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Wang Z, Liu J, Qi X, Su D, Yang J, Cui X. Study of Endogenous Viruses in the Strawberry Plants. Viruses 2024; 16:1306. [PMID: 39205280 PMCID: PMC11359110 DOI: 10.3390/v16081306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 08/12/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Endogenous viral elements (EVEs) have been reported to exist widely in the genomes of eukaryotic organisms, and they are closely associated with the growth, development, genetics, adaptation, and evolution of their hosts. In this study, two methods-homologous sequence search and genome alignment-were used to explore the endogenous viral sequences in the genomes of Fragaria species. Results revealed abundant endogenous pararetroviruses (EPRVs) in the genomes of Fragaria species, including 786 sequences belonging to five known taxa such as Caulimovirus and other unclassified taxa. Differences were observed in the detected EPRVs between the two methods, with the homologous sequence search having a greater number of EPRVs. On the contrary, genome alignment identified various types and sources of virus-like sequences. Furthermore, through genome alignment, a 267-bp sequence with 95% similarity to the gene encoding the aphid-transmitted protein of Strawberry vein banding virus (Caulimovirus venafragariae) was discovered in the F. chiloensis genome, which was likely a recent insertion. In addition, the statistical analysis of the genome alignment results indicated a remarkably higher abundance of virus-like sequences in the genomes of polyploid strawberries compared with diploid ones. Moreover, the differences in virus-like sequences were observed between the genomes of Fragaria species and those of their close relatives. This study enriched the diversity of viruses that infect strawberries, and laid a theoretical foundation for further research on the origin of endogenous viruses in the strawberry genome, host-virus interactions, adaptation, evolution, and their functions.
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Affiliation(s)
- Zongneng Wang
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
| | - Jian Liu
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
| | - Xingyang Qi
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
| | - Daifa Su
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
| | - Junyu Yang
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
- Yunnan International Joint Laboratory of Virology and Immunology, Kunming 650500, China
| | - Xiaolong Cui
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
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2
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Cao X, Tang L, Song J. Circular Single-Stranded DNA: Discovery, Biological Effects, and Applications. ACS Synth Biol 2024; 13:1038-1058. [PMID: 38501391 DOI: 10.1021/acssynbio.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The field of nucleic acid therapeutics has witnessed a significant surge in recent times, as evidenced by the increasing number of approved genetic drugs. However, current platform technologies containing plasmids, lipid nanoparticle-mRNAs, and adeno-associated virus vectors encounter various limitations and challenges. Thus, we are devoted to finding a novel nucleic acid vector and have directed our efforts toward investigating circular single-stranded DNA (CssDNA), an ancient form of nucleic acid. CssDNAs are ubiquitous, but generally ignored. Accumulating evidence suggests that CssDNAs possess exceptional properties as nucleic acid vectors, exhibiting great potential for clinical applications in genetic disorders, gene editing, and immune cell therapy. Here, we comprehensively review the discovery and biological effects of CssDNAs as well as their applications in the field of biomedical research for the first time. Undoubtedly, as an ancient form of DNA, CssDNA holds immense potential and promises novel insights for biomedical research.
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Affiliation(s)
- Xisen Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
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3
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Clemons RA, Yacoub MN, Faust E, Toledo LF, Jenkinson TS, Carvalho T, Simmons DR, Kalinka E, Fritz-Laylin LK, James TY, Stajich JE. An endogenous DNA virus in an amphibian-killing fungus associated with pathogen genotype and virulence. Curr Biol 2024; 34:1469-1478.e6. [PMID: 38490202 DOI: 10.1016/j.cub.2024.02.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/18/2023] [Accepted: 02/26/2024] [Indexed: 03/17/2024]
Abstract
The global panzootic lineage (GPL) of the pathogenic fungus Batrachochytrium dendrobatidis (Bd) has caused severe amphibian population declines, yet the drivers underlying the high frequency of GPL in regions of amphibian decline are unclear. Using publicly available Bd genome sequences, we identified multiple non-GPL Bd isolates that contain a circular Rep-encoding single-stranded (CRESS)-like DNA virus, which we named Bd DNA virus 1 (BdDV-1). We further sequenced and constructed genome assemblies with long read sequences to find that the virus is integrated into the nuclear genome in some strains. Attempts to cure virus-positive isolates were unsuccessful; however, phenotypic differences between naturally virus-positive and virus-negative Bd isolates suggested that BdDV-1 decreases the growth of its host in vitro but increases the virulence of its host in vivo. BdDV-1 is the first-described CRESS DNA mycovirus of zoosporic true fungi, with a distribution inversely associated with the emergence of the panzootic lineage.
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Affiliation(s)
- Rebecca A Clemons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mark N Yacoub
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA
| | - Evelyn Faust
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - L Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal Instituto de Biologia (IB), Universidade Estadual de Campinas, Campinas, SP 13083-862, Brazil
| | - Thomas S Jenkinson
- Department of Biological Sciences, California State University, East Bay, Hayward, CA 94592, USA
| | - Tamilie Carvalho
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - D Rabern Simmons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erik Kalinka
- Department of Biology, University of Massachusetts, Amherst, Amherst, MA 01003, USA
| | | | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA.
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4
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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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5
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Rieux A, Campos P, Duvermy A, Scussel S, Martin D, Gaudeul M, Lefeuvre P, Becker N, Lett JM. Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history. Sci Rep 2021; 11:21280. [PMID: 34711837 PMCID: PMC8553777 DOI: 10.1038/s41598-021-00518-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/13/2021] [Indexed: 12/30/2022] Open
Abstract
Emerging viral diseases of plants are recognised as a growing threat to global food security. However, little is known about the evolutionary processes and ecological factors underlying the emergence and success of viruses that have caused past epidemics. With technological advances in the field of ancient genomics, it is now possible to sequence historical genomes to provide a better understanding of viral plant disease emergence and pathogen evolutionary history. In this context, herbarium specimens represent a valuable source of dated and preserved material. We report here the first historical genome of a crop pathogen DNA virus, a 90-year-old African cassava mosaic virus (ACMV), reconstructed from small RNA sequences bearing hallmarks of small interfering RNAs. Relative to tip-calibrated dating inferences using only modern data, those performed with the historical genome yielded both molecular evolution rate estimates that were significantly lower, and lineage divergence times that were significantly older. Crucially, divergence times estimated without the historical genome appeared in discordance with both historical disease reports and the existence of the historical genome itself. In conclusion, our study reports an updated time-frame for the history and evolution of ACMV and illustrates how the study of crop viral diseases could benefit from natural history collections.
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Affiliation(s)
- Adrien Rieux
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France.
| | - Paola Campos
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
| | | | - Sarah Scussel
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France
| | - Darren Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
- Herbier national (P), Muséum national d'Histoire Naturelle, CP39, 57 Rue Cuvier, 75005, Paris, France
| | | | - Nathalie Becker
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
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6
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Zhao L, Lavington E, Duffy S. Truly ubiquitous CRESS DNA viruses scattered across the eukaryotic tree of life. J Evol Biol 2021; 34:1901-1916. [PMID: 34498333 DOI: 10.1111/jeb.13927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/05/2021] [Accepted: 08/18/2021] [Indexed: 11/29/2022]
Abstract
Until recently, most viruses detected and characterized were of economic significance, associated with agricultural and medical diseases. This was certainly true for the eukaryote-infecting circular Rep (replication-associated protein)-encoding single-stranded DNA (CRESS DNA) viruses, which were thought to be a relatively small group of viruses. With the explosion of metagenomic sequencing over the past decade and increasing use of rolling-circle replication for sequence amplification, scientists have identified and annotated copious numbers of novel CRESS DNA viruses - many without known hosts but which have been found in association with eukaryotes. Similar advances in cellular genomics have revealed that many eukaryotes have endogenous sequences homologous to viral Reps, which not only provide 'fossil records' to reconstruct the evolutionary history of CRESS DNA viruses but also reveal potential host species for viruses known by their sequences alone. The Rep protein is a conserved protein that all CRESS DNA viruses use to assist rolling-circle replication that is known to be endogenized in a few eukaryotic species (notably tobacco and water yam). A systematic search for endogenous Rep-like sequences in GenBank's non-redundant eukaryotic database was performed using tBLASTn. We utilized relaxed search criteria for the capture of integrated Rep sequence within eukaryotic genomes, identifying 93 unique species with an endogenized fragment of Rep in their nuclear, plasmid (one species), mitochondrial (six species) or chloroplast (eight species) genomes. These species come from 19 different phyla, scattered across the eukaryotic tree of life. Exogenous and endogenous CRESS DNA viral Rep tree topology suggested potential hosts for one family of uncharacterized viruses and supports a primarily fungal host range for genomoviruses.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA.,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Erik Lavington
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
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7
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Barreat JGN, Katzourakis A. Paleovirology of the DNA viruses of eukaryotes. Trends Microbiol 2021; 30:281-292. [PMID: 34483047 DOI: 10.1016/j.tim.2021.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022]
Abstract
Paleovirology is the study of ancient viruses and how they have coevolved with their hosts. An increasingly detailed understanding of the diversity, origins, and evolution of the DNA viruses of eukaryotes has been obtained through the lens of paleovirology in recent years. Members of multiple viral families have been found integrated in the genomes of eukaryotes, providing a rich fossil record to study. These elements have extended our knowledge of exogenous viral diversity, host ranges, and the timing of viral evolution, and are revealing the existence of entire new families of eukaryotic integrating dsDNA viruses and transposons. Future work in paleovirology will continue to provide insights into antiviral immunity, viral diversity, and potential applications, and reveal other secrets of the viral world.
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Affiliation(s)
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK.
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8
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Bagayoko I, Celli MG, Romay G, Poulicard N, Pinel-Galzi A, Julian C, Filloux D, Roumagnac P, Sérémé D, Bragard C, Hébrard E. Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus. Viruses 2021; 13:v13050737. [PMID: 33922593 PMCID: PMC8145960 DOI: 10.3390/v13050737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/12/2021] [Accepted: 04/21/2021] [Indexed: 01/02/2023] Open
Abstract
The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.
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Affiliation(s)
- Issiaka Bagayoko
- Earth and Life Institute, Applied Microbiology-Phytopathology, Université Catholique de Louvain (UCLouvain), Croix du Sud 2 Bte L07.05.03, 1348 Louvain-la-Neuve, Belgium; (I.B.); (G.R.); (C.B.)
| | - Marcos Giovanni Celli
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires 1425, Argentina;
- Instituto de Patología Vegetal (IPAVE, CIAP, INTA), Camino 60 cuadras Km 5, Cordoba 5119, Argentina
| | - Gustavo Romay
- Earth and Life Institute, Applied Microbiology-Phytopathology, Université Catholique de Louvain (UCLouvain), Croix du Sud 2 Bte L07.05.03, 1348 Louvain-la-Neuve, Belgium; (I.B.); (G.R.); (C.B.)
| | - Nils Poulicard
- PHIM, Plant Health Institute, Université de Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France; (N.P.); (A.P.-G.); (C.J.); (D.F.); (P.R.)
| | - Agnès Pinel-Galzi
- PHIM, Plant Health Institute, Université de Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France; (N.P.); (A.P.-G.); (C.J.); (D.F.); (P.R.)
| | - Charlotte Julian
- PHIM, Plant Health Institute, Université de Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France; (N.P.); (A.P.-G.); (C.J.); (D.F.); (P.R.)
- CIRAD, UMR PHIM, Campus International de Montferrier-Baillarguet, 34398 Montpellier, France
| | - Denis Filloux
- PHIM, Plant Health Institute, Université de Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France; (N.P.); (A.P.-G.); (C.J.); (D.F.); (P.R.)
- CIRAD, UMR PHIM, Campus International de Montferrier-Baillarguet, 34398 Montpellier, France
| | - Philippe Roumagnac
- PHIM, Plant Health Institute, Université de Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France; (N.P.); (A.P.-G.); (C.J.); (D.F.); (P.R.)
- CIRAD, UMR PHIM, Campus International de Montferrier-Baillarguet, 34398 Montpellier, France
| | - Drissa Sérémé
- Laboratoire de Laboratoire de Virologie et de Biotechnologies Végétales, INERA—Institut de l’Environnement et de Recherches Agricoles, LMI Patho-Bios, Ouagadougou 01 BP 476, Burkina Faso;
| | - Claude Bragard
- Earth and Life Institute, Applied Microbiology-Phytopathology, Université Catholique de Louvain (UCLouvain), Croix du Sud 2 Bte L07.05.03, 1348 Louvain-la-Neuve, Belgium; (I.B.); (G.R.); (C.B.)
| | - Eugénie Hébrard
- PHIM, Plant Health Institute, Université de Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France; (N.P.); (A.P.-G.); (C.J.); (D.F.); (P.R.)
- Correspondence:
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Chiumenti M, Greco C, De Stradis A, Loconsole G, Cavalieri V, Altamura G, Zicca S, Saldarelli P, Saponari M. Olea Europaea Geminivirus: A Novel Bipartite Geminivirid Infecting Olive Trees. Viruses 2021; 13:v13030481. [PMID: 33804134 PMCID: PMC8000510 DOI: 10.3390/v13030481] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/05/2021] [Accepted: 03/11/2021] [Indexed: 12/29/2022] Open
Abstract
In 2014, high-throughput sequencing of libraries of total DNA from olive trees allowed the identification of two geminivirus-like contigs. After conventional resequencing of the two genomic DNAs, their analysis revealed they belonged to the same viral entity, for which the provisional name of Olea europaea geminivirus (OEGV) was proposed. Although DNA-A showed a genome organization similar to that of New World begomoviruses, DNA-B had a peculiar ORF arrangement, consisting of a movement protein (MP) in the virion sense and a protein with unknown function on the complementary sense. Phylogenetic analysis performed either on full-length genome or on coat protein, replication associated protein (Rep), and MP sequences did not endorse the inclusion of this virus in any of the established genera in the family Geminiviridae. A survey of 55 plants revealed that the virus is widespread in Apulia (Italy) with 91% of the samples testing positive, although no correlation of OEGV with a disease or specific symptoms was encountered. Southern blot assay suggested that the virus is not integrated in the olive genome. The study of OEGV-derived siRNA obtained from small RNA libraries of leaves and fruits of three different cultivars, showed that the accumulation of the two genomic components is influenced by the plant genotype while virus-derived-siRNA profile is in line with other geminivirids reported in literature. Single-nucleotide polymorphism (SNP) analysis unveiled a low intra-specific variability.
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Affiliation(s)
- Michela Chiumenti
- Institute for Sustainable Plant Protection, CNR, Via Amendola 122/D, 70126 Bari, Italy; (C.G.); (A.D.S.); (V.C.); (G.A.); (S.Z.); (P.S.); (M.S.)
- Correspondence: (M.C.); (G.L.)
| | - Claudia Greco
- Institute for Sustainable Plant Protection, CNR, Via Amendola 122/D, 70126 Bari, Italy; (C.G.); (A.D.S.); (V.C.); (G.A.); (S.Z.); (P.S.); (M.S.)
- Dipartimento di Scienze del suolo, della Pianta e degli Alimenti, University of Bari “Aldo Moro”, Via Amendola, 165/A, 70126 Bari, Italy
| | - Angelo De Stradis
- Institute for Sustainable Plant Protection, CNR, Via Amendola 122/D, 70126 Bari, Italy; (C.G.); (A.D.S.); (V.C.); (G.A.); (S.Z.); (P.S.); (M.S.)
| | - Giuliana Loconsole
- Institute for Sustainable Plant Protection, CNR, Via Amendola 122/D, 70126 Bari, Italy; (C.G.); (A.D.S.); (V.C.); (G.A.); (S.Z.); (P.S.); (M.S.)
- Correspondence: (M.C.); (G.L.)
| | - Vincenzo Cavalieri
- Institute for Sustainable Plant Protection, CNR, Via Amendola 122/D, 70126 Bari, Italy; (C.G.); (A.D.S.); (V.C.); (G.A.); (S.Z.); (P.S.); (M.S.)
| | - Giuseppe Altamura
- Institute for Sustainable Plant Protection, CNR, Via Amendola 122/D, 70126 Bari, Italy; (C.G.); (A.D.S.); (V.C.); (G.A.); (S.Z.); (P.S.); (M.S.)
| | - Stefania Zicca
- Institute for Sustainable Plant Protection, CNR, Via Amendola 122/D, 70126 Bari, Italy; (C.G.); (A.D.S.); (V.C.); (G.A.); (S.Z.); (P.S.); (M.S.)
| | - Pasquale Saldarelli
- Institute for Sustainable Plant Protection, CNR, Via Amendola 122/D, 70126 Bari, Italy; (C.G.); (A.D.S.); (V.C.); (G.A.); (S.Z.); (P.S.); (M.S.)
| | - Maria Saponari
- Institute for Sustainable Plant Protection, CNR, Via Amendola 122/D, 70126 Bari, Italy; (C.G.); (A.D.S.); (V.C.); (G.A.); (S.Z.); (P.S.); (M.S.)
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10
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Serfraz S, Sharma V, Maumus F, Aubriot X, Geering ADW, Teycheney PY. Insertion of Badnaviral DNA in the Late Blight Resistance Gene (R1a) of Brinjal Eggplant ( Solanum melongena). FRONTIERS IN PLANT SCIENCE 2021; 12:683681. [PMID: 34367211 PMCID: PMC8346255 DOI: 10.3389/fpls.2021.683681] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/30/2021] [Indexed: 05/20/2023]
Abstract
Endogenous viral elements (EVEs) are widespread in plant genomes. They result from the random integration of viral sequences into host plant genomes by horizontal DNA transfer and have the potential to alter host gene expression. We performed a large-scale search for co-transcripts including caulimovirid and plant sequences in 1,678 plant and 230 algal species and characterized 50 co-transcripts in 45 distinct plant species belonging to lycophytes, ferns, gymnosperms and angiosperms. We found that insertion of badnavirus EVEs along with Ty-1 copia mobile elements occurred into a late blight resistance gene (R1) of brinjal eggplant (Solanum melongena) and wild relatives in genus Solanum and disrupted R1 orthologs. EVEs of two previously unreported badnaviruses were identified in the genome of S. melongena, whereas EVEs from an additional novel badnavirus were identified in the genome of S. aethiopicum, the cultivated scarlet eggplant. Insertion of these viruses in the ancestral lineages of the direct wild relatives of the eggplant would have occurred during the last 3 Myr, further supporting the distinctiveness of the group of the eggplant within the giant genus Solanum.
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Affiliation(s)
- Saad Serfraz
- CIRAD, UMR AGAP Institut, F-97130, Capesterre-Belle-Eau, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre-Belle-Eau, France
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Vikas Sharma
- URGI, INRAE, Université Paris-Saclay, Versailles, France
| | - Florian Maumus
- URGI, INRAE, Université Paris-Saclay, Versailles, France
| | - Xavier Aubriot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Andrew D. W. Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Pierre-Yves Teycheney
- CIRAD, UMR AGAP Institut, F-97130, Capesterre-Belle-Eau, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre-Belle-Eau, France
- *Correspondence: Pierre-Yves Teycheney,
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11
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Sharma V, Lefeuvre P, Roumagnac P, Filloux D, Teycheney PY, Martin DP, Maumus F. Large-scale survey reveals pervasiveness and potential function of endogenous geminiviral sequences in plants. Virus Evol 2020; 6:veaa071. [PMID: 33391820 PMCID: PMC7758297 DOI: 10.1093/ve/veaa071] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The family Geminiviridae contains viruses with single-stranded DNA genomes that have been found infecting a wide variety of angiosperm species. The discovery within the last 25 years of endogenous geminivirus-like (EGV) elements within the nuclear genomes of several angiosperms has raised questions relating to the pervasiveness of EGVs and their impacts on host biology. Only a few EGVs have currently been characterized and it remains unclear whether any of these have influenced, or are currently influencing, the evolutionary fitness of their hosts. We therefore undertook a large-scale search for evidence of EGVs within 134 genome and 797 transcriptome sequences of green plant species. We detected homologues of geminivirus replication-associated protein (Rep) genes in forty-two angiosperm species, including two monocots, thirty-nine dicots, and one ANITA-grade basal angiosperm species (Amborella trichopoda). While EGVs were present in the members of many different plant orders, they were particularly common within the large and diverse order, Ericales, with the highest copy numbers of EGVs being found in two varieties of tea plant (Camellia sinensis). Phylogenetic and clustering analyses revealed multiple highly divergent previously unknown geminivirus Rep lineages, two of which occur in C.sinensis alone. We find that some of the Camellia EGVs are likely transcriptionally active, sometimes co-transcribed with the same host genes across several Camellia species. Overall, our analyses expand the known breadths of both geminivirus diversity and geminivirus host ranges, and strengthens support for the hypothesis that EGVs impact the biology of their hosts.
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Affiliation(s)
- Vikas Sharma
- URGI, INRAE, Université Paris-Saclay, Plant Breeding Division, 78026, Versailles, France.,Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425 Jülich, Germany
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, Department of Biological Systems, F-97410 St Pierre, La Réunion, France
| | - Philippe Roumagnac
- CIRAD, BGPI, Department of Biological Systems, 34398 Montpellier CEDEX 5, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Department of Biological Systems, 34398 Montpellier CEDEX 5, France
| | - Denis Filloux
- CIRAD, BGPI, Department of Biological Systems, 34398 Montpellier CEDEX 5, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Department of Biological Systems, 34398 Montpellier CEDEX 5, France
| | - Pierre-Yves Teycheney
- CIRAD, UMR AGAP, Department of Biological Systems, F-97130, Capesterre Belle-Eau, Guadeloupe, France.,AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Department of Biological Systems, F-97130 Capesterre Belle-Eau, Guadeloupe, France
| | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of infectious Diseases and molecular Medicine, University of Cape Town, OBSERVATORY 7925 Cape Town, South Africa
| | - Florian Maumus
- URGI, INRAE, Université Paris-Saclay, Plant Breeding Division, 78026, Versailles, France
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12
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Torres-Herrera SI, Romero-Osorio A, Moreno-Valenzuela O, Pastor-Palacios G, Cardenas-Conejo Y, Ramírez-Prado JH, Riego-Ruiz L, Minero-García Y, Ambriz-Granados S, Argüello-Astorga GR. A Lineage of Begomoviruses Encode Rep and AC4 Proteins of Enigmatic Ancestry: Hints on the Evolution of Geminiviruses in the New World. Viruses 2019; 11:E644. [PMID: 31337020 PMCID: PMC6669703 DOI: 10.3390/v11070644] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/16/2022] Open
Abstract
The begomoviruses (BGVs) are plant pathogens that evolved in the Old World during the Cretaceous and arrived to the New World (NW) in the Cenozoic era. A subgroup of NW BGVs, the "Squash leaf curl virus (SLCV) lineage" (S-Lin), includes viruses with unique characteristics. To get clues on the evolutionary origin of this lineage, a search for divergent members was undertaken. Four novel BGVs were characterized, including one that is basal to the group. Comparative analyses led to discover a ~670 bp genome module that is nearly exclusive of this lineage, encompassing the replication origin, the AC4 gene, and 480 bp of the Rep gene. A similar DNA module was found in two curtoviruses, hence suggesting that the S-Lin ancestor acquired its distinctive genomic segment by recombination with a curtovirus. This hypothesis was definitely disproved by an in-depth sequence analysis. The search for homologs of S-Lin Rep uncover the common origin of Rep proteins encoded by diverse Geminiviridae genera and viral "fossils" integrated at plant genomes. In contrast, no homolog of S-Lin Rep was found in public databases. Consequently, it was concluded that the SLCV clade ancestor evolved by a recombination event between a primitive NW BGV and a virus from a hitherto unknown lineage.
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Affiliation(s)
- Sandra Iliana Torres-Herrera
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., México
- Facultad de Ciencias Forestales, Universidad Juárez del Estado de Durango, Río Papaloapan Esquina con Blvd Durango (s/n), Col. Valle del Sur. 34120, Durango, Dgo, México
| | - Angélica Romero-Osorio
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., México
| | | | - Guillermo Pastor-Palacios
- CONACYT-CIIDZA-Instituto Potosino de Investigación Científica y Tecnológica A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., México
| | - Yair Cardenas-Conejo
- CONACyT-Universidad de Colima, Laboratorio de Agrobiotecnología, Carretera Los Limones-Loma de Juarez (s/n), Tecnoparque CLQ Colima 28629, Colima, México
| | | | - Lina Riego-Ruiz
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., México
| | - Yereni Minero-García
- Centro de Investigación Científica de Yucatán, A.C., Mérida 97000, Yucatán, México
| | - Salvador Ambriz-Granados
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., México
| | - Gerardo R Argüello-Astorga
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., México.
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13
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Abstract
Single-stranded (ss)DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens. Most ssDNA viruses possess small genomes that replicate by the rolling-circle-like mechanism initiated by a distinct virus-encoded endonuclease. High throughput genome sequencing and improved bioinformatics tools have yielded vast information on presence of ssDNA viruses in diverse habitats. The simple genome of ssDNA viruses have high propensity to undergo mutation and recombination often emerging as threat to human civilization. Interestingly their genome is found embedded in fossils dating back to million years. The unusual evolutionary history of ssDNA viruses reveal evidences of horizontal gene transfer, sometimes between different species and genera.
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14
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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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15
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Filloux D, Fernandez E, Loire E, Claude L, Galzi S, Candresse T, Winter S, Jeeva ML, Makeshkumar T, Martin DP, Roumagnac P. Nanopore-based detection and characterization of yam viruses. Sci Rep 2018; 8:17879. [PMID: 30552347 PMCID: PMC6294787 DOI: 10.1038/s41598-018-36042-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/04/2018] [Indexed: 01/07/2023] Open
Abstract
We here assessed the capability of the MinION sequencing approach to detect and characterize viruses infecting a water yam plant. This sequencing platform consistently revealed the presence of several plant virus species, including Dioscorea bacilliform virus, Yam mild mosaic virus and Yam chlorotic necrosis virus. A potentially novel ampelovirus was also detected by a complimentary Illumina sequencing approach. The full-length genome sequence of yam chlorotic necrosis virus was determined using Sanger sequencing, which enabled determination of the coverage and sequencing accuracy of the MinION technology. Whereas the total mean sequencing error rate of yam chlorotic necrosis virus-related MinION reads was 11.25%, we show that the consensus sequence obtained either by de novo assembly or after mapping the MinION reads on the virus genomic sequence was >99.8% identical with the Sanger-derived reference sequence. From the perspective of potential plant disease diagnostic applications of MinION sequencing, these degrees of sequencing accuracy demonstrate that the MinION approach can be used to both reliably detect and accurately sequence nearly full-length positive-sense single-strand polyadenylated RNA plant virus genomes.
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Affiliation(s)
- Denis Filloux
- CIRAD, BGPI, Montpellier, France
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, BGPI, Montpellier, France
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, Montpellier, France
| | - Etienne Loire
- CIRAD, UMR ASTRE, F-34398, Montpellier, France
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Lisa Claude
- CIRAD, BGPI, Montpellier, France
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, Montpellier, France
| | - Serge Galzi
- CIRAD, BGPI, Montpellier, France
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, Montpellier, France
| | - Thierry Candresse
- UMR 1332 BFP, INRA, University Bordeaux, CS20032, 33882, Villenave d'Ornon cedex, France
| | - Stephan Winter
- DSMZ Plant Virus Department, Messeweg 11/12, 38102, Braunschweig, Germany
| | - M L Jeeva
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, Kerala, India
| | - T Makeshkumar
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, Kerala, India
| | - Darren P Martin
- Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Philippe Roumagnac
- CIRAD, BGPI, Montpellier, France.
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, Montpellier, France.
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16
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Catoni M, Noris E, Vaira AM, Jonesman T, Matić S, Soleimani R, Behjatnia SAA, Vinals N, Paszkowski J, Accotto GP. Virus-mediated export of chromosomal DNA in plants. Nat Commun 2018; 9:5308. [PMID: 30546019 PMCID: PMC6293997 DOI: 10.1038/s41467-018-07775-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/23/2018] [Indexed: 11/09/2022] Open
Abstract
The propensity of viruses to acquire genetic material from relatives and possibly from infected hosts makes them excellent candidates as vectors for horizontal gene transfer. However, virus-mediated acquisition of host genetic material, as deduced from historical events, appears to be rare. Here, we report spontaneous and surprisingly efficient generation of hybrid virus/host DNA molecules in the form of minicircles during infection of Beta vulgaris by Beet curly top Iran virus (BCTIV), a single-stranded DNA virus. The hybrid minicircles replicate, become encapsidated into viral particles, and spread systemically throughout infected plants in parallel with the viral infection. Importantly, when co-infected with BCTIV, B. vulgaris DNA captured in minicircles replicates and is transcribed in other plant species that are sensitive to BCTIV infection. Thus, we have likely documented in real time the initial steps of a possible path of virus-mediated horizontal transfer of chromosomal DNA between plant species.
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Affiliation(s)
- Marco Catoni
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Emanuela Noris
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, 10135, Italy
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, 10135, Italy
| | - Thomas Jonesman
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Slavica Matić
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, 10135, Italy
| | - Reihaneh Soleimani
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
- Department of Plant Protection, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, 81595-158, Iran
| | - Seyed Ali Akbar Behjatnia
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| | - Nestor Vinals
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, 10135, Italy
| | - Jerzy Paszkowski
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, 10135, Italy.
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17
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Zhao L, Rosario K, Breitbart M, Duffy S. Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range. Adv Virus Res 2018; 103:71-133. [PMID: 30635078 DOI: 10.1016/bs.aivir.2018.10.001] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States.
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18
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Pooggin MM. Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization. Front Microbiol 2018; 9:2779. [PMID: 30524398 PMCID: PMC6256188 DOI: 10.3389/fmicb.2018.02779] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for virus, satellite or viroid identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.
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Affiliation(s)
- Mikhail M. Pooggin
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
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19
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Fondong VN. The Search for Resistance to Cassava Mosaic Geminiviruses: How Much We Have Accomplished, and What Lies Ahead. FRONTIERS IN PLANT SCIENCE 2017; 8:408. [PMID: 28392798 PMCID: PMC5365051 DOI: 10.3389/fpls.2017.00408] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/09/2017] [Indexed: 05/23/2023]
Abstract
The cassava mosaic disease (CMD), which occurs in all cassava growing regions of Africa and the Indian subcontinent, is caused by cassava mosaic geminiviruses (CMGs). CMGs are considered to be the most damaging vector-borne plant pathogens. So far, the most successful approach used to control these viruses has been the transfer of a polygenic recessive resistance locus, designated CMD1, from wild cassava to cassava cultivars. Further progress in harnessing natural resistance to contain CMGs has come from the discovery of the dominant monogenic resistance locus, CMD2, in some West African cassava cultivars. CMD2 has been combined with CMD1 through genetic crosses. Because of the limitations of the cassava breeding approach, especially with regard to time required to produce a variety and the loss of preferred agronomic attributes, efforts have been directed toward the deployment of genetic engineering approaches. Most of these approaches have been centered on RNA silencing strategies, developed mainly in the model plant Nicotiana benthamiana. Early RNA silencing platforms assessed for CMG resistance have been use of viral genes for co-suppression, antisense suppression or for hairpin RNAs-mediated gene silencing. Here, progress and challenges in the deployment of these approaches in the control of CMGs are discussed. Novel functional genomics approaches with potential to overcome some of the drawbacks of the current strategies are also discussed.
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Affiliation(s)
- Vincent N. Fondong
- Department of Biological Sciences, Delaware State UniversityDover, DE, USA
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20
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Bernardo P, Muhire B, François S, Deshoux M, Hartnady P, Farkas K, Kraberger S, Filloux D, Fernandez E, Galzi S, Ferdinand R, Granier M, Marais A, Monge Blasco P, Candresse T, Escriu F, Varsani A, Harkins GW, Martin DP, Roumagnac P. Molecular characterization and prevalence of two capulaviruses: Alfalfa leaf curl virus from France and Euphorbia caput-medusae latent virus from South Africa. Virology 2016; 493:142-53. [PMID: 27038709 DOI: 10.1016/j.virol.2016.03.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 01/25/2023]
Abstract
Little is known about the prevalence, diversity, evolutionary processes, genomic structures and population dynamics of viruses in the divergent geminivirus lineage known as the capulaviruses. We determined and analyzed full genome sequences of 13 Euphorbia caput-medusae latent virus (EcmLV) and 26 Alfalfa leaf curl virus (ALCV) isolates, and partial genome sequences of 23 EcmLV and 37 ALCV isolates. While EcmLV was asymptomatic in uncultivated southern African Euphorbia caput-medusae, severe alfalfa disease symptoms were associated with ALCV in southern France. The prevalence of both viruses exceeded 10% in their respective hosts. Besides using patterns of detectable negative selection to identify ORFs that are probably functionally expressed, we show that ALCV and EcmLV both display evidence of inter-species recombination and biologically functional genomic secondary structures. Finally, we show that whereas the EcmLV populations likely experience restricted geographical dispersion, ALCV is probably freely moving across the French Mediterranean region.
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Affiliation(s)
- Pauline Bernardo
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - Brejnev Muhire
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Sarah François
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France; INRA, UMR 1333, DGIMI, Montpellier, France; CNRS-IRD-UM1-UM2, UMR 5290, MIVEGEC, Avenue Agropolis, Montpellier, France
| | - Maëlle Deshoux
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - Penelope Hartnady
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Kata Farkas
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Denis Filloux
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - Emmanuel Fernandez
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - Serge Galzi
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - Romain Ferdinand
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - Martine Granier
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France
| | - Armelle Marais
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon Cedex, France; Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon Cedex, France
| | - Pablo Monge Blasco
- Unidad de Sanidad Vegetal, Centro de Investigacion y Tecnologıa Agroalimentaria de Aragon (CITA), Av. Montañana 930, 50059 Zaragoza, Spain
| | - Thierry Candresse
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon Cedex, France; Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon Cedex, France
| | - Fernando Escriu
- Unidad de Sanidad Vegetal, Centro de Investigacion y Tecnologıa Agroalimentaria de Aragon (CITA), Av. Montañana 930, 50059 Zaragoza, Spain; Unidad de Sanidad Vegetal, Instituto Agroalimentario de Aragón IA2 (CITA - Universidad de Zaragoza), Av. Montañana 930, 50059 Zaragoza, Spain
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, USA; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, South Africa
| | - Gordon W Harkins
- South African National Bioinformatics Institute, MRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Cape Town, South Africa
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Philippe Roumagnac
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France.
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Gibbs AJ, Wood J, Garcia-Arenal F, Ohshima K, Armstrong JS. Tobamoviruses have probably co-diverged with their eudicotyledonous hosts for at least 110 million years. Virus Evol 2015; 1:vev019. [PMID: 27774289 PMCID: PMC5014485 DOI: 10.1093/ve/vev019] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A phylogeny has been calculated by maximum likelihood comparisons of the concatenated consensus protein sequences of 29 tobamoviruses shown to be non-recombinant. This phylogeny has statistically significant support throughout, including its basal branches. The viruses form eight lineages that are congruent with the taxonomy of the hosts from which each was first isolated and, with the exception of three of the twenty-nine species, all fall into three clusters that have either asterid or rosid or caryophyllid hosts (i.e. the major subdivisions of eudicotyledonous plants). A modified Mantel permutation test showed that the patristic distances of virus and host phylogenies are significantly correlated, especially when the three anomalously placed viruses are removed. When the internal branches of the virus phylogeny were collapsed the congruence decreased. The simplest explanation of this congruence of the virus and host phylogenies is that most tobamovirus lineages have co-diverged with their primary plant hosts for more than 110 million years, and only the brassica-infecting lineage originated from a major host switch from asterids to rosids. Their co-divergence seems to have been ‘fuzzy’ rather than ‘strict’, permitting viruses to switch hosts within major host clades. Our conclusions support those of a coalesence analysis of tobamovirus sequences, that used proxy node dating, but not a similar analysis of nucleotide sequences from dated samples, which concluded that the tobamoviruses originated only 100 thousand years ago.
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Affiliation(s)
- Adrian J Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia
| | - Jeffrey Wood
- Statistical Consulting Unit, Australian National University, Canberra, ACT 2601, Australia
| | - Fernando Garcia-Arenal
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Madrid, Spain and
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
| | - John S Armstrong
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia
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