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Huang A, Svanella-Dumas L, Vitry C, Marais A, Faure C, Candresse T. A new geminialphasatellite associated with wheat dwarf virus identified in winter barley in France. Arch Virol 2024; 169:162. [PMID: 38985350 DOI: 10.1007/s00705-024-06090-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/21/2024] [Indexed: 07/11/2024]
Abstract
Using a high-throughput sequencing (HTS) approach, we report the discovery of a new alphasatellite identified in a winter barley plant collected in France in 2022 that was also infected by wheat dwarf virus (WDV). The presence of the satellite and of WDV was confirmed by several independent PCR assays, and the complete genome sequence was determined. The circular satellite genome is 1424 nt long and shows typical hallmarks of members of the subfamily Geminialphasatellitinae, including a replication-associated hairpin with a CAGTATTAC sequence and a Rep-encoding open reading frame (ORF). It also possesses a second ORF, embedded in a different frame within the Rep ORF, which is also observed in clecrusatellites and a few other members of the family Alphasatellitidae. Pairwise sequence comparisons and phylogenetic analysis showed that this satellite represents a novel species. Its closest relatives are in the genus Colecusatellite, but it likely represents a new genus given its divergence from other genera of the subfamily Geminialphasatellitinae. Given that WDV was the only virus observed in coinfection with the satellite, the name "wheat dwarf virus-associated alphasatellite" is proposed for this novel agent.
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Affiliation(s)
- Aijun Huang
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, Villenave d'Ornon Cedex, 33882, France
- College of Life Science, Gannan Normal University, Ganzhou, 341000, Jiangxi, PR China
| | - Laurence Svanella-Dumas
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, Villenave d'Ornon Cedex, 33882, France
| | - C Vitry
- ARVALIS, Institut du Végétal, Boigneville, 91720, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, Villenave d'Ornon Cedex, 33882, France
| | - Chantal Faure
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, Villenave d'Ornon Cedex, 33882, France
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, Villenave d'Ornon Cedex, 33882, France.
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Claverie S, Hoareau M, Chéhida SB, Filloux D, Varsani A, Roumagnac P, Martin DP, Lett JM, Lefeuvre P. Metagenomics reveals the structure of Mastrevirus-host interaction network within an agro-ecosystem. Virus Evol 2023; 9:vead043. [PMID: 37475836 PMCID: PMC10354507 DOI: 10.1093/ve/vead043] [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: 02/16/2023] [Revised: 05/24/2023] [Accepted: 07/04/2023] [Indexed: 07/22/2023] Open
Abstract
As highly pervasive parasites that sometimes cause disease, viruses are likely major components of all natural ecosystems. An important step towards both understanding the precise ecological roles of viruses and determining how natural communities of viral species are assembled and evolve is obtaining full descriptions of viral diversity and distributions at ecosystem scales. Here, we focused on obtaining such 'community-scale' data for viruses in a single genus. We chose the genus Mastrevirus (family Geminiviridae), members of which have predominantly been found infecting uncultivated grasses (family Poaceae) throughout the tropical and sub-tropical regions of the world. We sampled over 3 years, 2,884 individual Poaceae plants belonging to thirty different species within a 2-ha plot which included cultivated and uncultivated areas on the island of Reunion. Mastreviruses were found in ∼8 per cent of the samples, of which 96 per cent did not have any discernible disease symptoms. The multitude of host-virus associations that we uncovered reveals both the plant species that most commonly host mastreviruses and the mastrevirus species (such as maize streak virus and maize streak Reunion virus) that have especially large host ranges. Our findings are consistent with the hypothesis that perennial plant species capable of hosting years-long mixed mastrevirus infections likely play a disproportionately important role in the generation of inter-species and inter-strain mastrevirus recombinants.
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Affiliation(s)
- Sohini Claverie
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France
- Université de La Réunion, UMR PVBMT, F-97410 St Pierre, La Réunion, France
| | | | | | - Denis Filloux
- CIRAD, UMR PHIM, Montpellier F-34090, France
- PHIM Plant Health Institute, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier 34090, France
| | | | - Philippe Roumagnac
- CIRAD, UMR PHIM, Montpellier F-34090, France
- PHIM Plant Health Institute, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier 34090, France
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa
| | | | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town 7700, South Africa
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Complete nucleotide sequence of a begomovirus associated with an alphasatellite and a betasatellite naturally infecting okra in Jordan. Arch Virol 2021; 166:2033-2036. [PMID: 33900467 DOI: 10.1007/s00705-021-05075-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 03/03/2021] [Indexed: 10/21/2022]
Abstract
The complete nucleotide sequences of a monopartite begomovirus and an associated alphasatellite and betasatellite isolated from naturally infected okra (Abelmoschus esculentus) plants originating from Jordan were determined. The sequences of the begomovirus, alphasatellite, and betasatellites were determined to be 2,764, 1,307, and 1,354 nucleotides in length, respectively. Sequence Demarcation Tool (SDT) and phylogenetic analysis revealed that the begomovirus isolate shared the highest (99.5-99.8%) nt sequence identity with isolates of cotton leaf curl Gezira virus (CLCuGeV), a begomovirus found to exclusively infect cotton in Africa, and recently, in Asia and the Middle East. The DNA sequences of the alphasatellite and betasatellite exhibited the highest nt sequence identity (98.7-98.9% and 92.2-95.3%, respectively) to cotton leaf curl Gezira alphasatellite and cotton leaf curl Gezira betasatellite, respectively. This is the first identification of an African begomovirus, associated with DNA satellites, infecting okra in Jordan.
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Saunders K, Richardson J, Lawson DM, Lomonossoff GP. Requirements for the Packaging of Geminivirus Circular Single-Stranded DNA: Effect of DNA Length and Coat Protein Sequence. Viruses 2020; 12:E1235. [PMID: 33143128 PMCID: PMC7694086 DOI: 10.3390/v12111235] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 11/16/2022] Open
Abstract
Geminivirus particles, consisting of a pair of twinned isometric structures, have one of the most distinctive capsids in the virological world. Until recently, there was little information as to how these structures are generated. To address this, we developed a system to produce capsid structures following the delivery of geminivirus coat protein and replicating circular single-stranded DNA (cssDNA) by the infiltration of gene constructs into plant leaves. The transencapsidation of cssDNA of the Begomovirus genus by coat protein of different geminivirus genera was shown to occur with full-length but not half-length molecules. Double capsid structures, distinct from geminate capsid structures, were also generated in this expression system. By increasing the length of the encapsidated cssDNA, triple geminate capsid structures, consisting of straight, bent and condensed forms were generated. The straight geminate triple structures generated were similar in morphology to those recorded for a potato-infecting virus from Peru. These finding demonstrate that the length of encapsidated DNA controls both the size and stability of geminivirus particles.
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Affiliation(s)
- Keith Saunders
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (D.M.L.); (G.P.L.)
| | - Jake Richardson
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK;
| | - David M. Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (D.M.L.); (G.P.L.)
| | - George P. Lomonossoff
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (D.M.L.); (G.P.L.)
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