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Ishwara Bhat A, Selvarajan R, Balasubramanian V. Emerging and Re-Emerging Diseases Caused by Badnaviruses. Pathogens 2023; 12:pathogens12020245. [PMID: 36839517 PMCID: PMC9963457 DOI: 10.3390/pathogens12020245] [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: 12/23/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
New and emerging plant diseases are caused by different pathogens including viruses that often cause significant crop losses. Badnaviruses are pararetroviruses that contain a single molecule of ds DNA genome of 7 to 9 kb in size and infect a large number of economically important crops such as banana and plantains, black pepper, cacao, citrus, grapevine, pineapple, sugarcane, sweet potato, taro, and yam, causing significant yield losses. Many of the species in the genus have a restricted host range and several of them are known to infect a single crop. Combined infections of different virus species and strains offer conditions that favor the development of new strains via recombination, especially in vegetatively propagated crops. The primary spread of badnaviruses is through vegetative propagating materials while for the secondary spread, they depend on insects such as mealybugs and aphids. Disease emerges as a consequence of the interactions between host and pathogens under favorable environmental conditions. The viral genome of the pararetroviruses is known to be integrated into the chromosome of the host and a few plants with integrants when subjected to different kinds of abiotic stress will give rise to episomal forms of the virus and cause disease. Attempts have been made to develop management strategies for badnaviruses both conventionally and using precision breeding techniques such as genome editing. Until 2016 only 32 badnavirus species infecting different crops were known, but in a span of six years, this number has gone up to 68. The current review highlights the emerging disease problems and management options for badnaviruses infecting economically important crops.
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Affiliation(s)
- Alangar Ishwara Bhat
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Kozhikode 673012, Kerala, India
| | - Ramasamy Selvarajan
- Division of Crop Protection, ICAR-National Research Centre for Banana, Trichy 620102, Tamil Nadu, India
| | - Velusamy Balasubramanian
- Division of Crop Protection, ICAR-National Research Centre for Banana, Trichy 620102, Tamil Nadu, India
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2
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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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3
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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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4
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Silva G, Bömer M, Turaki AA, Nkere CK, Kumar PL, Seal SE. Homing in on Endogenous Badnaviral Elements: Development of Multiplex PCR-DGGE for Detection and Rapid Identification of Badnavirus Sequences in Yam Germplasm. FRONTIERS IN PLANT SCIENCE 2022; 13:846989. [PMID: 35620696 PMCID: PMC9127665 DOI: 10.3389/fpls.2022.846989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Viruses of the genus Badnavirus (family Caulimoviridae) are double-stranded DNA-reverse transcribing (dsDNA-RT) plant viruses and have emerged as serious pathogens of tropical and temperate crops globally. Endogenous badnaviral sequences are found integrated in the genomes of several economically important plant species. Infection due to activation of replication-competent integrated copies of the genera Badnavirus, Petuvirus and Cavemovirus has been described. Such endogenous badnaviral elements pose challenges to the development of nucleic acid-based diagnostic methods for episomal virus infections and decisions on health certification for international movement of germplasm and seed. One major food security crop affected is yam (Dioscorea spp.). A diverse range of Dioscorea bacilliform viruses (DBVs), and endogenous DBV (eDBV) sequences have been found to be widespread in yams cultivated in West Africa and other parts of the world. This study outlines the development of multiplex PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE) to assist in the detection and analysis of eDBVs, through the example of analysing yam germplasm from Nigeria and Ghana. Primers targeting the three most prevalent DBV monophyletic species groups in West Africa were designed to improve DGGE resolution of complex eDBV sequence fingerprints. Multiplex PCR-DGGE with the addition of a tailor-made DGGE sequence marker enables rapid comparison of endogenous badnaviral sequence diversity across germplasm, as illustrated in this study for eDBV diversity in yam.
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Affiliation(s)
- Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
| | - Moritz Bömer
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
| | - Aliyu A. Turaki
- Kebbi State University of Science and Technology Aliero, Birnin Kebbi, Nigeria
| | - Chukwuemeka K. Nkere
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Department of Crop Protection and Environmental Biology (CPEB), University of Ibadan, Ibadan, Nigeria
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - P. Lava Kumar
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Susan E. Seal
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
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5
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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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6
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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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Identification and distribution of novel badnaviral sequences integrated in the genome of cacao (Theobroma cacao). Sci Rep 2021; 11:8270. [PMID: 33859254 PMCID: PMC8050207 DOI: 10.1038/s41598-021-87690-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 03/22/2021] [Indexed: 12/03/2022] Open
Abstract
Theobroma cacao is one of the most economically important tropical trees, being the source of chocolate. As part of an ongoing study to understand the diversity of the badnavirus complex, responsible for the cacao swollen shoot virus disease in West Africa, evidence was found recently of virus-like sequences in asymptomatic cacao plants. The present study exploited the wealth of genomic resources in this crop, and combined bioinformatic, molecular, and genetic approaches to report for the first time the presence of integrated badnaviral sequences in most of the cacao genetic groups. These sequences, which we propose to name eTcBV for endogenous T. cacao bacilliform virus, varied in type with each predominating in a specific genetic group. A diagnostic multiplex PCR method was developed to identify the homozygous or hemizygous condition of one specific insert, which was inherited as a single Mendelian trait. These data suggest that these integration events occurred before or during the species diversification in Central and South America, and prior to its cultivation in other regions. Such evidence of integrated sequences is relevant to the management of cacao quarantine facilities and may also aid novel methods to reduce the impact of such viruses in this crop.
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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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9
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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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10
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Sukal AC, Kidanemariam DB, Dale JL, Harding RM, James AP. Characterization of a novel member of the family Caulimoviridae infecting Dioscorea nummularia in the Pacific, which may represent a new genus of dsDNA plant viruses. PLoS One 2018; 13:e0203038. [PMID: 30208072 PMCID: PMC6135502 DOI: 10.1371/journal.pone.0203038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/14/2018] [Indexed: 12/17/2022] Open
Abstract
We have characterized the complete genome of a novel circular double-stranded DNA virus, tentatively named Dioscorea nummularia-associated virus (DNUaV), infecting Dioscorea nummularia originating from Samoa. The genome of DNUaV comprised 8139 bp and contained four putative open reading frames (ORFs). ORFs 1 and 2 had no identifiable conserved domains, while ORF 3 had conserved motifs typical of viruses within the family Caulimoviridae including coat protein, movement protein, aspartic protease, reverse transcriptase and ribonuclease H. A transactivator domain, similar to that present in members of several caulimoviridae genera, was also identified in the putative ORF 4. The genome size, organization, and presence of conserved amino acid domains are similar to other viruses in the family Caulimoviridae. However, based on nucleotide sequence similarity and phylogenetic analysis, DNUaV appears to be a distinct novel member of the family and may represent a new genus.
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Affiliation(s)
- Amit C. Sukal
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
- Centre for Pacific Crops and Trees, Pacific Community, Suva, Fiji
| | - Dawit B. Kidanemariam
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
| | - James L. Dale
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Robert M. Harding
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Anthony P. James
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, Australia
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11
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Bömer M, Turaki AA, Rathnayake AI, Silva G, Kumar PL, Seal SE. Rolling Circle Amplification to Screen Yam Germplasm for Badnavirus Infections and to Amplify and Characterise Novel Badnavirus Genomes. Bio Protoc 2018; 8:e2672. [PMID: 34179227 DOI: 10.21769/bioprotoc.2672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 12/11/2017] [Accepted: 12/18/2017] [Indexed: 11/02/2022] Open
Abstract
Since the first discovery of badnaviruses (family Caulimoviridae, genus Badnavirus) in yam (Dioscorea spp.) germplasm in the 1970s (Harrison and Roberts, 1973), several hundred partial badnavirus reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences have been characterised ( Kenyon et al., 2008 ; Bousalem et al., 2009 ), but only a few complete Dioscorea bacilliform virus (DBV) genome sequences have been reported ( Phillips et al., 1999 ; Seal and Muller, 2007; Bömer et al., 2016 and 2017; Sukal et al., 2017 ; Umber et al., 2017 ). We have optimised a workflow involving total nucleic acid extractions and rolling circle amplification (RCA) combined with restriction enzyme analysis for the detection and amplification of DBVs present in yam germplasm. We have employed this approach successfully revealing three novel episomal yam badnaviruses ( Bömer et al., 2016 ). We proposed this to be a complementary method to denaturing gradient gel electrophoresis, which enables a rapid indication of badnavirus diversity as well as the identification of potentially integrated badnavirus sequences in the host genome ( Turaki et al., 2017 ). Here, we describe the step-by-step protocol to screen yam germplasm for badnavirus infections using RCA as an efficient research tool in the amplification and characterization of novel badnavirus genomes.
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Affiliation(s)
- Moritz Bömer
- Natural Resources Institute, University of Greenwich, London, UK
| | - Aliyu A Turaki
- Kebbi State University of Science and Technology Aliero, Birnin Kebbi, Nigeria
| | | | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, London, UK
| | - P Lava Kumar
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, London, UK
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12
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Bömer M, Rathnayake AI, Visendi P, Silva G, Seal SE. Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Arch Virol 2017; 163:533-538. [PMID: 29134336 PMCID: PMC5799344 DOI: 10.1007/s00705-017-3605-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/27/2017] [Indexed: 11/03/2022]
Abstract
Yams (Dioscorea spp.) host a diverse range of badnaviruses (genus Badnavirus, family Caulimoviridae). The first complete genome sequence of Dioscorea bacilliform RT virus 3 (DBRTV3), which belongs to the monophyletic species group K5, is described. This virus is most closely related to Dioscorea bacilliform SN virus (DBSNV, group K4) based on a comparison of genome sequences. Recombination analysis identified a unique recombination event in DBRTV3, with DBSNV likely to be the major parent and Dioscorea bacilliform AL virus (DBALV) the minor parent, providing the first evidence for recombination in yam badnaviruses. This has important implications for yam breeding programmes globally.
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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
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - 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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PCR-DGGE Analysis: Unravelling Complex Mixtures of Badnavirus Sequences Present in Yam Germplasm. Viruses 2017; 9:v9070181. [PMID: 28696406 PMCID: PMC5537673 DOI: 10.3390/v9070181] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/29/2017] [Accepted: 07/04/2017] [Indexed: 12/19/2022] Open
Abstract
Badnaviruses (family Caulimoviridae, genus Badnavirus) have emerged as serious pathogens especially affecting the cultivation of tropical crops. Badnavirus sequences can be integrated in host genomes, complicating the detection of episomal infections and the assessment of viral genetic diversity in samples containing a complex mixture of sequences. Yam (Dioscorea spp.) plants are hosts to a diverse range of badnavirus species, and recent findings have suggested that mixed infections occur frequently in West African yam germplasm. Historically, the determination of the diversity of badnaviruses present in yam breeding lines has been achieved by cloning and sequencing of polymerase chain reaction (PCR) products. In this study, the molecular diversity of partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences from yam badnaviruses was analysed using PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE). This resulted in the identification of complex ‘fingerprints’ composed of multiple sequences of Dioscorea bacilliform viruses (DBVs). Many of these sequences show high nucleotide identities to endogenous DBV (eDBV) sequences deposited in GenBank, and fall into six monophyletic species groups. Our findings highlight PCR-DGGE as a powerful tool in badnavirus diversity studies enabling a rapid indication of sequence diversity as well as potential candidate integrated sequences revealed by their conserved nature across germplasm.
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14
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Sukal A, Kidanemariam D, Dale J, James A, Harding R. Characterization of badnaviruses infecting Dioscorea spp. in the Pacific reveals two putative novel species and the first report of dioscorea bacilliform RT virus 2. Virus Res 2017; 238:29-34. [PMID: 28591557 DOI: 10.1016/j.virusres.2017.05.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 01/20/2023]
Abstract
The complete genome sequences of three new badnaviruses associated with yam (Dioscorea spp.) originating from Fiji, Papua New Guinea and Samoa were determined following rolling circle amplification of the virus genomes. The full-length genomes consisted of a single molecule of circular double-stranded DNA of 8106bp for isolate FJ14, 7871bp for isolate PNG10 and 7426bp for isolate SAM01. FJ14 and PNG10 contained three open reading frames while SAM01 had an additional open reading frame which partially overlapped the 3' end of ORF 3. Amino acid sequence analysis of ORF 3 from the three isolates confirmed the presence of conserved motifs typical of other badnaviruses. Phylogenetic analysis revealed the sequences to be closely related to other Dioscorea-infecting badnaviruses. FJ14 and PNG10 appear to be new species, which we have tentatively named dioscorea bacilliform ES virus (DBESV) and dioscorea bacilliform AL virus 2 (DBALV2), respectively, while SAM01 represents a Pacific isolate of the recently published dioscorea bacilliform RT virus 2 and is described as dioscorea bacilliform RT virus 2-[4RT] (DBRTV2-[4RT]).
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Affiliation(s)
- Amit Sukal
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology (QUT), 2 George St, Brisbane, 4001, Australia
| | - Dawit Kidanemariam
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology (QUT), 2 George St, Brisbane, 4001, Australia
| | - James Dale
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology (QUT), 2 George St, Brisbane, 4001, Australia
| | - Anthony James
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology (QUT), 2 George St, Brisbane, 4001, Australia
| | - Robert Harding
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology (QUT), 2 George St, Brisbane, 4001, Australia.
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