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Bandoo RA, Kraberger S, Varsani A. Two Novel Geminiviruses Identified in Bees ( Apis mellifera and Nomia sp.). Viruses 2024; 16:602. [PMID: 38675943 PMCID: PMC11053556 DOI: 10.3390/v16040602] [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: 03/30/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Members of the Geminviridae family are circular single-stranded DNA plant-infecting viruses, some of which impact global food production. Geminiviruses are vectored by sap-feeding insects such as leafhoppers, treehoppers, aphids, and whiteflies. Additionally, geminivirus sequences have also been identified in other insects such as dragonflies, mosquitoes, and stingless bees. As part of a viral metagenomics study on honeybees and solitary bees (Nomia sp.), two geminivirus genomes were identified. These represent a novel citlodavirus (from honeybees collected from Westmoreland, Jamaica) and a mastrevirus-like genome (from a solitary bee collected from Tempe, Arizona, USA). The novel honeybee-derived citlodavirus genome shares ~61 to 69% genome-wide nucleotide pairwise identity with other citlodavirus genome sequences and is most closely related to the passion fruit chlorotic mottle virus identified in Brazil. Whereas the novel solitary bee-derived mastrevirus-like genome shares ~55 to 61% genome-wide nucleotide identity with other mastreviruses and is most closely related to tobacco yellow dwarf virus identified in Australia, based on pairwise identity scores of the full genome, replication-associated protein, and capsid protein sequences. Previously, two geminiviruses in the Begomovirus genus were identified in samples of stingless bee (Trigona spp.) samples. Here, we identify viruses that represent two new species of geminiviruses from a honeybee and a solitary bee, which continues to demonstrate that plant pollinators can be utilized for the identification of plant-infecting DNA viruses in ecosystems.
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Affiliation(s)
- Rohan Antonio Bandoo
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town 7700, South Africa
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da Silva JPH, Zerbini FM. Taxonomic Classification of Geminiviruses Based on Pairwise Sequence Comparisons. Methods Mol Biol 2024; 2724:21-31. [PMID: 37987895 DOI: 10.1007/978-1-0716-3485-1_2] [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: 11/22/2023]
Abstract
Geminiviridae is the largest and one of the most diverse families of plant viruses, comprising 14 genera demarcated based on host range, type of insect vector, and phylogenetic relationships. The use of unbiased, whole-genome multiple displacement amplification techniques coupled with high-throughput sequencing has greatly expanded our knowledge of geminivirus diversity over the last two decades. As a result, a large number of new species have been described in recent years. Species demarcation criteria in the family are entirely based on sequence comparisons, but the specific cutoff values vary for each genus. The purpose of this chapter is to provide a step-by-step pipeline to classify new species in the family Geminiviridae.
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Affiliation(s)
| | - F Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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Lin J, Yang S, Ji J, Xiang P, Wu L, Chen H. Natural or artificial: An example of topographic spatial distribution analysis of mescaline in cactus plants by matrix-assisted laser desorption/ionization mass spectrometry imaging. FRONTIERS IN PLANT SCIENCE 2023; 14:1066595. [PMID: 36844095 PMCID: PMC9950628 DOI: 10.3389/fpls.2023.1066595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Differentiating whether plant products are natural or artificial is of great importance in many practical fields, including forensic science, food safety, cosmetics, and fast-moving consumer goods. Information about the topographic distribution of compounds is an important criterion for answering this question. However, of equal importance is the likelihood that topographic spatial distribution information may provide important and valuable information for molecular mechanism study. METHODS In this study, we took mescaline, a substance with hallucinogenic properties in cacti of the species Trichocereus pachanoi and Lophophora williamsii, as an example to characterize the spatial distribution of mescaline in plants and flowers by liquid chromatograph-mass spectrometry-matrix-assisted laser desorption/ionization mass spectrometry imaging at the macroscopic, tissue structure, and even cellular levels. RESULTS According to our results, the distribution of mescaline in natural plant was concentrated on the active meristems, epidermal tissues, and protruding parts of Trichocereus pachanoi and Lophophora williamsii, while artificially spiked Lophophora diffusa products showed no such difference in their topographic spatial distribution. DISCUSSION This difference in distribution pattern allowed us to distinguish between flowers that could synthesize mescaline on their own and those that had been artificially spiked with mescaline. The interesting topographic spatial distribution results, such as the overlap of the mescaline distribution map and micrographs of the vascular bundles, were consistent with the synthesis and transport theory of mescaline, indicating the potential for applying matrix-assisted laser desorption/ionization mass spectrometry imaging in botanical research.
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Menezes RCFD, Gomes QCDC, Almeida BSD, Matos MFRD, Pinto LC. Plant-based mayonnaise: Trending ingredients for innovative products. Int J Gastron Food Sci 2022. [DOI: 10.1016/j.ijgfs.2022.100599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Jiang N, Gai X, Yin D, Zhang G, Lu C, Guo J, Ma J, Xia Z. Tobacco leaf curl Puer virus: a novel monopartite begomovirus infecting Nicotiana tabacum in China. Arch Virol 2022; 167:229-232. [PMID: 34652555 DOI: 10.1007/s00705-021-05267-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
Begomoviruses (family Geminiviridae) cause serious diseases in many crops. In this study, we characterized a begomovirus isolated from a tobacco plant with leaf curl in Puer, Yunnan Province, China. Analysis of the viral genome obtained from a symptomatic Nicotiana tabacum plant showed that it belonged to a novel monopartite begomovirus. The genome (2741 nt) shared the highest nucleotide sequence identity (83.43%) with that of tomato yellow leaf curl Vietnam virus (TYLCVV). Based on the current taxonomic criteria of the International Committee on Taxonomy of Viruses, this virus, for which the name "tobacco leaf curl Puer virus" is proposed, represents a new species of begomovirus.
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Affiliation(s)
- Ning Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China.
| | - Xiaotong Gai
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Duan Yin
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Guanghai Zhang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Canhua Lu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Jian Guo
- Yunnan Tobacco Company, Honghe Branch, Honghe, 652399, Yunnan Province, China
| | - Junhong Ma
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
| | - Zhenyuan Xia
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, China
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Roumagnac P, Lett JM, Fiallo-Olivé E, Navas-Castillo J, Zerbini FM, Martin DP, Varsani A. Establishment of five new genera in the family Geminiviridae: Citlodavirus, Maldovirus, Mulcrilevirus, Opunvirus, and Topilevirus. Arch Virol 2021; 167:695-710. [PMID: 34837111 DOI: 10.1007/s00705-021-05309-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Geminiviruses are plant-infecting, circular single-stranded DNA viruses that have a geminate virion morphology. These viruses infect both cultivated and non-cultivated monocotyledonous and dicotyledonous plants and have a wide geographical distribution. Nine genera had been established within the family Geminiviridae (Becurtovirus, Begomovirus, Capulavirus, Curtovirus, Eragrovirus, Grablovirus, Mastrevirus, Topocuvirus, and Turncurtovirus) as of 2020. In the last decade, metagenomics approaches have facilitated the discovery and identification of many novel viruses, among them numerous highly divergent geminiviruses. Here, we report the establishment of five new genera in the family Geminiviridae (Citlodavirus, Maldovirus, Mulcrilevirus, Opunvirus, and Topilevirus) to formally classify twelve new, divergent geminiviruses.
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Affiliation(s)
- Philippe Roumagnac
- CIRAD, UMR PHIM, 34090, Montpellier, France.
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
| | | | - Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, 29750, Algarrobo-Costa, Málaga, Spain
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, 29750, Algarrobo-Costa, Málaga, Spain
| | - F Murilo Zerbini
- Dep. de Fitopatologia/Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Darren P Martin
- Department of Integrative Biomedical Sciences, Computational Biology Division, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa.
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Fontenele RS, Köhler M, Majure LC, Avalos-Calleros JA, Argüello-Astorga GR, Font F, Vidal AH, Roumagnac P, Kraberger S, Martin DP, Lefeuvre P, Varsani A. Novel circular DNA virus identified in Opuntia discolor ( Cactaceae) that codes for proteins with similarity to those of geminiviruses. J Gen Virol 2021; 102. [PMID: 34726588 DOI: 10.1099/jgv.0.001671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Viral metagenomic studies have enabled the discovery of many unknown viruses and revealed that viral communities are much more diverse and ubiquitous than previously thought. Some viruses have multiple genome components that are encapsidated either in separate virions (multipartite viruses) or in the same virion (segmented viruses). In this study, we identify what is possibly a novel bipartite plant-associated circular single-stranded DNA virus in a wild prickly pear cactus, Opuntia discolor, that is endemic to the Chaco ecoregion in South America. Two ~1.8 kb virus-like circular DNA components were recovered, one encoding a replication-associated protein (Rep) and the other a capsid protein (CP). Both of the inferred protein sequences of the Rep and CP are homologous to those encoded by members of the family Geminiviridae. These two putatively cognate components each have a nonanucleotide sequence within a likely hairpin structure that is homologous to the origins of rolling-circle replication (RCR), found in diverse circular single-stranded DNA viruses. In addition, the two components share similar putative replication-associated iterative sequences (iterons), which in circular single-stranded DNA viruses are important for Rep binding during the initiation of RCR. Such molecular features provide support for the possible bipartite nature of this virus, which we named utkilio virus (common name of the Opuntia discolor in South America) components A and B. In the infectivity assays conducted in Nicotiana benthamiana plants, only the A component of utkilio virus, which encodes the Rep protein, was found to move and replicate systemically in N. benthamiana. This was not true for component B, for which we did not detect replication, which may have been due to this being a defective molecule or because of the model plants (N. benthamiana) used for the infection assays. Future experiments need to be conducted with other plants, including O. discolor, to understand more about the biology of these viral components.
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Affiliation(s)
- Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, 85287, USA
| | - Matias Köhler
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lucas C Majure
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Jesús A Avalos-Calleros
- 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, Mexico
| | - 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, Mexico
| | - Fabián Font
- Herbario Museo de Farmacobotánica 'Juan A. Domínguez' (BAF), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andreza H Vidal
- Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília, Brasília, Brazil
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, 85287, USA
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, 7925, Cape Town, South Africa
| | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, 85287, USA.,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925, Cape Town, South Africa
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Identification of the Begomoviruses Squash Leaf Curl Virus and Watermelon Chlorotic Stunt Virus in Various Plant Samples in North America. Viruses 2021; 13:v13050810. [PMID: 33946382 PMCID: PMC8147125 DOI: 10.3390/v13050810] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022] Open
Abstract
Geminiviruses are a group of plant-infecting viruses with single-stranded DNA genomes. Within this family, viruses in the genus Begomovirus are known to have a worldwide distribution causing a range of severe diseases in a multitude of dicotyledonous plant species. Begomoviruses are transmitted by the whitefly Bemisia tabaci, and their ssDNA genomes can be either monopartite or bipartite. As part of a viral survey, various plants including those in the families Alliaceae, Amaranthaceae, Apiaceae, Asteraceae, Brassicaceae, Cactaceae, Cucurbitaceae, Lamiaceae, Lauraceae, Malvaceae, Oleaceae and Solanaceae were sampled and screened for begomoviruses using both a high-throughput sequencing and a begomovirus-specific primer pair approach. Based on the sequences derived using these approaches, the full-length genome of various begomoviruses were amplified from plants using abutting primers. Squash leaf curl virus (SLCV) and watermelon chlorotic stunt virus (WCSV) were identified in Cactaceae (n = 25), Solanaceae (n = 7), Cucurbitaceae (n = 2) and Lamiaceae (n = 1) samples. WCSV is an Old World bipartite begomovirus that has only recently been discovered infecting watermelons in the Americas. Our discovery of WCSV in the USA is the first indication that it has reached this country and indicates that this virus might be widespread throughout North America. Phylogenetic analysis suggests WCSV was introduced to the New World twice. The detection of begomoviruses in cactus plants suggests possible spillover events from agricultural areas into native vegetation. Since WCSV and SLCV have previously been found in mixed infections, pseudo-recombination infection experiments were conducted. We demonstrate that WCSV DNA-B is successfully trans-replicated by SLCV DNA-A despite very low degree of similarity between the replication-associated iterative sequences present in their common region, an essential feature for binding of the replication associated protein. This study highlights the importance of viral surveys for the detection of spillover events into native vegetation, but also suggests the need for more surveillance of WCSV in the USA, as this virus is a serious threat to watermelon cultivation in the Middle East.
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