the wild, and insights into evolutionary questions, regarding the origins of viruses. While much work has been done, we have merely scratched the surface of the diversity that is estimated to exist. In this chapter we discuss the state of our knowledge of virus diversity, both in agricultural systems as well as in native wild systems, the border between these two systems and how viruses adapt and move across this border into an artificial, domesticated environment. We look at how this diversity has affected our outlook on viruses as a whole, shifting our past view of viruses as purely antagonistic entities of destruction to one where viruses are in a mutually beneficial relationship with their hosts. Additionally, we discuss the current work that plant virology has put forth regarding the evolutionary mechanisms, the life histories, and the deep evolution of viruses.
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16
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Zhou GC, Shao ZQ, Ma FF, Wu P, Wu XY, Xie ZY, Yu DY, Cheng H, Liu ZH, Jiang ZF, Chen QS, Wang B, Chen JQ. The evolution of soybean mosaic virus: An updated analysis by obtaining 18 new genomic sequences of Chinese strains/isolates. Virus Res 2015; 208:189-98. [PMID: 26103098 DOI: 10.1016/j.virusres.2015.06.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/12/2015] [Accepted: 06/13/2015] [Indexed: 10/23/2022]
Abstract
Soybean mosaic virus (SMV) is widely recognized as a highly damaging pathogen of soybean, and various strains/isolates have been reported to date. However, the pathogenic differences and phylogenetic relationships of these SMV strains/isolates have not been extensively studied. In the present work, by first obtaining 18 new genomic sequences of Chinese SMV strains/isolates and further compiling these with available data, we have explored the evolution of SMV from multiple aspects. First, as in other potyviruses, recombination has occurred frequently during SMV evolution, and a total of 32 independent events were detected. Second, using a maximum-likelihood method and removing recombinant fragments, a phylogeny covering 83 SMV sequences sampled from all over the world was reconstructed and the results showed four separate SMV clades, with clade I and II recovered for the first time. Third, the population structure analysis of SMV revealed significant genetic differentiations between China and two other countries (Korea and U.S.A.). Fourth, certain SMV-encoded genes, such as P1, HC-Pro and P3, exhibited higher non-synonymous substitution rate (dN) than synonymous substitution rate (dS), indicating that positive selection has influenced these genes. Finally, four Chinese SMV strains/isolates were selected for inoculation of both USA and Chinese differential soybean cultivars, and their pathogenic phenotypes were significantly different from that of the American strains. Overall, these findings have further broadened our understanding on SMV evolution, which would assist researchers to better deal with this harmful virus.
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Affiliation(s)
- Guang-Can Zhou
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhu-Qing Shao
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Fang-Fang Ma
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ping Wu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiao-Yi Wu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhong-Yun Xie
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - De-Yue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing 210095, China
| | - Hao Cheng
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing 210095, China
| | - Zhi-Hua Liu
- College of Resources and Environment, Northeast Agriculture University, Harbin 150030, China
| | - Zhen-Feng Jiang
- College of Agriculture, Northeast Agriculture University, Harbin 150030, China
| | - Qing-Shan Chen
- College of Agriculture, Northeast Agriculture University, Harbin 150030, China
| | - Bin Wang
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China.
| | - Jian-Qun Chen
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China.
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17
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Recombination analysis of Maize dwarf mosaic virus (MDMV) in the Sugarcane mosaic virus (SCMV) subgroup of potyviruses. Virus Genes 2014; 50:79-86. [PMID: 25392089 DOI: 10.1007/s11262-014-1142-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 11/01/2014] [Indexed: 10/24/2022]
Abstract
Recombination among RNA viruses is a natural phenomenon that appears to have played a significant role in the species development and the evolution of many strains. It also has particular significance for the risk assessment of plants which have been genetically modified for disease resistance by incorporating viral sequences into their genomes. However, the exact recombination events taking place in viral genomes are not investigated in detail for many virus groups. In this analysis, different single-stranded positive-sense RNA potyviruses were compared using various in silico recombination detection methods and new recombination events in the Sugarcane mosaic virus (SCMV) subgroup were detected. For an extended in silico recombination analysis, two of the analyzed Maize dwarf mosaic virus full-length genomes were sequenced additionally during this work. These results strengthen the evidence that recombination is a major driving force in virus evolution, and the emergence of new virus variants in the SCMV subgroup, paired with mutations, could generate viruses with altered biological properties. The intra- and interspecific homolog recombinations seem to be a general trait in this virus group, causing little or no changes to the amino acid of the progenies. However, we found a few breakpoints between the members of SCMV subgroup and the weed-infecting distant relatives, but only a few methods of the RDP3 package predicted these events with low significance level.
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18
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Zhou GC, Wu XY, Zhang YM, Wu P, Wu XZ, Liu LW, Wang Q, Hang YY, Yang JY, Shao ZQ, Wang B, Chen JQ. A genomic survey of thirty soybean-infecting bean common mosaic virus (BCMV) isolates from China pointed BCMV as a potential threat to soybean production. Virus Res 2014; 191:125-33. [PMID: 25107622 DOI: 10.1016/j.virusres.2014.07.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/23/2014] [Accepted: 07/26/2014] [Indexed: 10/24/2022]
Abstract
Widely known as a severe pathogen of bean plants, the bean common mosaic virus (BCMV) has been reported to infect soybeans only sporadically and the involved strains were all found in China regions. To explore variations among soybean-infecting BCMV strains, hundreds of soybean mosaic leave samples were collected throughout China, with a total of 30 BCMV isolates detected and their genomes sequenced. These newly obtained genomes, together with 16 other BCMV genomes available in GenBank were examined from multiple aspects to characterize BCMV evolutionary processes. Phylogenetic analysis showed that both soybean-infecting BCMVs (group I) and peanut-infecting BCMVs (group II) are distantly related to other BCMVs, suggesting ancestral differentiation and host adaptation. Genetic variation analysis showed that P1, P3 and 6K2 genes and the beginning portion of CP gene showed higher levels of variation relative to other genes. Moreover, selection analyses further confirmed that a number of sites within the P1 and P3 genes have suffered positive selection. These obtained BCMV sequences also exhibit high recombination frequencies, indicating a more dynamic evolutionary history. Finally, 12 different soybean cultivars were challenged with two BCMV isolates (DXH015 and HZZB011), with most of the cultivars successfully infected. These findings suggest that BCMV is indeed a potential threat to soybean production.
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Affiliation(s)
- Guang-Can Zhou
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Xiao-Yi Wu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yan-Mei Zhang
- Jiangsu Province & Chinese Academy of Science, Institute of Botany, Nanjing 210014, China
| | - Ping Wu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Xun-Zong Wu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Li-Wei Liu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Qiang Wang
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yue-Yu Hang
- Jiangsu Province & Chinese Academy of Science, Institute of Botany, Nanjing 210014, China
| | - Jia-Yin Yang
- Crop Research & Development Center, Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an 223001, China
| | - Zhu-Qing Shao
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China.
| | - Bin Wang
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China.
| | - Jian-Qun Chen
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210093, China.
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19
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Balasubramanian V, Selvarajan R. Genetic diversity and recombination analysis in the coat protein gene of Banana bract mosaic virus. Virus Genes 2014; 48:509-17. [DOI: 10.1007/s11262-014-1056-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 03/06/2014] [Indexed: 11/29/2022]
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20
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Li Y, Liu R, Zhou T, Fan Z. Genetic diversity and population structure of Sugarcane mosaic virus. Virus Res 2013; 171:242-6. [DOI: 10.1016/j.virusres.2012.10.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Revised: 10/12/2012] [Accepted: 10/22/2012] [Indexed: 11/16/2022]
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21
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Abdalla OA, Ali A. Genetic diversity in the 3'-terminal region of papaya ringspot virus (PRSV-W) isolates from watermelon in Oklahoma. Arch Virol 2011; 157:405-12. [PMID: 22160129 DOI: 10.1007/s00705-011-1184-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Accepted: 11/01/2011] [Indexed: 11/28/2022]
Abstract
The 3'-terminal region (1191 nt) containing part of the NIb gene, complete coat protein (CP) and poly-A tail of 64 papaya ringspot virus (PRSV-W) isolates collected during 2008-2009 from watermelon in commercial fields of four different counties of Oklahoma were cloned and sequenced. Nucleotide and amino acid sequence identities ranged from 95.2-100% and 97.1-100%, respectively, among the Oklahoman PRSV-W isolates. Phylogenetic analysis showed that PRSW-W isolates clustered according to the locations where they were collected within Oklahoma, and each cluster contained two subgroups. All subgroups of Oklahoman PRSV-W isolates were on separate branches when compared to 35 known isolates originating from other parts of the world, including the one reported previously from the USA. This study helps in our understanding about the genetic diversity of PRSV-W isolates infecting cucurbits in Oklahoma.
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Affiliation(s)
- Osama A Abdalla
- Department of Biological Science, The University of Tulsa, 800 S. Tucker Dr, Tulsa, OK 74104, USA
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22
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Sztuba-Solińska J, Urbanowicz A, Figlerowicz M, Bujarski JJ. RNA-RNA recombination in plant virus replication and evolution. ANNUAL REVIEW OF PHYTOPATHOLOGY 2011; 49:415-43. [PMID: 21529157 DOI: 10.1146/annurev-phyto-072910-095351] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
RNA-RNA recombination is one of the strongest forces shaping the genomes of plant RNA viruses. The detection of recombination is a challenging task that prompted the development of both in vitro and in vivo experimental systems. In the divided genome of Brome mosaic virus system, both inter- and intrasegmental crossovers are described. Other systems utilize satellite or defective interfering RNAs (DI-RNAs) of Turnip crinkle virus, Tomato bushy stunt virus, Cucumber necrosis virus, and Potato virus X. These assays identified the mechanistic details of the recombination process, revealing the role of RNA structure and proteins in the replicase-mediated copy-choice mechanism. In copy choice, the polymerase and the nascent RNA chain from which it is synthesized switch from one RNA template to another. RNA recombination was found to mediate the rearrangement of viral genes, the repair of deleterious mutations, and the acquisition of nonself sequences influencing the phylogenetics of viral taxa. The evidence for recombination, not only between related viruses but also among distantly related viruses, and even with host RNAs, suggests that plant viruses unabashedly test recombination with any genetic material at hand.
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Affiliation(s)
- Joanna Sztuba-Solińska
- Plant Molecular Biology Center, Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
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23
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Bousalem M, Viader V, Mariac C, Gomez RM, Hochu I, Santoni S, David J. Evidence of diploidy in the wild Amerindian yam, a putative progenitor of the endangered species Dioscorea trifida (Dioscoreaceae). Genome 2010; 53:371-83. [DOI: 10.1139/g10-016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The fundamental question about Dioscorea trifida (Dioscoreaceae), the most important Amerindian yam, that remains unresolved concerns its evolutionary origin, since no wild relative has been reported. In this paper we report the existence of D. trifida’s wild relative for the first time. The diploidy of wild D. trifida (2n = 40) is clearly demonstrated by flow cytometry, chromosome counts, and microsatellite pattern analysis, whereas the cultivated form was previously shown to be autotetraploid (2n = 80). In the coastal region where the wild and cultivated forms are sympatric, tetraploid and triploid cytotypes coexist within the same populations. In the sites where the wild and cultivated forms are allopatric, the wild diploid cytotype predominates. AFLP (amplified fragment length polymorphism) analyses gave an initial idea of the position of the wild forms in relation to the cultivated forms. All the wild and cultivated types form a monophyletic group structured into two major subgroups corresponding to the tetraploid cytotype of the cultivated form and the diploid cytotype of the wild form. The triploid cytotypes of the wild form are in an intermediary position. Wild accessions are grouped on the basis of their geographic origin. The data presented in this paper are significant for the effective breeding and conservation of D. trifida and to assess its genetic diversity and population structure for the general understanding of the evolution and domestication of the species.
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Affiliation(s)
- Mustapha Bousalem
- INRA-URPV, Domaine Duclos, Prise d’Eau, 97170 Petit-Bourg, Guadeloupe, France
- UMR Diversité et Génomes des Plantes Cultivées, Station d’Amélioration des Plantes, INRA, 2, place Viala, 34060 Montpellier, France
| | - Véronique Viader
- INRA-URPV, Domaine Duclos, Prise d’Eau, 97170 Petit-Bourg, Guadeloupe, France
- UMR Diversité et Génomes des Plantes Cultivées, Station d’Amélioration des Plantes, INRA, 2, place Viala, 34060 Montpellier, France
| | - Cedric Mariac
- INRA-URPV, Domaine Duclos, Prise d’Eau, 97170 Petit-Bourg, Guadeloupe, France
- UMR Diversité et Génomes des Plantes Cultivées, Station d’Amélioration des Plantes, INRA, 2, place Viala, 34060 Montpellier, France
| | - Rose-Marie Gomez
- INRA-URPV, Domaine Duclos, Prise d’Eau, 97170 Petit-Bourg, Guadeloupe, France
- UMR Diversité et Génomes des Plantes Cultivées, Station d’Amélioration des Plantes, INRA, 2, place Viala, 34060 Montpellier, France
| | - Isabelle Hochu
- INRA-URPV, Domaine Duclos, Prise d’Eau, 97170 Petit-Bourg, Guadeloupe, France
- UMR Diversité et Génomes des Plantes Cultivées, Station d’Amélioration des Plantes, INRA, 2, place Viala, 34060 Montpellier, France
| | - Sylvain Santoni
- INRA-URPV, Domaine Duclos, Prise d’Eau, 97170 Petit-Bourg, Guadeloupe, France
- UMR Diversité et Génomes des Plantes Cultivées, Station d’Amélioration des Plantes, INRA, 2, place Viala, 34060 Montpellier, France
| | - Jacques David
- INRA-URPV, Domaine Duclos, Prise d’Eau, 97170 Petit-Bourg, Guadeloupe, France
- UMR Diversité et Génomes des Plantes Cultivées, Station d’Amélioration des Plantes, INRA, 2, place Viala, 34060 Montpellier, France
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24
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Boulila M. Putative recombination events and evolutionary history of five economically important viruses of fruit trees based on coat protein-encoding gene sequence analysis. Biochem Genet 2009; 48:357-75. [PMID: 20035376 DOI: 10.1007/s10528-009-9317-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 09/09/2009] [Indexed: 10/20/2022]
Abstract
To enhance the knowledge of recombination as an evolutionary process, 267 accessions retrieved from GenBank were investigated, all belonging to five economically important viruses infecting fruit crops (Plum pox, Apple chlorotic leaf spot, Apple mosaic, Prune dwarf, and Prunus necrotic ringspot viruses). Putative recombinational events were detected in the coat protein (CP)-encoding gene using RECCO and RDP version 3.31beta algorithms. Based on RECCO results, all five viruses were shown to contain potential recombination signals in the CP gene. Reconstructed trees with modified topologies were proposed. Furthermore, RECCO performed better than the RDP package in detecting recombination events and exhibiting their evolution rate along the sequences of the five viruses. RDP, however, provided the possible major and minor parents of the recombinants. Thus, the two methods should be considered complementary.
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25
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Gell G, Balázs E, Petrik K. Genetic diversity of Hungarian Maize dwarf mosaic virus isolates. Virus Genes 2009; 40:277-81. [PMID: 20033839 DOI: 10.1007/s11262-009-0434-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 12/09/2009] [Indexed: 10/20/2022]
Abstract
The genetic diversity of the coat-protein (CP) region and the untranslated C-terminal region (3'UTR) of Maize dwarf mosaic virus (MDMV) was analyzed to evaluate the variability between isolates (inter-isolate sequence diversity). The results of inter-isolate sequence diversity analysis showed that the diversity of the MDMV CP gene is fairly high (p-distance: up to 0.136). During sequence analysis, a 13 amino-acid residue insertion and an 8 amino-acid residue deletion were found within the N-terminal region of the CP gene. The phylogenetic analysis showed that-unlike other potyvirus species in this subgroup-the MDMV isolates could not be distinguished on the basis of their host plants or geographic origins.
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Affiliation(s)
- Gyöngyvér Gell
- Department of Applied Genomics, Agricultural Research Institute of the Hungarian Academy of Sciences, Brunszvik u 2, 2462 Martonvásár, Hungary
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26
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Seo JK, Ohshima K, Lee HG, Son M, Choi HS, Lee SH, Sohn SH, Kim KH. Molecular variability and genetic structure of the population of soybean mosaic virus based on the analysis of complete genome sequences. Virology 2009; 393:91-103. [PMID: 19716150 DOI: 10.1016/j.virol.2009.07.007] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 07/01/2009] [Accepted: 07/06/2009] [Indexed: 11/18/2022]
Abstract
The complete genomes of 30 Soybean mosaic virus (SMV) isolates and strains were sequenced in this study. Together with fourteen previously reported sequences, we analyzed the genetic structure of the SMV population. Analyses of genetic diversity showed that different genomic regions of SMV are under different evolutionary constraints and that there was no significant genetic differentiation between East Asian and North American populations of SMV. Phylogenetic analyses revealed a significant correlation between phylogeny of the cylindrical inclusion (CI) gene of SMV and SMV resistance gene 3 (Rsv3)-relating pathogenicity of SMV, suggesting CI might be a pathogenic determinant in Rsv3-mediated disease response. Interestingly, recombination analyses identified 19 'clear' recombination events in the SMV population. Furthermore, as several resistance-breaking strains were identified as recombinants, it appears that recombination might contribute to overcome host resistance in SMV-soybean pathosystem. Our finding suggests that recombination as well as mutation is an important evolutionary process in the genetic diversification of SMV population.
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Affiliation(s)
- Jang-Kyun Seo
- Department of Agricultural Biotechnology and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
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27
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Molecular characterization of Korean Pepper mottle virus isolates and its relationship to symptom variations. Virus Res 2009; 144:83-8. [DOI: 10.1016/j.virusres.2009.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 03/25/2009] [Accepted: 04/05/2009] [Indexed: 11/17/2022]
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28
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Bousalem M, Durand O, Scarcelli N, Lebas BSM, Kenyon L, Marchand JL, Lefort F, Seal SE. Dilemmas caused by endogenous pararetroviruses regarding the taxonomy and diagnosis of yam (Dioscorea spp.) badnaviruses: analyses to support safe germplasm movement. Arch Virol 2009; 154:297-314. [PMID: 19190853 DOI: 10.1007/s00705-009-0311-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 12/12/2008] [Indexed: 11/25/2022]
Abstract
The discovery of endogenous pararetroviral sequences (EPRVs) has had a deep impact on the approaches needed for diagnosis, taxonomy, safe movement of germplasm and management of diseases caused by pararetroviruses. In this article, we illustrate this through the example of yam (Dioscorea spp.) badnaviruses. To enable progress, it is first necessary to clarify the taxonomical status of yam badnavirus sequences. Phylogeny and pairwise sequence comparison of 121 yam partial reverse transcriptase sequences provided strong support for the identification of 12 yam badnavirus species, of which ten have not been previously named. Virus prevalence data were obtained, and they support the presence of EPRVs in D. rotundata, but not in D. praehensilis, D. abyssinica, D. alata or D. trifida. Five yam badnavirus species characterised by a wide host range seem to be of African origin. Seven other yam badnavirus species with a limited host range are probably of Asian-Pacific origin. Recombination under natural circumstances appears to be rare. Average values of nucleotide intra-species genetic distances are comparable to data obtained for other RNA and DNA virus families. The dispersion scenarios proposed here, combined with the fact that host-switching events appear common for some yam badnaviruses, suggest that the risks linked to introduction via international plant material exchanges are high.
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Affiliation(s)
- Mustapha Bousalem
- INRA-URPV, Domaine Duclos, Prise d'Eau, 9170 Petit-Bourg, Guadeloupe, France.
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Bousalem M, Douzery EJP, Seal SE. Taxonomy, molecular phylogeny and evolution of plant reverse transcribing viruses (family Caulimoviridae) inferred from full-length genome and reverse transcriptase sequences. Arch Virol 2008; 153:1085-102. [PMID: 18483693 DOI: 10.1007/s00705-008-0095-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 03/20/2008] [Indexed: 11/26/2022]
Abstract
This study constitutes the first evaluation and application of quantitative taxonomy to the family Caulimoviridae and the first in-depth phylogenetic study of the family Caulimoviridae that integrates the common origin between LTR retrotransposons and caulimoviruses. The phylogenetic trees and PASC analyses derived from the full genome and from the corresponding partial RT concurred, providing strong support for the current genus classification based mainly on genome organisation and use of partial RT sequence as a molecular marker. The PASC distributions obtained are multimodal, making it possible to distinguish between genus, species and strain. The taxonomy of badnaviruses infecting banana (Musa spp.) was clarified, and the consequence of endogenous badnaviruses on the genetic diversity and evolution of caulimoviruses is discussed. The use of LTR retrotransposons as outgroups reveals a structured bipolar topology separating the genus Badnavirus from the other genera. Badnaviruses appear to be the most recent genus, with the genus Tungrovirus in an intermediary position. This structuring intersects the one established by genomic and biological properties and allows us to make a correlation between phylogeny and biogeography. The variability shown between members of the family Caulimoviridae is in a similar range to that reported within other DNA and RNA plant virus families.
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Affiliation(s)
- M Bousalem
- INRA Antilles-Guyane, UR979 Productions Végétales, Domaine Duclos, 97170 Petit-Bourg, Guadeloupe.
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30
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Molecular variability of sweet potato feathery mottle virus and other potyviruses infecting sweet potato in Peru. Arch Virol 2008; 153:473-83. [PMID: 18172571 DOI: 10.1007/s00705-007-0019-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 11/21/2007] [Indexed: 10/22/2022]
Abstract
Several potyviruses are found infecting sweet potato (Ipomoea batatas) in Peru, of which sweet potato feathery mottle virus (SPFMV, genus Potyvirus) is the most common. However, sequence data for these viruses are not available from Peru. In this study, the 3'-terminal approximately 1,800 nucleotide sequences of 17 potyvirus samples collected from the six main sweet potato-producing areas of Peru over the past 20 years were determined and analyzed. Results of sequence comparisons and phylogenetic analysis showed that three of the four recognized SPFMV strain groups, including the East African strain, are established in Peru as well as two other potyviruses: sweet potato virus G (SPVG) and sweet potato virus 2 (SPV2). The analysis further revealed that SPFMV, SPVG and SPV2 are related and form an Ipomoea-specific phylogenetic lineage within the genus Potyvirus and identified for the first time recombination events between viruses from different strain groups of SPFMV.
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31
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Genetic variation of papaya ringspot virus in Venezuela. Arch Virol 2007; 153:343-9. [DOI: 10.1007/s00705-007-1091-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 09/26/2007] [Indexed: 10/22/2022]
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32
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Iglesias NG, Gago-Zachert SP, Robledo G, Costa N, Plata MI, Vera O, Grau O, Semorile LC. Population structure of Citrus tristeza virus from field Argentinean isolates. Virus Genes 2007; 36:199-207. [DOI: 10.1007/s11262-007-0169-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Accepted: 09/28/2007] [Indexed: 11/30/2022]
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Zhang C, Gu H, Ghabrial SA. Molecular Characterization of Naturally Occurring RNA1 Recombinants of the Comovirus Bean pod mottle virus. PHYTOPATHOLOGY 2007; 97:1255-1262. [PMID: 18943683 DOI: 10.1094/phyto-97-10-1255] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT The Bean pod mottle virus, a member of the genus Comovirus, has a bipartite genome consisting of RNA1 and RNA2. We previously reported the occurrence in nature of two distinct subgroups of BPMV strains (subgroups I and II), as well as reassortants between the two subgroups. Here, we report on the isolation and molecular characterization of RNA1 recombinants from soybean plants infected with the partial diploid reassortant strain IL-Cb1, which induces very severe symptoms on soybean. cDNA cloning and sequencing of RNA1 from strain IL-Cb1 revealed the presence of chimeric and mosaic recombinant RNA1s. The full-length mosaic and chimeric recombinant RNA1s were infectious and induced mild symptoms on soybean. Although the recombinant RNA1 accumulated to high levels in the absence of wild-type RNA1, its accumulation level was low in mixed infections with wild-type RNA1. Recombinant RNA1 molecules with similar structures to the naturally occurring recombinant RNA1s were generated in soybean after four passages following inoculation with RNA1 transcripts derived from cDNAs of two distinct strains. This suggests that recombination events are frequent and that a recombination hot spot exists. Sequence analysis of the recombination region showed that it has AU-rich sequences characteristic of recombination hot spots.
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Janssen D, Velasco L, Martín G, Segundo E, Cuadrado IM. Low genetic diversity among Cucumber vein yellowing virus isolates from Spain. Virus Genes 2007; 34:367-71. [PMID: 16927122 DOI: 10.1007/s11262-006-0026-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 01/20/2006] [Indexed: 11/25/2022]
Abstract
The population structure and genetic diversity of Cucumber vein yellowing virus (CVYV) from Spain were estimated by analyses of partial nucleotide sequences of the P1-proteinase (P1-Pro), P3 protein (P3), and the coat protein (CP) coding regions. Analysis of 56 CVYV Spanish field isolates collected from 2001 to 2005 showed low genetic diversity (0.0026, 0.0013, and 0.0012 for the P1-Pro, P3, and CP regions, respectively). The ratio between nonsynonymous and synonymous substitutions was among the lowest found in a plant virus, indicating a strong negative selective pressure in the regions analyzed. Nonsynonymous nucleotide substitutions were only found within the P1-Pro regions, although these do not appear to have been selected with time. The results support the hypothesis that the Spanish CVYV population could derive from a single origin of recent introduction.
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Affiliation(s)
- Dirk Janssen
- Centro de Investigación y Formación Agraria, I.F.A.P.A., C.I.C.E. (Junta de Andalucía), Autovía del Mediterraneo Km 420, 04745 La Mojonera, Almeria, Spain.
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35
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Valli A, López-Moya JJ, García JA. Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae. J Gen Virol 2007; 88:1016-1028. [PMID: 17325376 DOI: 10.1099/vir.0.82402-0] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genome structure and sequence are notably conserved between members of the family Potyviridae. However, some genomic regions of these viruses, such as that encoding the P1 protein, show strikingly high variability. In this study, some partially conserved motifs were identified upstream of the quite well-conserved protease domain located near the P1 C terminus. The irregular distribution of these motifs suggests that the potyviral P1 proteins have undergone complex evolutionary diversification. Evidence was found of recombination events in the P1 N-terminal region, similar to those reported in potyviruses of the bean common mosaic virus subgroup, but also affecting other potyviruses. Moreover, intergeneric recombination events affecting potyviruses and ipomoviruses were also observed. Evidence that these recombination events could be linked to host adaptation is provided. Specific sequence features and differences in net charge help to classify the P1 proteins of members of the family Potyviridae into two groups: those from potyviruses and rymoviruses and those from tritimoviruses. The ipomovirus Cucumber vein yellowing virus has two P1 copies arranged in tandem, the most N-terminal one being of the potyvirus type and the other being of the tritimovirus type. These findings suggest that both recombination and gene duplication have contributed to P1 evolution and helped to facilitate successful adaptation of members of the family Potyviridae to a wide range of host species.
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Affiliation(s)
- Adrian Valli
- Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan José López-Moya
- Laboratori de Genètica Molecular Vegetal, Consorci CSIC-IRTA, IBMB, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Juan Antonio García
- Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
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36
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Chung BN, Canto T, Palukaitis P. Stability of recombinant plant viruses containing genes of unrelated plant viruses. J Gen Virol 2007; 88:1347-1355. [PMID: 17374781 DOI: 10.1099/vir.0.82477-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The stability of hybrid plant viruses that might arise by recombination in transgenic plants was examined using hybrid viruses derived from the viral expression vectors potato virus X (PVX) and tobacco rattle virus (TRV). The potato virus Y (PVY) NIb and HCPro open reading frames (ORFs) were introduced into PVX to generate PVX-NIb and PVX-HCPro, while the PVY NIb ORF was introduced into a vector derived from TRV RNA2 to generate TRV-NIb. All three viruses were unstable and most of the progeny viruses had lost the inserted sequences between 2 and 4 weeks post-inoculation. There was some variation in the rate of loss of part or all of the inserted sequence and the number of plants containing the deleted viruses, depending on the sequence, the host (Nicotiana tabacum vs Nicotiana benthamiana) or the vector, although none of these factors was associated consistently with the preferential loss of the inserted sequences. PVX-NIb was unable to accumulate in NIb-transgenic tobacco resistant to infection by PVY and also showed loss of the NIb insert from PVX-NIb in some NIb-transgenic tobacco plants susceptible to infection by PVY. These data indicate that such hybrid viruses, formed in resistant transgenic plants from a transgene and an unrelated virus, would be at a selective disadvantage, first by being targeted by the resistance mechanism and second by not being competitive with the parental virus.
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Affiliation(s)
- Bong-Nam Chung
- National Horticultural Research Institute, Rural Development Administration, 475 Imok-Dong, Suwon 440-310, Korea
- Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Tomas Canto
- Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Peter Palukaitis
- Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK
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37
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Ohshima K, Tomitaka Y, Wood JT, Minematsu Y, Kajiyama H, Tomimura K, Gibbs AJ. Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination. J Gen Virol 2007; 88:298-315. [PMID: 17170463 DOI: 10.1099/vir.0.82335-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Potyviruses have variable single-stranded RNA genomes and many show clear evidence of recombination. This report studied the distribution of recombination sites in the genomes of 92 isolates of the potyvirus Turnip mosaic virus (TuMV); 42 came from the international gene sequence databases and an additional 50 complete genomic sequences were generated from field samples collected in Europe and Asia. The sequences were examined for evidence of recombination using seven different sequence comparison methods and the exact position of each site was confirmed by sequence composition analysis. Recombination sites were found throughout the genomes, except in the small 6K1 protein gene, and only 24 of the genomes (26%) showed no evidence of recombination. Statistically significant clusters of recombination sites were found in the P1 gene and in the CI/6K2/VPg gene region. Most recombination sites were bordered by an upstream (5') region of GC-rich and downstream (3') region of AU-rich sequence of a similar length. Correlations between the presence and type of recombination site and provenance, host type and phylogenetic relationships are discussed, as is the role of recombination in TuMV evolution.
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Affiliation(s)
- Kazusato Ohshima
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Yasuhiro Tomitaka
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Jeffery T Wood
- Statistical Consulting Unit, Graduate School, Australian National University, Canberra, ACT 0200, Australia
| | - Yoshiteru Minematsu
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Hiromi Kajiyama
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Kenta Tomimura
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
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38
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Voth PD, Mairura L, Lockhart BE, May G. Phylogeography of Ustilago maydis virus H1 in the USA and Mexico. J Gen Virol 2006; 87:3433-3441. [PMID: 17030880 DOI: 10.1099/vir.0.82149-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ustilago maydis virus H1 (Umv-H1) is a mycovirus that infects Ustilago maydis, a fungal pathogen of maize. As Zea mays was domesticated, it carried with it many associated symbionts, such that the subsequent range expansion and cultivation of maize should have affected maize symbionts' evolutionary history dramatically. Because transmission of Umv-H1 takes place only through cytoplasmic fusion during mating of U. maydis individuals, the population dynamics of U. maydis and maize are expected to affect the population structure of the viral symbiont strongly. Here, the impact of changes in the evolutionary history of U. maydis on that of Umv-H1 was investigated. The high mutation rate of this virus allows inferences to be made about the evolution and divergence of Umv-H1 lineages as a result of the recent changes in U. maydis geographical and genetic structure. The phylogeographical history and genetic structure of Umv-H1 populations in the USA and Mexico were determined by using analyses of viral nucleotide sequence variation. Infection and recombination frequencies, genetic diversity and rates of neutral evolution were also assessed, to make inferences regarding evolutionary processes underlying the population genetic structure of ancestral and descendent populations. The results suggest that Mexico represents the ancestral population of Umv-H1, from which the virus has been carried with U. maydis populations into the USA. Thus, the population dynamics of one symbiont represent a major evolutionary force on the co-evolutionary dynamics of symbiotic partners.
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Affiliation(s)
- Peter D Voth
- Plant Biological Sciences Graduate Program, University of Minnesota, 100 Ecology, 1987 Upper Buford Circle, St Paul, MN 55108, USA
| | - Linah Mairura
- Department of Ecology, Evolution, and Behaviour, University of Minnesota, 100 Ecology, 1987 Upper Buford Circle, St Paul, MN 55108, USA
| | - Ben E Lockhart
- Department of Plant Pathology, University of Minnesota, 100 Ecology, 1987 Upper Buford Circle, St Paul, MN 55108, USA
| | - Georgiana May
- Department of Ecology, Evolution, and Behaviour, University of Minnesota, 100 Ecology, 1987 Upper Buford Circle, St Paul, MN 55108, USA
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39
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Meier M, Truve E. An attempt to identify recombinants between two sobemoviruses in doubly infected oat plants. ACTA ACUST UNITED AC 2006; 5:47-56. [PMID: 16978574 DOI: 10.1051/ebr:2006013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Recombination in RNA viruses is considered to play a major role as a driving force in virus variability to counterbalance loss in fitness that can be due to the accumulation of detrimental mutations. Studies on mixed infections are pertinent for understanding the role of recombination in virus evolution. They also provide important baseline information for studying the biosafety of plants expressing viral sequences. To investigate the possibility of RNA recombination occurrence between two sobemoviruses under little or no selection pressure, we co-infected test plants with Cocksfoot mottle virus (CfMV) and Ryegrass mottle virus (RGMoV). CfMV and RGMoV were selected because of their overlapping host range and geographical distribution. First, symptom development of both viruses in barley (Hordeum vulgare) and oat (Avena sativa) was examined. Both viruses generated quite strong infection symptoms in oat, but synergism was not detected. RGMoV was lethal for barley, whereas CfMV infection in barley was nearly symptomless. RT-PCR analysis revealed 100% infection with both viruses in oat but not in barley. Therefore, an RNA recombination study of CfMV and RGMoV was performed in oat. 105 plants were co-inoculated with both viruses and putative recombinational hot spot regions were screened for recombination events by RT-PCR analysis at a sensitivity level down to 0.1-100 pg of viral genomic RNA. No recombination events between the two sobemoviruses were detected.
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Affiliation(s)
- Merike Meier
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 19086 Tallinn, Estonia
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40
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Bousalem M, Arnau G, Hochu I, Arnolin R, Viader V, Santoni S, David J. Microsatellite segregation analysis and cytogenetic evidence for tetrasomic inheritance in the American yam Dioscorea trifida and a new basic chromosome number in the Dioscoreae. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:439-51. [PMID: 16775695 DOI: 10.1007/s00122-006-0309-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Accepted: 05/06/2006] [Indexed: 05/10/2023]
Abstract
Despite the economic and cultural importance of the indigenous "Amerindian" yam Dioscorea trifida, very little is known about their origin, phylogeny, diversity and genetics. Consequently, conventional breeding efforts for the selection of D. trifida genotypes resistant to potyviruses which are directly involved in the regression of this species have been seriously limited. Our objective of this paper is to contribute to the clarification of the cytogenetic status, i.e., inheritance and chromosome number. Our results provide genetic evidence supporting tetrasomic behaviour of the genome of D. trifida based on chromosomal segregation pattern analysis using eight SSRs markers in three different crosses. This is the first reliable evidence of an autopolyploid species in the genus Dioscorea. The second major result in this study is the revealing of a new base chromosome number in the botanical section Macrogynodium to which D. trifida belongs. To date, our assumptions about the ploidy level of yams are based on the observations that the basic chromosome number is 10 or 9, and D. trifida was described as octoploid. The chromosome number of D. trifida accessions was also assessed using somatic chromosomic count techniques. Flow cytometry did not show significant variation of 2C DNA content among 80 accessions indicating homogeneity of the ploidy level of the cultivated D. trifida. This suggests that autotetraploidy is well established as well as the rule for the cultivated pool of D. trifida, even if the direct diploid ancestor remains to be identified. The data presented in this paper are significant and important for the effective breeding and conservation of the species and for elucidating the phylogeny and the origins of the yam and the evolution of the genus Dioscorea.
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Affiliation(s)
- Mustapha Bousalem
- INRA-URPV, Domaine Duclos, prise d'eau, 97170, Petit-Bourg, Guadeloupe, France.
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41
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Wierzchoslawski R, Bujarski JJ. Efficient in vitro system of homologous recombination in brome mosaic bromovirus. J Virol 2006; 80:6182-7. [PMID: 16731958 PMCID: PMC1472593 DOI: 10.1128/jvi.02447-05] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Accepted: 03/26/2006] [Indexed: 12/26/2022] Open
Abstract
Recent in vivo studies have revealed that the subgenomic promoter (sgp) in brome mosaic bromovirus (BMV) RNA3 supports frequent homologous recombination events (R. Wierzchoslawski, A. Dzianott, and J. Bujarski, J. Virol. 78:8552-8564, 2004). In this paper, we describe an sgp-driven in vitro system that supports efficient RNA3 crossovers. A 1:1 mixture of two (-)-sense RNA3 templates was copied with either a BMV replicase (RdRp) preparation or recombinant BMV protein 2a. The BMV replicase enzyme supported a lower recombination frequency than 2a, demonstrating a role of other viral and/or host factors. The described in vitro system will allow us to study the mechanism of homologous RNA recombination.
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Affiliation(s)
- Rafal Wierzchoslawski
- Plant Molecular Biology Center, Department of Biological Sciences, Northern Illinois University, De Kalb, IL 60115, USA
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42
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Rebenstorf K, Candresse T, Dulucq MJ, Büttner C, Obermeier C. Host species-dependent population structure of a pollen-borne plant virus, Cherry leaf roll virus. J Virol 2006; 80:2453-62. [PMID: 16474152 PMCID: PMC1395386 DOI: 10.1128/jvi.80.5.2453-2462.2006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cherry leaf roll virus (CLRV) belongs to the Nepovirus genus within the family Comoviridae. It has a host range which includes a number of wild tree and shrub species. The serological and molecular diversity of CLRV was assessed using a collection of isolates and samples recovered from woody and herbaceous host plants from different geographical origins. Molecular diversity was assessed by sequencing a short (375-bp) region of the 3' noncoding region (NCR) of the genomic RNAs while serological diversity was assessed using a panel of seven monoclonal antibodies raised initially against a walnut isolate of CLRV. The genomic region analyzed was shown to exhibit a significant degree of molecular variability with an average pairwise divergence of 8.5% (nucleotide identity). Similarly, serological variability proved to be high, with no single monoclonal antibody being able to recognize all isolates analyzed. Serological and molecular phylogenetic reconstructions showed a strong correlation. Remarkably, the diversity of CLRV populations is to a large extent defined by the host plant from which the viral samples are originally obtained. There are relatively few reports of plant viruses for which the genetic diversity is structured by the host plant. In the case of CLRV, we hypothesize that this situation may reflect the exclusive mode of transmission in natural plant populations by pollen and by seeds. These modes of transmission are likely to impose barriers to host change by the virus, leading to rapid biological and genetic separation of CLRV variants coevolving with different plant host species.
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Affiliation(s)
- Kathrin Rebenstorf
- Section Phytomedicine, Institute for Horticultural Sciences, Humboldt-Universität zu Berlin, Germany
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43
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HOCHU I, SANTONI S, BOUSALEM M. Isolation, characterization and cross-species amplification of microsatellite DNA loci in the tropical American yam Dioscorea trifida. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2005.01166.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Myrta A, Varga A, James D. The complete genome sequence of an El Amar isolate of plum pox virus (PPV) and its phylogenetic relationship to other PPV strains. Arch Virol 2006; 151:1189-98. [PMID: 16397750 DOI: 10.1007/s00705-005-0703-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Accepted: 12/01/2005] [Indexed: 10/25/2022]
Abstract
The genomic sequence of an El Amar isolate of plum pox virus (PPV) from Egypt was determined by sequencing overlapping cDNA fragments. This is the first complete sequence of a member of the El Amar (EA) strain of PPV. The genome consists of 9791 nt, excluding a poly(A) tail at the 3' terminus. The complete nt sequence of PPV EA is 79-80%, 80%, 77%, and 77% homologous with isolates of strains D/M, Rec (BOR3), C, and W, respectively. The polyprotein identity ranged from 87-91%. Phylogenetic analysis using the complete genome sequence of PPV EA confirmed its strain status. No significant recombination signals were identified using PhylPro and SimPlot scans of the PPV EA sequence, however an interesting recombination signal was identified in the P1/HC-Pro region of PPV W3174.
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Affiliation(s)
- A Myrta
- Istituto Agronomico Mediterraneo, Bari, Italy
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45
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Affiliation(s)
- M J Jeger
- Division of Biology, Imperial College London, Wye Campus, Wye Ashford TN25 5AH, United Kingdom
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46
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Chare ER, Holmes EC. A phylogenetic survey of recombination frequency in plant RNA viruses. Arch Virol 2005; 151:933-46. [PMID: 16292597 DOI: 10.1007/s00705-005-0675-x] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 10/04/2005] [Indexed: 11/27/2022]
Abstract
The severe economic consequences of emerging plant viruses highlights the importance of studies of plant virus evolution. One question of particular relevance is the extent to which the genomes of plant viruses are shaped by recombination. To this end we conducted a phylogenetic survey of recombination frequency in a wide range of positive-sense RNA plant viruses, utilizing 975 capsid gene sequences and 157 complete genome sequences. In total, 12 of the 36 RNA virus species analyzed showed evidence for recombination, comprising 17% of the capsid gene sequence alignments and 44% of the genome sequence alignments. Given the conservative nature of our analysis, we propose that recombination is a relatively common process in some plant RNA viruses, most notably the potyviruses.
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Affiliation(s)
- E R Chare
- Department of Zoology, University of Oxford, Oxford, UK
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Choi BK, Koo JM, Ahn HJ, Yum HJ, Choi CW, Ryu KH, Chen P, Tolin SA. Emergence of Rsv-resistance breaking Soybean mosaic virus isolates from Korean soybean cultivars. Virus Res 2005; 112:42-51. [PMID: 15869819 DOI: 10.1016/j.virusres.2005.03.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Revised: 03/09/2005] [Accepted: 03/09/2005] [Indexed: 11/28/2022]
Abstract
Twelve Rsv resistance-breaking (RB) isolates of Soybean mosaic virus (SMV) were obtained from field-grown soybean plants showing mosaic symptoms and subsequently examined biologically and molecularly. All of these RB isolates were identified as SMV based on serological and infectivity assays, and the amplification of P1 gene products by reverse transcription-polymerase chain reaction (RT-PCR). Differential soybean cultivars, lines or accessions Lee 68 (rsv), PI 96983, York, Marshall, Ogden, Kwanggyo, Suweon 97 (Rsv1 alleles), L29 (Rsv3), and V94-5152 (Rsv4), following inoculation with each RB isolate, showed similar systemic symptoms suggesting that these RB isolates can overcome Rsv resistance at three loci. To differentiate the 12 RB isolates molecularly, the P1 coding region for each isolate was amplified, cloned, sequenced and compared to known SMV strains. The P1 region from the RB isolates shared 86-90% and 90-99% similarities in amino acid (aa) and nucleotide sequence, respectively, with known SMV strains. Comparison of aa sequences indicated that these RB isolates are newly emerging isolates capable of breaking Rsv resistance. Phylogenetic analysis further suggested that the RB isolates can be classified as three major types. However, recombination was not observed within the coding region of P1 protein among the types. This is the first report on the emergence of SMV isolates capable of overcoming all of the known resistance alleles at the Rsv1 locus, as well as distinct resistance genes at Rsv3 and Rsv4.
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Affiliation(s)
- B K Choi
- Department of Biology and Medicinal Science, Pai Chai University, Daejeon 302-735, Republic of Korea
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Zhong Y, Guo A, Li C, Zhuang B, Lai M, Wei C, Luo J, Li Y. Identification of a naturally occurring recombinant isolate of Sugarcane mosaic virus causing maize dwarf mosaic disease. Virus Genes 2005; 30:75-83. [PMID: 15744565 DOI: 10.1007/s11262-004-4584-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2004] [Accepted: 07/15/2004] [Indexed: 11/29/2022]
Abstract
The complete nucleotide sequence of a potyvirus causing severe maize dwarf mosaic disease in Shaanxi province, northwestern China was determined (GenBank accession No. AY569692). The full genome is 9596 nucleotides in length excluding the 3 '-terminal poly (A) sequence. It contains a large open reading frame (ORF) flanked by a 149 nt 5'-untranslated region (UTR) and a 255 nt 3'-UTR. The putative polyprotein encoded by this large ORF comprises of 3063 amino acid residues. Sequence comparisons and phylogenetic analyses showed that this potyvirus is an isolate of Sugarcane mosaic virus (SCMV). The entire sequences shared identities of 89.6-97.6 % and 79.3-93.3% with 9 sequenced SCMV isolates at the nucleotide and deduced amino acid levels, respectively. But it showed much lower identities with Maize dwarf mosaic virus (MDMV), Sorghum mosaic virus (SrMV) and Johnsongrass mosaic virus (JGMV) isolates. The putative coat protein sequence is identical to that of a Chinese maize isolate SCMV-HZ. However, partition comparisons and phylogenetic profile analyses of the viral nucleotide sequences indicated that it is a recombinant isolate of SCMV. The recombination sites are located within the 6K1 and CI coding regions.
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Affiliation(s)
- Yongwang Zhong
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
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Glasa M, Paunovic S, Jevremovic D, Myrta A, Pittnerová S, Candresse T. Analysis of recombinant Plum pox virus (PPV) isolates from Serbia confirms genetic homogeneity and supports a regional origin for the PPV-Rec subgroup. Arch Virol 2005; 150:2051-60. [PMID: 15906106 DOI: 10.1007/s00705-005-0548-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2005] [Accepted: 03/18/2005] [Indexed: 10/25/2022]
Abstract
The recent observation of the frequent occurrence of natural recombinant Plum pox virus (PPV) isolates has led to the identification of a distinct PPV subgroup, named PPV-Rec. The diversity, origin and geographical spread of the recombinant PPV isolates belonging to this subgroup remain, however, relatively poorly known. In an effort to further our understanding of these isolates, eight PPV isolates from Serbia, the country from which the first such recombinant (PPV-o6) originated, were characterized. Depending on the genomic region targeted by different typing assays, seven of the eight isolates tested presented discrepancies in their typing behavior. Sequence analysis of the (Cter)NIb-(Nter)CP region confirmed the recombinant nature of these seven isolates which all presented an identical recombination breakpoint identical to previously characterized PPV-Rec isolates. Biological indexing and immunoblot analysis provided indications that asymptomatic infection of the GF305 peach indicator and migration of the coat protein as a double-band in immunoblots may represent conserved and discriminating properties of PPV-Rec isolates. The genetic diversity of PPV-Rec isolates from former Yugoslavia (Serbia, Bosnia and Herzegovina) was estimated to be twice as large as that of the PPV-Rec isolates obtained from all other countries to date (Albania, Bulgaria, Czech republic, Germany, Hungary and Slovakia). These last results are consistent with the hypothesis that former Yugoslavia is the center of dispersion of PPV-Rec. Taken together, the results presented here provide further evidence for the wide distribution and temporal genetic stability of these natural PPV recombinant isolates and provide for the first time a possible scenario for their dispersion throughout central and eastern Europe.
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Affiliation(s)
- M Glasa
- Department of Plant Virology, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia.
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Tan Z, Gibbs AJ, Tomitaka Y, Sánchez F, Ponz F, Ohshima K. Mutations in Turnip mosaic virus genomes that have adapted to Raphanus sativus. J Gen Virol 2005; 86:501-510. [PMID: 15659771 DOI: 10.1099/vir.0.80540-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic basis for virulence in potyviruses is largely unknown. Earlier studies showed that there are two host types of Turnip mosaic virus (TuMV); the Brassica/Raphanus (BR)-host type infects both Brassica and Raphanus systemically, whereas the Brassica (B)-host type infects Brassica fully and systemically, but not Raphanus. The genetic basis of this difference has been explored by using the progeny of an infectious clone, p35Tunos; this clone is derived from the UK1 isolate, which is of the B-host type, but rarely infects Raphanus systemically and then only asymptomatically. Two inocula from one such infection were adapted to Raphanus by passaging, during which the infectivity and concentration of the virions of successive infections increased. The variant genomes in the samples, 16 in total, were sequenced fully. Four of the 39 nucleotide substitutions that were detected among the Raphanus sativus-adapted variant genomes were probably crucial for adaptation, as they were found in several variants with independent passage histories. These four were found in the protein 1 (P1), protein 3 (P3), cylindrical inclusion protein (CI) and genome-liked viral protein (VPg) genes. One of four 'parallel evolution' substitutions, 3430G-->A, resulted in a 1100Met-->Ile amino acid change in the C terminus of P3. It seems likely that this site is important in the initial stages of adaptation to R. sativus. Other independent substitutions were mostly found in the P3, CI and VPg genes.
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Affiliation(s)
- Zhongyang Tan
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Adrian J Gibbs
- School of Botany and Zoology, Australian National University, Canberra, ACT 0200, Australia
| | - Yasuhiro Tomitaka
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Flora Sánchez
- Departamento de Biotecnologia, INIA, Autopista A-6 km 7, 28040 Madrid, Spain
| | - Fernando Ponz
- Departamento de Biotecnologia, INIA, Autopista A-6 km 7, 28040 Madrid, Spain
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga 840-8502, Japan
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