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Varma A, Singh MK. The Role of Satellites in the Evolution of Begomoviruses. Viruses 2024; 16:970. [PMID: 38932261 PMCID: PMC11209209 DOI: 10.3390/v16060970] [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: 03/29/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Begomoviruses have emerged as destructive pathogens of crops, particularly in the tropics and subtropics, causing enormous economic losses and threatening food security. Epidemics caused by begomoviruses have even spread in regions and crops that were previously free from these viruses. The most seriously affected crops include cassava; cotton; grain legumes; and cucurbitaceous, malvaceous, and solanaceous vegetables. Alphasatellites, betasatellites, and deltasatellites are associated with the diseases caused by begomoviruses, but begomovirus-betasatellite complexes have played significant roles in the evolution of begomoviruses, causing widespread epidemics in many economically important crops throughout the world. This article provides an overview of the evolution, distribution, and approaches used by betasatellites in the suppression of host plant defense responses and increasing disease severity.
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Affiliation(s)
- Anupam Varma
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India;
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Vo TTB, Wira Sanjaya IGNP, Kil EJ, Lal A, Ho PT, Nattanong B, Tabassum M, Qureshi MA, Lee TK, Lee S. Transreplication Preference of the Tomato Leaf Curl Joydebpur Virus for a Noncognate Betasatellite through Iteron Resemblance on Nicotiana bethamiana. Microorganisms 2023; 11:2907. [PMID: 38138051 PMCID: PMC10745424 DOI: 10.3390/microorganisms11122907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Pepper plants (Capsicum annuum) with severe leaf curl symptoms were collected in 2013 from Bangalore, Karnataka, India. The detection results showed a co-infection between the tomato leaf curl Joydebpur virus (ToLCJoV) and tomato leaf curl Bangladesh betasatellite (ToLCBDB) through the sequencing analysis of PCR amplicons. To pinpoint the molecular mechanism of this uncommon combination, infectious clones of ToLCJoV and two different betasatellites-ToLCBDB and tomato leaf curl Joydebpur betasatellite (ToLCJoB)-were constructed and tested for their infectivity in Nicotiana benthamiana. Together, we conducted various combined agroinoculation studies to compare the interaction of ToLCJoV with non-cognate and cognate betasatellites. The natural non-cognate interaction between ToLCJoV and ToLCBDB showed severe symptoms compared to the mild symptoms of a cognate combination (ToLCJoV × ToLCJoB) in infected plants. A sequence comparison among betasatellites and their helper virus wasperformed and the iteron resemblances in ToLCBDB as well as ToLCJoB clones were processed. Mutant betasatellites that comprised iteron modifications revealed that changes in iteron sequences could disturb the transreplication process between betasatellites and their helper virus. Our study might provide an important consideration for determining the efficiency of transreplication activity between betasatellites and their helper virus.
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Affiliation(s)
- Thuy T. B. Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea; (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.); (B.N.); (M.T.); (M.A.Q.)
| | - I Gusti Ngurah Prabu Wira Sanjaya
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea; (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.); (B.N.); (M.T.); (M.A.Q.)
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong 36729, Republic of Korea; (E.-J.K.); (A.L.)
| | - Aamir Lal
- Department of Plant Medicals, Andong National University, Andong 36729, Republic of Korea; (E.-J.K.); (A.L.)
| | - Phuong T. Ho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea; (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.); (B.N.); (M.T.); (M.A.Q.)
| | - Bupi Nattanong
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea; (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.); (B.N.); (M.T.); (M.A.Q.)
| | - Marjia Tabassum
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea; (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.); (B.N.); (M.T.); (M.A.Q.)
| | - Muhammad Amir Qureshi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea; (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.); (B.N.); (M.T.); (M.A.Q.)
| | - Taek-Kyun Lee
- Ecological Risk Research Department, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea; (T.T.B.V.); (I.G.N.P.W.S.); (P.T.H.); (B.N.); (M.T.); (M.A.Q.)
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Rajabu CA, Dallas MM, Chiunga E, De León L, Ateka EM, Tairo F, Ndunguru J, Ascencio-Ibanez JT, Hanley-Bowdoin L. SEGS-1 a cassava genomic sequence increases the severity of African cassava mosaic virus infection in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1250105. [PMID: 37915512 PMCID: PMC10616593 DOI: 10.3389/fpls.2023.1250105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023]
Abstract
Cassava is a major crop in Sub-Saharan Africa, where it is grown primarily by smallholder farmers. Cassava production is constrained by Cassava mosaic disease (CMD), which is caused by a complex of cassava mosaic begomoviruses (CMBs). A previous study showed that SEGS-1 (sequences enhancing geminivirus symptoms), which occurs in the cassava genome and as episomes during viral infection, enhances CMD symptoms and breaks resistance in cassava. We report here that SEGS-1 also increases viral disease severity in Arabidopsis thaliana plants that are co-inoculated with African cassava mosaic virus (ACMV) and SEGS-1 sequences. Viral disease was also enhanced in Arabidopsis plants carrying a SEGS-1 transgene when inoculated with ACMV alone. Unlike cassava, no SEGS-1 episomal DNA was detected in the transgenic Arabidopsis plants during ACMV infection. Studies using Nicotiana tabacum suspension cells showed that co-transfection of SEGS-1 sequences with an ACMV replicon increases viral DNA accumulation in the absence of viral movement. Together, these results demonstrated that SEGS-1 can function in a heterologous host to increase disease severity. Moreover, SEGS-1 is active in a host genomic context, indicating that SEGS-1 episomes are not required for disease enhancement.
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Affiliation(s)
- Cyprian A. Rajabu
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Mary M. Dallas
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Evangelista Chiunga
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Leandro De León
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Elijah M. Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Fred Tairo
- Tanzania Agricultural Research Institute-Mikocheni, Dar Es Salaam, Tanzania
| | - Joseph Ndunguru
- Tanzania Agricultural Research Institute-Mikocheni, Dar Es Salaam, Tanzania
| | - Jose T. Ascencio-Ibanez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Fiallo-Olivé E, Bastidas L, Chirinos DT, Navas-Castillo J. Insights into Emerging Begomovirus-Deltasatellite Complex Diversity: The First Deltasatellite Infecting Legumes. BIOLOGY 2021; 10:1125. [PMID: 34827118 PMCID: PMC8615175 DOI: 10.3390/biology10111125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/30/2022]
Abstract
Begomoviruses and associated DNA satellites are involved in pathosystems that include many cultivated and wild dicot plants and the whitefly vector Bemisia tabaci. A survey of leguminous plants, both crops and wild species, was conducted in Venezuela, an understudied country, to determine the presence of begomoviruses. Molecular analysis identified the presence of bipartite begomoviruses in 37% of the collected plants. Four of the six begomoviruses identified constituted novel species, and two others had not been previously reported in Venezuela. In addition, a novel deltasatellite (cabbage leaf curl deltasatellite, CabLCD) was found to be associated with cabbage leaf curl virus (CabLCV) in several plant species. CabLCD was the first deltasatellite found to infect legumes and the first found in the New World to infect a crop plant. Agroinoculation experiments using Nicotiana benthamiana plants and infectious viral clones confirmed that CabLCV acts as a helper virus for CabLCD. The begomovirus-deltasatellite complex described here is also present in wild legume plants, suggesting the possible role of these plants in the emergence and establishment of begomoviral diseases in the main legume crops in the region. Pathological knowledge of these begomovirus-deltasatellite complexes is fundamental to develop control methods to protect leguminous crops from the diseases they cause.
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Affiliation(s)
- Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Avenida Dr. Wienberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
| | - Liseth Bastidas
- Departamento Fitosanitario, Facultad de Agronomía, Universidad del Zulia, Maracaibo 4005, Zulia, Venezuela;
| | - Dorys T. Chirinos
- Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Portoviejo 130105, Manabí, Ecuador;
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Avenida Dr. Wienberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
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Aimone CD, De León L, Dallas MM, Ndunguru J, Ascencio-Ibáñez JT, Hanley-Bowdoin L. A New Type of Satellite Associated with Cassava Mosaic Begomoviruses. J Virol 2021; 95:e0043221. [PMID: 34406866 PMCID: PMC8513466 DOI: 10.1128/jvi.00432-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/10/2021] [Indexed: 12/29/2022] Open
Abstract
Cassava mosaic disease (CMD), which is caused by single-stranded DNA begomoviruses, severely limits cassava production across Africa. A previous study showed that CMD symptom severity and viral DNA accumulation increase in cassava in the presence of a DNA sequence designated SEGS-2 (sequence enhancing geminivirus symptoms). We report here that when SEGS-2 is coinoculated with African cassava mosaic virus (ACMV) onto Arabidopsis thaliana, viral symptoms increase. Transgenic Arabidopsis with an integrated copy of SEGS-2 inoculated with ACMV also display increased symptom severity and viral DNA levels. Moreover, SEGS-2 enables Cabbage leaf curl virus (CaLCuV) to infect a geminivirus-resistant Arabidopsis thaliana accession. Although SEGS-2 is related to cassava genomic sequences, an earlier study showed that it occurs as episomes and is packaged into virions in CMD-infected cassava and viruliferous whiteflies. We identified SEGS-2 episomes in SEGS-2 transgenic Arabidopsis. The episomes occur as both double-stranded and single-stranded DNA, with the single-stranded form packaged into virions. In addition, SEGS-2 episomes replicate in tobacco protoplasts in the presence, but not the absence, of ACMV DNA-A. SEGS-2 episomes contain a SEGS-2 derived promoter and an open reading frame with the potential to encode a 75-amino acid protein. An ATG mutation at the beginning of the SEGS-2 coding region does not enhance ACMV infection in A. thaliana. Together, the results established that SEGS-2 is a new type of begomovirus satellite that enhances viral disease through the action of an SEGS-2-encoded protein that may also be encoded by the cassava genome. IMPORTANCE Cassava is an important root crop in the developing world and a food and income crop for more than 300 million African farmers. Cassava is rising in global importance and trade as the demands for biofuels and commercial starch increase. More than half of the world's cassava is produced in Africa, where it is primarily grown by smallholder farmers, many of whom are from the poorest villages. Although cassava can grow under high temperature, drought, and poor soil conditions, its production is severely limited by viral diseases. Cassava mosaic disease (CMD) is one of the most important viral diseases of cassava and can cause up to 100% yield losses. We provide evidence that SEGS-2, which was originally isolated from cassava crops displaying severe and atypical CMD symptoms in Tanzanian fields, is a novel begomovirus satellite that can compromise the development of durable CMD resistance.
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Affiliation(s)
- Catherine D. Aimone
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Leandro De León
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Mary M. Dallas
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | | | - José T. Ascencio-Ibáñez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
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The Association between New World Alphasatellites and Bipartite Begomoviruses: Effects on Infection and Vector Transmission. Pathogens 2021; 10:pathogens10101244. [PMID: 34684193 PMCID: PMC8538204 DOI: 10.3390/pathogens10101244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 11/17/2022] Open
Abstract
Begomoviruses can be found in association with alphasatellites, which are capable of autonomous replication but are dependent on the helper begomovirus for systemic infection, encapsidation and vector transmission. Previous studies suggest that the presence of NW alphasatellites (genus Clecrusatellite) is associated with more severe symptoms. To better understand this interaction, we investigated the effects of two alphasatellites on infectivity, symptom development, viral DNA accumulation and vector transmission of three begomoviruses in three hosts. In tomato and Nicotiana benthamiana, all combinations were infectious. In Leonurus sibiricus, only the ToYSV/ToYSA combination was infectious. The presence of EuYMA increased symptom severity of EuYMV and ToYSV in N. benthamiana, and the presence of ToYSA was associated with more severe symptoms of ToYSV in N. benthamiana and L. sibiricus. EuYMA increased the accumulation of ToYSV in N. benthamiana but reduced the accumulation of EuYMV in tomato and of ToSRV in N. benthamiana. The presence of ToYSA decreased the accumulation of ToYSV in N. benthamiana and L. sibiricus. ToYSA negatively affected transmission of ToSRV by Bemisia tabaci MEAM1. Together, our results indicate that NW alphasatellites can interact with different begomoviruses, increasing symptom severity and interfering in the transmission of the helper begomovirus. Understanding this interaction is important as it may affect the emergence of diseases caused by begomovirus-alphasatellite complexes in the field.
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Nigam D. Genomic Variation and Diversification in Begomovirus Genome in Implication to Host and Vector Adaptation. PLANTS (BASEL, SWITZERLAND) 2021; 10:1706. [PMID: 34451752 PMCID: PMC8398267 DOI: 10.3390/plants10081706] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 01/02/2023]
Abstract
Begomoviruses (family Geminiviridae, genus Begomovirus) are DNA viruses transmitted in a circulative, persistent manner by the whitefly Bemisia tabaci (Gennadius). As revealed by their wide host range (more than 420 plant species), worldwide distribution, and effective vector transmission, begomoviruses are highly adaptive. Still, the genetic factors that facilitate their adaptation to a diverse array of hosts and vectors remain poorly understood. Mutations in the virus genome may confer a selective advantage for essential functions, such as transmission, replication, evading host responses, and movement within the host. Therefore, genetic variation is vital to virus evolution and, in response to selection pressure, is demonstrated as the emergence of new strains and species adapted to diverse hosts or with unique pathogenicity. The combination of variation and selection forms a genetic imprint on the genome. This review focuses on factors that contribute to the evolution of Begomovirus and their global spread, for which an unforeseen diversity and dispersal has been recognized and continues to expand.
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Affiliation(s)
- Deepti Nigam
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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Revealing the Complexity of Sweepovirus-Deltasatellite-Plant Host Interactions: Expanded Natural and Experimental Helper Virus Range and Effect Dependence on Virus-Host Combination. Microorganisms 2021; 9:microorganisms9051018. [PMID: 34068583 PMCID: PMC8150397 DOI: 10.3390/microorganisms9051018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022] Open
Abstract
Sweepoviruses are begomoviruses (genus Begomovirus, family Geminiviridae) with ssDNA genomes infecting sweet potato and other species of the family Convolvulaceae. Deltasatellites (genus Deltasatellite, family Tolecusatellitidae) are small-size non-coding DNA satellites associated with begomoviruses. In this study, the genetic diversity of deltasatellites associated with sweepoviruses infecting Ipomoea indica plants was analyzed by further sampling the populations where the deltasatellite sweet potato leaf curl deltasatellite 1 (SPLCD1) was initially found, expanding the search to other geographical areas in southern continental Spain and the Canary Islands. The sweepoviruses present in the samples coinfected with deltasatellites were also fully characterized by sequencing in order to define the range of viruses that could act as helper viruses in nature. Additionally, experiments were performed to assess the ability of a number of geminivirids (the monopartite tomato leaf deformation virus and the bipartite NW begomovirus Sida golden yellow vein virus, the bipartite OW begomovirus tomato leaf curl New Delhi virus, and the curtovirus beet curly top virus) to transreplicate SPLCD1 in their natural plant hosts or the experimental host Nicotiana benthamiana. The results show that SPLCD1 can be transreplicated by all the geminivirids assayed in N. benthamiana and by tomato leaf curl New Delhi virus in zucchini. The presence of SPLCD1 did not affect the symptomatology caused by the helper viruses, and its effect on viral DNA accumulation depended on the helper virus-host plant combination.
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François S, Antoine-Lorquin A, Kulikowski M, Frayssinet M, Filloux D, Fernandez E, Roumagnac P, Froissart R, Ogliastro M. Characterisation of the Viral Community Associated with the Alfalfa Weevil ( Hypera postica) and Its Host Plant, Alfalfa ( Medicago sativa). Viruses 2021; 13:791. [PMID: 33925168 PMCID: PMC8145008 DOI: 10.3390/v13050791] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 12/22/2022] Open
Abstract
Advances in viral metagenomics have paved the way of virus discovery by making the exploration of viruses in any ecosystem possible. Applied to agroecosystems, such an approach opens new possibilities to explore how viruses circulate between insects and plants, which may help to optimise their management. It could also lead to identifying novel entomopathogenic viral resources potentially suitable for biocontrol strategies. We sampled the larvae of a natural population of alfalfa weevils (Hypera postica), a major herbivorous pest feeding on legumes, and its host plant alfalfa (Medicago sativa). Insect and plant samples were collected from a crop field and an adjacent meadow. We characterised the diversity and abundance of viruses associated with weevils and alfalfa, and described nine putative new virus species, including four associated with alfalfa and five with weevils. In addition, we found that trophic accumulation may result in a higher diversity of plant viruses in phytophagous pests compared to host plants.
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Affiliation(s)
- Sarah François
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, South Park Road, Oxford OX1 3SY, UK
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
| | - Aymeric Antoine-Lorquin
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
| | - Maximilien Kulikowski
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
| | - Marie Frayssinet
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France; (D.F.); (E.F.); (P.R.)
- PHIM Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34090 Montpellier, France; (D.F.); (E.F.); (P.R.)
- PHIM Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France; (D.F.); (E.F.); (P.R.)
- PHIM Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Rémy Froissart
- MIVEGEC Infectious and Vector Diseases: Ecology, Genetics, Evolution and Control, University of Montpellier, CNRS, IRD, 34394 Montpellier, France;
| | - Mylène Ogliastro
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
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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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Fiallo-Olivé E, Navas-Castillo J. Molecular and Biological Characterization of a New World Mono-/Bipartite Begomovirus/Deltasatellite Complex Infecting Corchorus siliquosus. Front Microbiol 2020; 11:1755. [PMID: 32793176 PMCID: PMC7390960 DOI: 10.3389/fmicb.2020.01755] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/06/2020] [Indexed: 12/02/2022] Open
Abstract
The genus Begomovirus (family Geminiviridae) is the largest genus in the entire virosphere, with more than 400 species recognized. Begomoviruses are single-stranded DNA plant viruses transmitted by whiteflies of the Bemisia tabaci complex and are considered one of the most important groups of emerging plant viruses in tropical and subtropical regions. Several types of DNA satellites have been described to be associated with begomoviruses: betasatellites, alphasatellites, and deltasatellites. Recently, a family of single-stranded DNA satellites associated with begomoviruses has been created, Tolecusatellitidae, including the genera Betasatellite and Deltasatellite. In this work, we analyzed the population of begomoviruses and associated DNA satellites present in Corchorus siliquosus, a malvaceous plant growing wild in Central America, southeastern North America and the Caribbean, collected in Cuba. The genomes of isolates of two New World begomoviruses [(Desmodium leaf distortion virus (DesLDV) and Corchorus yellow vein Cuba virus (CoYVCUV)] and two deltasatellites [tomato yellow leaf distortion deltasatellite 2 (TYLDD2) and Desmodium leaf distortion deltasatellite (DesLDD)] have been cloned and sequenced from plants showing yellow vein symptoms. Isolates of one of the begomoviruses, CoYVCUV, and one of the deltasatellites, DesLDD, represent novel species. Experiments with infectious clones showed the monopartite nature of CoYVCUV and that DesLDD utilizes the bipartite DesLDV as helper virus, but not the monopartite CoYVCUV. Also, CoYVCUV was shown to infect common bean in addition to Nicotiana benthamiana. This is the first time that (i) a monopartite New World begomovirus is found in a host other than tomato and (ii) deltasatellites have been found in C. siliquosus, thus extending the host and helper virus ranges of this recently recognized class of DNA satellites.
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Affiliation(s)
- Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Cient ficas - Universidad de Málaga (IHSM-CSIC-UMA), Málaga, Spain
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Cient ficas - Universidad de Málaga (IHSM-CSIC-UMA), Málaga, Spain
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12
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Reconstruction and Characterization of Full-Length Begomovirus and Alphasatellite Genomes Infecting Pepper through Metagenomics. Viruses 2020; 12:v12020202. [PMID: 32054104 PMCID: PMC7077291 DOI: 10.3390/v12020202] [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] [Received: 12/08/2019] [Revised: 01/10/2020] [Accepted: 01/16/2020] [Indexed: 01/18/2023] Open
Abstract
In northwestern Argentina (NWA), pepper crops are threatened by the emergence of begomoviruses due to the spread of its vector, Bemisia tabaci (Gennadius). The genus Begomovirus includes pathogens that can have a monopartite or bipartite genome and are occasionally associated with sub-viral particles called satellites. This study characterized the diversity of begomovirus and alphasatellite species infecting pepper in NWA using a metagenomic approach. Using RCA-NGS (rolling circle amplification-next generation sequencing), 19 full-length begomovirus genomes (DNA-A and DNA-B) and one alphasatellite were assembled. This ecogenomic approach revealed six begomoviruses in single infections: soybean blistering mosaic virus (SbBMV), tomato yellow spot virus (ToYSV), tomato yellow vein streak virus (ToYVSV), tomato dwarf leaf virus (ToDfLV), sida golden mosaic Brazil virus (SiGMBRV), and a new proposed species, named pepper blistering leaf virus (PepBLV). SbBMV was the most frequently detected species, followed by ToYSV. Moreover, a new alphasatellite associated with ToYSV, named tomato yellow spot alphasatellite 2 (ToYSA-2), was reported for the first time in Argentina. For the Americas, this was the first report of an alphasatellite found in a crop (pepper) and in a weed (Leonurus japonicus). We also detected intra-species and inter-species recombination.
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13
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Abstract
Virus-virus interactions in plants can modify host symptoms. As a result, disease management strategies may be unsuccessful if they are based solely on visual assessment and diagnostic assays for known individual viruses. Papaya ringspot virus is an important limiting factor for papaya production and likely has interactions with other viruses that are not yet known. Using high-throughput sequencing, we recovered known and novel RNA and DNA viruses from papaya orchards in Chiapas, Mexico, and categorized them by host and, in the case of papaya, symptom type: asymptomatic papaya, papaya with ringspot virus symptoms, papaya with nonringspot symptoms, weeds, and insects. Using network analysis, we demonstrated virus associations within and among host types and described the ecological community patterns. Recovery of viruses from weeds and asymptomatic papaya suggests the need for additional management attention. These analyses contribute to the understanding of the community structure of viruses in the agroecological landscape. The study of complex ecological interactions, such as those among host, pathogen, and vector communities, can help to explain host ranges and the emergence of novel pathogens. We evaluated the viromes of papaya orchards, including weed and insect viromes, to identify common viruses in intensive production of papaya in the Pacific Coastal Plain and the Central Depression of Chiapas, Mexico. Samples of papaya cultivar Maradol, susceptible to papaya ringspot virus (PRSV), were categorized by symptoms by local farmers (papaya ringspot symptoms, non-PRSV symptoms, or asymptomatic). These analyses revealed the presence of 61 viruses, where only 4 species were shared among both regions, 16 showed homology to known viruses, and 36 were homologous with genera including Potyvirus, Comovirus, and Tombusvirus (RNA viruses) and Begomovirus and Mastrevirus (DNA viruses). We analyzed the network of associations between viruses and host-location combinations, revealing ecological properties of the network, such as an asymmetric nested pattern, and compared the observed network to null models of network association. Understanding the network structure informs management strategies, for example, revealing the potential role of PRSV in asymptomatic papaya and that weeds may be an important pathogen reservoir. We identify three key management implications: (i) each region may need a customized management strategy; (ii) visual assessment of papaya may be insufficient for PRSV, requiring diagnostic assays; and (iii) weed control within orchards may reduce the risk of virus spread to papaya. Network analysis advances understanding of host-pathogen interactions in the agroecological landscape. IMPORTANCE Virus-virus interactions in plants can modify host symptoms. As a result, disease management strategies may be unsuccessful if they are based solely on visual assessment and diagnostic assays for known individual viruses. Papaya ringspot virus is an important limiting factor for papaya production and likely has interactions with other viruses that are not yet known. Using high-throughput sequencing, we recovered known and novel RNA and DNA viruses from papaya orchards in Chiapas, Mexico, and categorized them by host and, in the case of papaya, symptom type: asymptomatic papaya, papaya with ringspot virus symptoms, papaya with nonringspot symptoms, weeds, and insects. Using network analysis, we demonstrated virus associations within and among host types and described the ecological community patterns. Recovery of viruses from weeds and asymptomatic papaya suggests the need for additional management attention. These analyses contribute to the understanding of the community structure of viruses in the agroecological landscape.
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14
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Rodríguez-Negrete EA, Morales-Aguilar JJ, Domínguez-Duran G, Torres-Devora G, Camacho-Beltrán E, Leyva-López NE, Voloudakis AE, Bejarano ER, Méndez-Lozano J. High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico. Viruses 2019; 11:v11070594. [PMID: 31261973 PMCID: PMC6669537 DOI: 10.3390/v11070594] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/28/2019] [Accepted: 06/17/2019] [Indexed: 12/24/2022] Open
Abstract
Plant DNA viruses of the genus Begomovirus have been documented as the most genetically diverse in the family Geminiviridae and present a serious threat for global horticultural production, especially considering climate change. It is important to characterize naturally existing begomoviruses, since viral genetic diversity in non-cultivated plants could lead to future disease epidemics in crops. In this study, high-throughput sequencing (HTS) was employed to determine viral diversity of samples collected in a survey performed during 2012–2016 in seven states of Northern-Pacific Mexico, areas of diverse climatic conditions where different vegetable crops are subject to intensive farming. In total, 132 plant species, belonging to 34 families, were identified and sampled in the natural ecosystems surrounding cultivated areas (agro-ecological interface). HTS analysis and subsequent de novo assembly revealed a number of geminivirus-related DNA signatures with 80 to 100% DNA similarity with begomoviral sequences present in the genome databank. The analysis revealed DNA signatures corresponding to 52 crop-infecting and 35 non-cultivated-infecting geminiviruses that, interestingly, were present in different plant species. Such an analysis deepens our knowledge of geminiviral diversity and could help detecting emerging viruses affecting crops in different agro-climatic regions.
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Affiliation(s)
- Edgar Antonio Rodríguez-Negrete
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Juan José Morales-Aguilar
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Gustavo Domínguez-Duran
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Gadiela Torres-Devora
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Erika Camacho-Beltrán
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Norma Elena Leyva-López
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Andreas E Voloudakis
- Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, 75 Iera Odos, Athens 11855, Greece
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
| | - Jesús Méndez-Lozano
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico.
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15
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Non-cultivated Cotton Species ( Gossypium spp.) Act as a Reservoir for Cotton Leaf Curl Begomoviruses and Associated Satellites. PLANTS 2019; 8:plants8050127. [PMID: 31091727 PMCID: PMC6571856 DOI: 10.3390/plants8050127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/02/2019] [Accepted: 05/10/2019] [Indexed: 11/17/2022]
Abstract
A collection of cultivated and non-cultivated species of cotton (Gossypium spp.) has been maintained for the last four decades in Multan, Pakistan. This geographical location has been observed as a hotspot for the evolution of begomoviruses and satellites associated with cotton leaf curl disease (CLCuD). Recent studies showed that begomoviruses responsible for the CLCuD epidemic in the 1990s, and that almost disappeared from the CLCuD complex in 2000s, have been observed again in CLCuD-infected cotton fields. To identify host species that acted as probable reservoirs for these viruses, we characterized begomoviruses and satellites in non-cultivated cotton species G. raimondii, G. thurberi and G. mustelinum and identified several species of CLCuD associated begomoviruses and satellites. Further, phylogenetic analysis indicated that the identified begomoviruses and beta/alphasatellites are closely related to the ones associated with the most recent CLCuD complex. qPCR indicated that the comparative level of virus significantly decreased in the presence of alphasatellites. Our results indicated that non-cultivated cotton species have been continuously challenged by diverse begomoviruses and associated satellites and act as reservoirs for CLCuD associated begomoviruses. These results provide novel insights into understanding the spread of begomoviruses and associated satellites in New World cotton species introduced into the Old World.
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16
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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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17
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Hasanvand V, Kamali M, Heydarnejad J, Massumi H, Kvarnheden A, Varsani A. Identification of a new turncurtovirus in the leafhopper Circulifer haematoceps and the host plant species Sesamum indicum. Virus Genes 2018; 54:840-845. [DOI: 10.1007/s11262-018-1604-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/01/2018] [Indexed: 12/17/2022]
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18
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Rosario K, Mettel KA, Benner BE, Johnson R, Scott C, Yusseff-Vanegas SZ, Baker CCM, Cassill DL, Storer C, Varsani A, Breitbart M. Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates. PeerJ 2018; 6:e5761. [PMID: 30324030 PMCID: PMC6186406 DOI: 10.7717/peerj.5761] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/16/2018] [Indexed: 11/20/2022] Open
Abstract
Viruses encoding a replication-associated protein (Rep) within a covalently closed, single-stranded (ss)DNA genome are among the smallest viruses known to infect eukaryotic organisms, including economically valuable agricultural crops and livestock. Although circular Rep-encoding ssDNA (CRESS DNA) viruses are a widespread group for which our knowledge is rapidly expanding, biased sampling toward vertebrates and land plants has limited our understanding of their diversity and evolution. Here, we screened terrestrial arthropods for CRESS DNA viruses and report the identification of 44 viral genomes and replicons associated with specimens representing all three major terrestrial arthropod lineages, namely Euchelicerata (spiders), Hexapoda (insects), and Myriapoda (millipedes). We identified virus genomes belonging to three established CRESS DNA viral families (Circoviridae, Genomoviridae, and Smacoviridae); however, over half of the arthropod-associated viral genomes are only distantly related to currently classified CRESS DNA viral sequences. Although members of viral and satellite families known to infect plants (Geminiviridae, Nanoviridae, Alphasatellitidae) were not identified in this study, these plant-infecting CRESS DNA viruses and replicons are transmitted by hemipterans. Therefore, members from six out of the seven established CRESS DNA viral families circulate among arthropods. Furthermore, a phylogenetic analysis of Reps, including endogenous viral sequences, reported to date from a wide array of organisms revealed that most of the known CRESS DNA viral diversity circulates among invertebrates. Our results highlight the vast and unexplored diversity of CRESS DNA viruses among invertebrates and parallel findings from RNA viral discovery efforts in undersampled taxa.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Kaitlin A Mettel
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Bayleigh E Benner
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Ryan Johnson
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Catherine Scott
- Department of Biological Sciences, University of Toronto, Scarborough, Scarborough, ON, Canada
| | | | - Christopher C M Baker
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Deby L Cassill
- Department of Biological Sciences, University of South Florida Saint Petersburg, Saint Petersburg, FL, USA
| | - Caroline Storer
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
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19
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Islam W, Akutse KS, Qasim M, Khan KA, Ghramh HA, Idrees A, Latif S. Bemisia tabaci-mediated facilitation in diversity of begomoviruses: Evidence from recent molecular studies. Microb Pathog 2018; 123:162-168. [PMID: 30017827 DOI: 10.1016/j.micpath.2018.07.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/08/2018] [Accepted: 07/10/2018] [Indexed: 12/12/2022]
Abstract
Begomoviruses are considered as one of the most notorious plant viruses worldwide, which cause substantial economic losses to various field crops. Management of begomoviruses has become a challenge due to the continuous evolution and the emergence of new strains. Bemisia tabaci is globally known to be the key vector of begomoviruses, having relatively high reproductivity, fast dispersal ability, high survival rate due to its polyphagous nature and high resistance to various groups of insecticides. Continuous transmission of begomoviruses by the vector has led to the development and spread of epidemics of various diseases worldwide. In this review, we have critically analyzed the various dynamics which facilitate the diversity of begomoviruses through their vector. The interaction of begomovirus-whitefly leads to continuous research activities regarding management of both virus and its vector, thus opening exciting new horizons to formulate potential control strategies to ensure a disease-free cropping environment.
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Affiliation(s)
- Waqar Islam
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Govt. of Punjab, Agriculture Department, Lahore, Pakistan.
| | - Komivi Senyo Akutse
- International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya
| | - Muhammad Qasim
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Khalid Ali Khan
- Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Hamed A Ghramh
- Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia; Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Atif Idrees
- Institute of Beneficial Insects, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Shahid Latif
- Department of Plant Pathology, Faculty of Agriculture Science and Technology, Bahauddin Zakariya University, Multan, Pakistan
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20
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From Spatial Metagenomics to Molecular Characterization of Plant Viruses: A Geminivirus Case Study. Adv Virus Res 2018; 101:55-83. [PMID: 29908594 DOI: 10.1016/bs.aivir.2018.02.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The number of plant viruses that are known likely remains only a vanishingly small fraction of all extant plant virus species. Consequently, the distribution and population dynamics of plant viruses within even the best-studied ecosystems have only ever been studied for small groups of virus species. Even for the best studied of these groups very little is known about virus diversity at spatial scales ranging from an individual host, through individual local host populations to global host populations. To date, metagenomics studies that have assessed the collective or metagenomes of viruses at the ecosystem scale have revealed many previously unrecognized viral species. More recently, novel georeferenced metagenomics approaches have been devised that can precisely link individual sequence reads to both the plant hosts from which they were obtained, and the spatial arrangements of these hosts. Besides illuminating the diversity and the distribution of plant viruses at the ecosystem scale, application of these "geometagenomics" approaches has enabled the direct testing of hypotheses relating to the impacts of host diversity, host spatial variations, and environmental conditions on plant virus diversity and prevalence. To exemplify how such top-down approaches can provide a far deeper understanding of host-virus associations, we provide a case-study focusing on geminiviruses within two complex ecosystems containing both cultivated and uncultivated areas. Geminiviruses are a highly relevant model for studying the evolutionary and ecological aspects of viral emergence because the family Geminiviridae includes many of the most important crop pathogens that have emerged over the past century. In addition to revealing unprecedented degrees of geminivirus diversity within the analyzed ecosystems, the geometagenomics-based approach enabled the focused in-depth analysis of the complex evolutionary dynamics of some of the highly divergent geminivirus species that were discovered.
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21
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Analysis of DNAs associated with coconut foliar decay disease implicates a unique single-stranded DNA virus representing a new taxon. Sci Rep 2018; 8:5698. [PMID: 29632309 PMCID: PMC5890292 DOI: 10.1038/s41598-018-23739-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/16/2018] [Indexed: 12/11/2022] Open
Abstract
The unique ecology, pathology and undefined taxonomy of coconut foliar decay virus (CFDV), found associated with coconut foliar decay disease (CFD) in 1986, prompted analyses of old virus samples by modern methods. Rolling circle amplification and deep sequencing applied to nucleic acid extracts from virion preparations and CFD-affected palms identified twelve distinct circular DNAs, eleven of which had a size of about 1.3 kb and one of 641 nt. Mass spectrometry-based protein identification proved that a 24 kDa protein encoded by two 1.3 kb DNAs is the virus capsid protein with highest sequence similarity to that of grabloviruses (family Geminiviridae), even though CFDV particles are not geminate. The nine other 1.3 kb DNAs represent alphasatellites coding for replication initiator proteins that differ clearly from those encoded by nanovirid DNA-R. The 641 nt DNA-gamma is unique and may encode a movement protein. Three DNAs, alphasatellite CFDAR, capsid protein encoding CFDV DNA-S.1 and DNA-gamma share sequence motifs near their replication origins and were consistently present in all samples analysed. These DNAs appear to be integral components of a possibly tripartite CFDV genome, different from those of any Geminiviridae or Nanoviridae family member, implicating CFDV as representative of a new genus and family.
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22
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Sseruwagi P, Wainaina J, Ndunguru J, Tumuhimbise R, Tairo F, Guo JY, Vrielink A, Blythe A, Kinene T, De Marchi B, Kehoe MA, Tanz S, Boykin LM. The first transcriptomes from field-collected individual whiteflies ( Bemisia tabaci, Hemiptera: Aleyrodidae): a case study of the endosymbiont composition. Gates Open Res 2018. [PMID: 29608200 DOI: 10.12688/gatesopenres.12783.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Bemisia tabaci species ( B. tabaci), or whiteflies, are the world's most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised a single whitefly RNA extraction procedure, and sequenced the transcriptome of four individual adult Sub-Saharan Africa 1 (SSA1) B. tabaci. Transcriptome sequencing resulted in 39-42 million raw reads. De novo assembly of trimmed reads yielded between 65,000-162,000 Contigs across B. tabaci transcriptomes. Results: Bayesian phylogenetic analysis of mitochondrion cytochrome I oxidase (mtCOI) grouped the four whiteflies within the SSA1 clade. BLASTn searches on the four transcriptomes identified five endosymbionts; the primary endosymbiont Portiera aleyrodidarum and four secondary endosymbionts: Arsenophonus, Wolbachia, Rickettsia, and Cardinium spp. that were predominant across all four SSA1 B. tabaci samples with prevalence levels of between 54.1 to 75%. Amino acid alignments of the NusG gene of P. aleyrodidarum for the SSA1 B. tabaci transcriptomes of samples WF2 and WF2b revealed an eleven amino acid residue deletion that was absent in samples WF1 and WF2a. Comparison of the protein structure of the NusG protein from P. aleyrodidarum in SSA1 with known NusG structures showed the deletion resulted in a shorter D loop. Conclusions: The use of field-collected specimens means time and money will be saved in future studies using single whitefly transcriptomes in monitoring vector and viral interactions. Our method is applicable to any small organism where RNA quantity has limited transcriptome studies.
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Affiliation(s)
- Peter Sseruwagi
- Mikocheni Agriculture Research Institute (MARI), Dar es Salaam, P.O. Box 6226, Tanzania
| | - James Wainaina
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, WA, 6009, Australia
| | - Joseph Ndunguru
- Mikocheni Agriculture Research Institute (MARI), Dar es Salaam, P.O. Box 6226, Tanzania
| | - Robooni Tumuhimbise
- National Agricultural Research Laboratories, P.O. Box 7065, Kampala Kawanda - Senge Rd, Kampala, Uganda
| | - Fred Tairo
- Mikocheni Agriculture Research Institute (MARI), Dar es Salaam, P.O. Box 6226, Tanzania
| | - Jian-Yang Guo
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China.,State Key Laboratory for the Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Alice Vrielink
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, WA, 6009, Australia
| | - Amanda Blythe
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, WA, 6009, Australia
| | - Tonny Kinene
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, WA, 6009, Australia
| | - Bruno De Marchi
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, WA, 6009, Australia.,Faculdade de Ciências Agronômicas, Universidade Estadual Paulista , Botucatu, Brazil
| | - Monica A Kehoe
- Department of Primary Industries and Regional Development, DPIRD Diagnostic Laboratory Services, South Perth, WA, Australia
| | - Sandra Tanz
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, WA, 6009, Australia
| | - Laura M Boykin
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, WA, 6009, Australia
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23
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Sseruwagi P, Wainaina J, Ndunguru J, Tumuhimbise R, Tairo F, Guo JY, Vrielink A, Blythe A, Kinene T, De Marchi B, Kehoe MA, Tanz S, Boykin LM. The first transcriptomes from field-collected individual whiteflies ( Bemisia tabaci, Hemiptera: Aleyrodidae): a case study of the endosymbiont composition. Gates Open Res 2018; 1:16. [PMID: 29608200 PMCID: PMC5872585 DOI: 10.12688/gatesopenres.12783.3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2018] [Indexed: 11/23/2022] Open
Abstract
Background: Bemisia tabaci species (
B. tabaci), or whiteflies, are the world’s most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for
B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised a single whitefly RNA extraction procedure, and sequenced the transcriptome of four individual adult Sub-Saharan Africa 1 (SSA1)
B. tabaci. Transcriptome sequencing resulted in 39-42 million raw reads.
De novo assembly of trimmed reads yielded between 65,000-162,000 Contigs across
B. tabaci transcriptomes. Results: Bayesian phylogenetic analysis of mitochondrion cytochrome I oxidase (mtCOI) grouped the four whiteflies within the SSA1 clade. BLASTn searches on the four transcriptomes identified five endosymbionts; the primary endosymbiont
Portiera aleyrodidarum and four secondary endosymbionts:
Arsenophonus, Wolbachia, Rickettsia, and
Cardinium spp. that were predominant across all four SSA1 B.
tabaci samples with prevalence levels of between 54.1 to 75%. Amino acid alignments of the
NusG gene of
P. aleyrodidarum for the SSA1
B. tabaci transcriptomes of samples WF2 and WF2b revealed an eleven amino acid residue deletion that was absent in samples WF1 and WF2a. Comparison of the protein structure of the
NusG protein from
P. aleyrodidarum in SSA1 with known
NusG structures showed the deletion resulted in a shorter D loop. Conclusions: The use of field-collected specimens means time and money will be saved in future studies using single whitefly transcriptomes in monitoring vector and viral interactions. Our method is applicable to any small organism where RNA quantity has limited transcriptome studies.
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Affiliation(s)
- Peter Sseruwagi
- Mikocheni Agriculture Research Institute (MARI), Dar es Salaam, P.O. Box 6226, Tanzania
| | - James Wainaina
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, WA, 6009, Australia
| | - Joseph Ndunguru
- Mikocheni Agriculture Research Institute (MARI), Dar es Salaam, P.O. Box 6226, Tanzania
| | - Robooni Tumuhimbise
- National Agricultural Research Laboratories, P.O. Box 7065, Kampala Kawanda - Senge Rd, Kampala, Uganda
| | - Fred Tairo
- Mikocheni Agriculture Research Institute (MARI), Dar es Salaam, P.O. Box 6226, Tanzania
| | - Jian-Yang Guo
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China.,State Key Laboratory for the Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Alice Vrielink
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, WA, 6009, Australia
| | - Amanda Blythe
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, WA, 6009, Australia
| | - Tonny Kinene
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, WA, 6009, Australia
| | - Bruno De Marchi
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, WA, 6009, Australia.,Faculdade de Ciências Agronômicas, Universidade Estadual Paulista , Botucatu, Brazil
| | - Monica A Kehoe
- Department of Primary Industries and Regional Development, DPIRD Diagnostic Laboratory Services, South Perth, WA, Australia
| | - Sandra Tanz
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, WA, 6009, Australia
| | - Laura M Boykin
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, WA, 6009, Australia
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24
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Sseruwagi P, Wainaina J, Ndunguru J, Tumuhimbise R, Tairo F, Guo JY, Vrielink A, Blythe A, Kinene T, De Marchi B, Kehoe MA, Tanz S, Boykin LM. The first transcriptomes from field-collected individual whiteflies (Bemisia tabaci, Hemiptera: Aleyrodidae). Gates Open Res 2018; 1:16. [DOI: 10.12688/gatesopenres.12783.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2018] [Indexed: 11/20/2022] Open
Abstract
Background: Bemisia tabaci species (B. tabaci), or whiteflies, are the world’s most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised a single whitefly RNA extraction procedure, and sequenced the transcriptome of four individual adult Sub-Saharan Africa 1 (SSA1) B. tabaci. Transcriptome sequencing resulted in 39-42 million raw reads. De novo assembly of trimmed reads yielded between 65,000-162,000 Contigs across B. tabaci transcriptomes. Results: Bayesian phylogenetic analysis of mitochondrion cytochrome I oxidase (mtCOI) grouped the four whiteflies within the SSA1 clade. BLASTn searches on the four transcriptomes identified five endosymbionts; the primary endosymbiont Portiera aleyrodidarum and four secondary endosymbionts: Arsenophonus, Wolbachia, Rickettsia, and Cardinium spp. that were predominant across all four SSA1 B. tabaci samples with prevalence levels of between 54.1 to 75%. Amino acid alignments of the NusG gene of P. aleyrodidarum for the SSA1 B. tabaci transcriptomes of samples WF2 and WF2b revealed an eleven amino acid residue deletion that was absent in samples WF1 and WF2a. Comparison of the protein structure of the NusG protein from P. aleyrodidarum in SSA1 with known NusG structures showed the deletion resulted in a shorter D loop. Conclusions: The use of field-collected specimens means time and money will be saved in future studies using single whitefly transcriptomes in monitoring vector and viral interactions. Our method is applicable to any small organism where RNA quantity has limited transcriptome studies.
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25
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Fontenele RS, Alves-Freitas DMT, Silva PIT, Foresti J, Silva PR, Godinho MT, Varsani A, Ribeiro SG. Discovery of the first maize-infecting mastrevirus in the Americas using a vector-enabled metagenomics approach. Arch Virol 2017; 163:263-267. [PMID: 28956174 DOI: 10.1007/s00705-017-3571-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 09/04/2017] [Indexed: 01/18/2023]
Abstract
The genus Mastrevirus (family Geminiviridae) is composed of single-stranded DNA viruses that infect mono- and dicotyledonous plants and are transmitted by leafhoppers. In South America, there have been only two previous reports of mastreviruses, both identified in sweet potatoes (from Peru and Uruguay). As part of a general viral surveillance program, we used a vector-enabled metagenomics (VEM) approach and sampled leafhoppers (Dalbulus maidis) in Itumbiara (State of Goiás), Brazil. High-throughput sequencing of viral DNA purified from the leafhopper sample revealed mastrevirus-like contigs. Using a set of abutting primers, a 2746-nt circular genome was recovered. The circular genome has a typical mastrevirus genome organization and shares <63% pairwise identity with other mastrevirus isolates from around the world. Therefore, the new mastrevirus was tentatively named "maize striate mosaic virus". Seventeen maize leaf samples were collected in the same field as the leafhoppers, and ten samples were found to be positive for this mastrevirus. Furthermore, the ten genomes recovered from the maize samples share >99% pairwise identity with the one from the leafhopper. This is the first report of a maize-infecting mastrevirus in the Americas, the first identified in a non-vegetatively propagated mastrevirus host in South America, and the first mastrevirus to be identified in Brazil.
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Affiliation(s)
- Rafaela S Fontenele
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil.,The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA, 85287
| | | | - Pedro I T Silva
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | - Josemar Foresti
- Faculdade de Agronomia e Medicina Veterinária, Campus Darcy Ribeiro, Universidade de Brasília, Brasília, DF, Brasil
| | - Paulo R Silva
- Faculdade de Agronomia e Medicina Veterinária, Campus Darcy Ribeiro, Universidade de Brasília, Brasília, DF, Brasil
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA, 85287. .,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa.
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26
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Mar TB, Mendes IR, Lau D, Fiallo-Olivé E, Navas-Castillo J, Alves MS, Murilo Zerbini F. Interaction between the New World begomovirus Euphorbia yellow mosaic virus and its associated alphasatellite: effects on infection and transmission by the whitefly Bemisia tabaci. J Gen Virol 2017; 98:1552-1562. [PMID: 28590236 DOI: 10.1099/jgv.0.000814] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The majority of Old World monopartite begomoviruses (family Geminiviridae) are associated with satellite DNAs. Alphasatellites are capable of autonomous replication, but depend on the helper virus for movement, encapsidation and transmission by the insect vector. Recently, Euphorbia yellow mosaic alphasatellite (EuYMA) was found in association with Euphorbia yellow mosaic virus (EuYMV) infecting Euphorbia heterophylla plants in Brazil. The geographical range of EuYMA was assessed in a representative sampling of E. heterophylla plants collected in several states of Brazil from 2009 to 2014. Infectious clones were generated and used to assess the phenotype of viral infection in the presence or absence of the alphasatellite in tomato, E. heterophylla, Nicotiana benthamiana, Arabidopsis thaliana and Crotalaria juncea. Phenotypic differences of EuYMV infection in the presence or absence of EuYMA were observed in A. thaliana, N. benthamiana and E. heterophylla. Symptoms were more severe when EuYMV was inoculated in combination with EuYMA in N. benthamiana and E. heterophylla, and the presence of the alphasatellite was determinant for symptom development in A. thaliana. Quantification of EuYMV and EuYMA indicated that EuYMA affects the accumulation of EuYMV during infection on a host-dependent basis. Transmission assays indicated that EuYMA negatively affects the transmission of EuYMV by Bemisia tabaci MEAM1. Together, these results indicate that EuYMA is capable of modulating symptoms, viral accumulation and whitefly transmission of EuYMV, potentially interfering with virus dissemination in the field.
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Affiliation(s)
- Talita Bernardon Mar
- Dep de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Igor Rodrigues Mendes
- Dep de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Douglas Lau
- Embrapa Trigo, Rodovia BR-285, CP 3081, Passo Fundo, RS, 99001-970, Brazil
| | - Elvira Fiallo-Olivé
- National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.,Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'', Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental ''La Mayora'', 29750 Algarrobo-Costa, Málaga, Spain
| | - Jesús Navas-Castillo
- National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.,Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'', Universidad de Málaga - Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental ''La Mayora'', 29750 Algarrobo-Costa, Málaga, Spain
| | - Murilo Siqueira Alves
- Dep de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - F Murilo Zerbini
- Dep de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.,National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
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27
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Silva JCF, Carvalho TFM, Basso MF, Deguchi M, Pereira WA, Sobrinho RR, Vidigal PMP, Brustolini OJB, Silva FF, Dal-Bianco M, Fontes RLF, Santos AA, Zerbini FM, Cerqueira FR, Fontes EPB. Geminivirus data warehouse: a database enriched with machine learning approaches. BMC Bioinformatics 2017; 18:240. [PMID: 28476106 PMCID: PMC5420152 DOI: 10.1186/s12859-017-1646-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/25/2017] [Indexed: 03/28/2023] Open
Abstract
BACKGROUND The Geminiviridae family encompasses a group of single-stranded DNA viruses with twinned and quasi-isometric virions, which infect a wide range of dicotyledonous and monocotyledonous plants and are responsible for significant economic losses worldwide. Geminiviruses are divided into nine genera, according to their insect vector, host range, genome organization, and phylogeny reconstruction. Using rolling-circle amplification approaches along with high-throughput sequencing technologies, thousands of full-length geminivirus and satellite genome sequences were amplified and have become available in public databases. As a consequence, many important challenges have emerged, namely, how to classify, store, and analyze massive datasets as well as how to extract information or new knowledge. Data mining approaches, mainly supported by machine learning (ML) techniques, are a natural means for high-throughput data analysis in the context of genomics, transcriptomics, proteomics, and metabolomics. RESULTS Here, we describe the development of a data warehouse enriched with ML approaches, designated geminivirus.org. We implemented search modules, bioinformatics tools, and ML methods to retrieve high precision information, demarcate species, and create classifiers for genera and open reading frames (ORFs) of geminivirus genomes. CONCLUSIONS The use of data mining techniques such as ETL (Extract, Transform, Load) to feed our database, as well as algorithms based on machine learning for knowledge extraction, allowed us to obtain a database with quality data and suitable tools for bioinformatics analysis. The Geminivirus Data Warehouse (geminivirus.org) offers a simple and user-friendly environment for information retrieval and knowledge discovery related to geminiviruses.
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Affiliation(s)
- Jose Cleydson F Silva
- Departamento de Informática, Universidade Federal de Viçosa, Viçosa, Brazil.,National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Marcos F Basso
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Michihito Deguchi
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Welison A Pereira
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Roberto R Sobrinho
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Pedro M P Vidigal
- Núcleo de Biomoléculas, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Otávio J B Brustolini
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Fabyano F Silva
- Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Maximiller Dal-Bianco
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Anésia A Santos
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil.,Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Francisco Murilo Zerbini
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil.,Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Fabio R Cerqueira
- Departamento de Informática, Universidade Federal de Viçosa, Viçosa, Brazil.,Departamento de Engenharia de Produção, Universidade Federal Fluminense, Petrópolis, Rio de Janeiro, Brazil
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil. .,Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil.
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28
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Genome Sequence of Cauliflower Mosaic Virus Identified in Earwigs ( Doru luteipes) through a Metagenomic Approach. GENOME ANNOUNCEMENTS 2017; 5:5/11/e00043-17. [PMID: 28302781 PMCID: PMC5356058 DOI: 10.1128/genomea.00043-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here we report the first complete genome sequence of a cauliflower mosaic virus from Brazil, obtained from the gut content of the predator earwig (Doru luteipes). This virus has a genome of 8,030 nucleotides (nt) and shares 97% genome-wide identity with an isolate from Argentina.
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29
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Genome Sequences of Beet curly top Iran virus, Oat dwarf virus, Turnip curly top virus, and Wheat dwarf virus Identified in Leafhoppers. GENOME ANNOUNCEMENTS 2017; 5:5/8/e01674-16. [PMID: 28232449 PMCID: PMC5323628 DOI: 10.1128/genomea.01674-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Implementation of a vector-enabled metagenomics approach resulted in the identification of various geminiviruses. We identified the genome sequences of Beet curly top Iran virus, Turnip curly top viruses, Oat dwarf viruses, the first from Iran, and Wheat dwarf virus from leafhoppers feeding on beet, parsley, pumpkin, and turnip plants.
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