1
|
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.
Collapse
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
| |
Collapse
|
2
|
Reingold V, Eliyahu A, Luria N, Leibman D, Sela N, Lachman O, Smith E, Mandelik Y, Sadeh A, Dombrovsky A. A Distinct Arabidopsis Latent Virus 1 Isolate Was Found in Wild Brassica hirta Plants and Bees, Suggesting the Potential Involvement of Pollinators in Virus Spread. PLANTS (BASEL, SWITZERLAND) 2024; 13:671. [PMID: 38475517 DOI: 10.3390/plants13050671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/08/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
During our search for aphid-pathogenic viruses, a comovirus was isolated from wild asymptomatic Brassica hirta (white mustard) plants harboring a dense population of Brevicoryne brassicae aphids. The transmission-electron-microscopy visualization of purified virions revealed icosahedral particles. The virus was mechanically transmitted to plants belonging to Brassicaceae, Solanaceae, Amaranthaceae, and Fabaceae families, showing unique ringspot symptoms only on B. rapa var. perviridis plants. The complete viral genome, comprised of two RNA segments, was sequenced. RNA1 and RNA2 contained 5921 and 3457 nucleotides, respectively, excluding the 3' terminal poly-adenylated tails. RNA1 and RNA2 each had one open-reading frame encoding a polyprotein of 1850 and 1050 amino acids, respectively. The deduced amino acids at the Pro-Pol region, delineated between a conserved CG motif of 3C-like proteinase and a GDD motif of RNA-dependent RNA polymerase, shared a 96.5% and 90% identity with the newly identified Apis mellifera-associated comovirus and Arabidopsis latent virus 1 (ArLV1), respectively. Because ArLV1 was identified early in 2018, the B. hirta comovirus was designated as ArLV1-IL-Bh. A high-throughput-sequencing-analyses of the extracted RNA from managed honeybees and three abundant wild bee genera, mining bees, long-horned bees, and masked bees, sampled while co-foraging in a Mediterranean ecosystem, allowed the assembly of ArLV1-IL-Bh, suggesting pollinators' involvement in comovirus spread in weeds.
Collapse
Affiliation(s)
- Victoria Reingold
- Department of Plant Pathology and Weed Research, ARO Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Avi Eliyahu
- Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
- Department of Natural Resources, Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay 3009500, Israel
- The Advanced School for Environmental Studies, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Neta Luria
- Department of Plant Pathology and Weed Research, ARO Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Diana Leibman
- Department of Plant Pathology and Weed Research, ARO Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Noa Sela
- Bioinformatics Unit, ARO Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Oded Lachman
- Department of Plant Pathology and Weed Research, ARO Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Elisheva Smith
- Department of Plant Pathology and Weed Research, ARO Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, Rishon LeZion 7528809, Israel
| | - Yael Mandelik
- Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Asaf Sadeh
- Department of Natural Resources, Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay 3009500, Israel
| | - Aviv Dombrovsky
- Department of Plant Pathology and Weed Research, ARO Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, Rishon LeZion 7528809, Israel
| |
Collapse
|
3
|
Smadi M, Lee E, Phelan J, Wang A, Bilodeau GJ, Pernal SF, Guarna MM, Rott M, Griffiths JS. Plant virus diversity in bee and pollen samples from apple ( Malus domestica) and sweet cherry ( Prunus avium) agroecosystems. FRONTIERS IN PLANT SCIENCE 2024; 15:1335281. [PMID: 38444533 PMCID: PMC10913894 DOI: 10.3389/fpls.2024.1335281] [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: 11/08/2023] [Accepted: 01/05/2024] [Indexed: 03/07/2024]
Abstract
Introduction Honey bee (Apis mellifera) pollination is widely used in tree fruit production systems to improve fruit set and yield. Many plant viruses can be associated with pollen or transmitted through pollination, and can be detected through bee pollination activities. Honey bees visit multiple plants and flowers in one foraging trip, essentially sampling small amounts of pollen from a wide area. Here we report metagenomics-based area-wide monitoring of plant viruses in cherry (Prunus avium) and apple (Malus domestica) orchards in Creston Valley, British Columbia, Canada, through bee-mediated pollen sampling. Methods Plant viruses were identified in total RNA extracted from bee and pollen samples, and compared with profiles from double stranded RNA extracted from leaf and flower tissues. CVA, PDV, PNRSV, and PVF coat protein nucleotide sequences were aligned and compared for phylogenetic analysis. Results A wide array of plant viruses were identified in both systems, with cherry virus A (CVA), prune dwarf virus (PDV), prunus necrotic ringspot virus (PNRSV), and prunus virus F (PVF) most commonly detected. Citrus concave gum associated virus and apple stem grooving virus were only identified in samples collected during apple bloom, demonstrating changing viral profiles from the same site over time. Different profiles of viruses were identified in bee and pollen samples compared to leaf and flower samples reflective of pollen transmission affinity of individual viruses. Phylogenetic and pairwise analysis of the coat protein regions of the four most commonly detected viruses showed unique patterns of nucleotide sequence diversity, which could have implications in their evolution and management approaches. Coat protein sequences of CVA and PVF were broadly diverse with multiple distinct phylogroups identified, while PNRSV and PDV were more conserved. Conclusion The pollen virome in fruit production systems is incredibly diverse, with CVA, PDV, PNRSV, and PVF widely prevalent in this region. Bee-mediated monitoring in agricultural systems is a powerful approach to study viral diversity and can be used to guide more targeted management approaches.
Collapse
Affiliation(s)
- Malek Smadi
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Eunseo Lee
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - James Phelan
- Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, North Saanich, BC, Canada
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | | | - Stephen F. Pernal
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, Beaverlodge, AB, Canada
| | - M. Marta Guarna
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, Beaverlodge, AB, Canada
- Department of Computer Science, University of Victoria, Victoria, BC, Canada
| | - Mike Rott
- Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, North Saanich, BC, Canada
| | - Jonathan S. Griffiths
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| |
Collapse
|
4
|
Lotos L, Katsiani A, Katis NI, Maliogka VI. Evaluation of the RNA Silencing Suppression Activity of Three Cherry Virus F-Encoded Proteins. PLANTS (BASEL, SWITZERLAND) 2024; 13:264. [PMID: 38256817 PMCID: PMC10819124 DOI: 10.3390/plants13020264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024]
Abstract
Cherry virus F (CVF) is a newly emerged sweet cherry virus. CVF has been identified in a small number of countries and it has not been associated with discrete symptomatology. RNA silencing is a natural defense mechanism of plants against invaders that degrades viral RNA in a sequence-specific manner. As a counter-defense, plant viruses encode one or more RNA silencing suppressors (RSSs) interfering with the silencing pathway via several mechanisms. To identify putative RSSs, the three proteins (MP, CPL, CPS) encoded by the RNA2 of CVF were selected and separately cloned into the binary vector pART27. The clones were used for transient expression experiments in Nicotiana benthamiana leaves, using co-agroinfiltration with a GFP-expressing vector. In both CPL and CPS, a rapid decrease in fluorescence was recorded, comparable to the negative control, whereas the MP of CVF retained the GFP's fluorescence for a few days longer even though this was observed in a small number of infiltrated leaves. Further experiments have shown that the protein was not able to inhibit the cell-to-cell spread of the silencing signal; however, a putative interference with systemic silencing was recorded especially when the induction was carried out with double-stranded GFP RNA. Overall, our results indicate that the MP of CVF is putatively implicated in the suppression of RNA silencing, though further experimentation is needed to unveil the exact mode of action.
Collapse
Affiliation(s)
| | | | | | - Varvara I. Maliogka
- Plant Pathology Laboratory, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (L.L.); (A.K.); (N.I.K.)
| |
Collapse
|