1,720,997 research outputs found
Exploring the tymovirales landscape through metatranscriptomics data
No full textTymovirales is an order of viruses with positive-sense RNA genomes that mostly infect plants, but also fungi and insects. The number of genome sequences of viruses that could fit this taxon has been growing in the last few years with the extensive use of high-throughput sequencing. Here, we report the discovery of 31 novel viral genome sequences associated with 27 different host plant species, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3,000 plant transcriptomes from the NCBI Sequence Read Archive (SRA) using known tymovirales sequences as queries. Identification, assembly, and curation of raw SRA reads resulted in 29 viral genome sequences with complete coding regions, and two representing partial genomes. Some of the obtained sequences highlight novel genome organizations for members of the order. Phylogenetic analysis showed that six of the novel viruses are related to alphaflexiviruses, 17 to betaflexiviruses, two to deltaflexiviruses, and six to tymovirids. These findings shed new light on the phylogenetic relationships and evolutionary landscape of this group of viruses. Furthermore, this study illustrates the complexity and genome diversity among members of the order and demonstrates that analyzing public SRA data provides an invaluable tool to accelerate virus discovery and refine virus taxonomy.Instituto de Patología VegetalFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentin
A glimpse into the DNA virome of the unique “living fossil” Welwitschia mirabilis
No full textHere, we report the identification and characterization of four novel DNA viruses from Welwitschia mirabilis
transcriptomic and genomic datasets. Complete circular virus-like sequences with affinity to members of the
Caulimoviridae and Geminiviridae families were detected and characterized from Welwitschia mirabilis genomic
data. The two newly members of the Caulimoviridae family have been tentatively named as Welwitschia mirabilis
virus 1 and 2 (WMV1-WMV2); whereas the two identified geminiviruses were named as Welwitschia mirabilis
associated geminivirus A and B (WMaGVA-WMaGVB). Phylogenetic analysis suggests that WMV1-2 belong to a
proposed genus of Caulimoviridae-infecting gymnosperms. WMaGVA-B are phylogenetically related with both
mastreviruses and capulaviruses and likely represent a distinct evolutionary lineage within geminiviruses.
Additionally, we detected several endogenous virus-like elements (EVE) linked to the discovered viruses in the
recently reported W. mirabilis genome, suggesting a shared ancient evolutionary history of these viruses and the
Welwithschia.Instituto de Patología VegetalFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentin
RNA Virus Discovery Sheds Light on the Virome of a Major Vineyard Pest, the European Grapevine Moth (Lobesia botrana)
No full textThe European grapevine moth (Lobesia botrana) poses a significant threat to vineyards worldwide, causing extensive economic losses. While its ecological interactions and control strategies have been well studied, its associated viral diversity remains unexplored. Here, we employ high-throughput sequencing data mining to comprehensively characterize the L. botrana virome, revealing novel and diverse RNA viruses. We characterized four new viral members belonging to distinct families, with evolutionary cues of cypoviruses (Reoviridae), sobemo-like viruses (Solemoviridae), phasmaviruses (Phasmaviridae), and carmotetraviruses (Carmotetraviridae). Phylogenetic analysis of the cypoviruses places them within the genus in affinity with other moth viruses. The bi-segmented and highly divergent sobemo-like virus showed a distinctive evolutionary trajectory of its encoding proteins at the periphery of recently reported invertebrate Sobelivirales. Notably, the presence of a novel phasmavirus, typically associated with mosquitoes, expands the known host range and diversity of this family to moths. Furthermore, the identification of a carmotetravirus branching in the same cluster as the Providence virus, a lepidopteran virus which replicates in plants, raises questions regarding the biological significance of this moth virus to the grapevine host. We further explored viral sequences in several publicly available transcriptomic datasets of the moth, indicating potential prevalence across distinct conditions. These results underscore the existence of a complex virome within L. botrana and lay the foundation for future studies investigating the ecological roles, evolutionary dynamics, and potential biocontrol applications of these viruses in the L. botrana–vineyard ecosystem.Instituto de Patología VegetalFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Gomez Talquenca, Sebastian. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentin
Two novel flavi-like viruses shed light on the plant-infecting koshoviruses
No full textThe family Flaviviridae is composed of viruses with a positive-sense single-stranded RNA genome and includes viruses that are important veterinary and human pathogens. Most members of the family are arthropod- and vertebrate-infecting viruses, but more recently, divergent flavi-like viruses have been identified in marine invertebrate and vertebrate hosts. The striking discovery of gentian Kobu-sho-associated virus (GKaV), along with a recent report of a related virus from carrot, has expanded the known host range of flavi-like viruses to plants, suggesting they could be grouped in a proposed genus tentatively named “Koshovirus”. Here, we report the identification and characterization of two novel RNA viruses that show a genetic and evolutionary relationship to the previously identified “koshoviruses”. Their genome sequences were obtained from transcriptomic datasets of the flowering plants Coptis teeta and Sonchus asper. These two new viruses, which we have named "coptis flavi-like virus 1" (CopFLV1) and "sonchus flavi-like virus 1" (SonFLV1), are members of novel species characterized by the longest monopartite RNA genome observed so far among plant-associated RNA viruses, which is ca. 24 kb in size. Structural and functional annotations of the polyproteins of all koshoviruses resulted in the detection not only of the expected helicase and RNA-dependent RNA polymerase but also of several additional divergent domains, including AlkB oxygenase, trypsin-like serine protease, methyltransferase, and envelope E1 flavi-like domains. Phylogenetic analysis showed that CopFLV1, SonFLV1, GKaV, and the carrot flavi-like virus were grouped together in a monophyletic clade, strongly supporting the recent proposal for creation of the genus “Koshovirus” for the group of related plant-infecting flavi-like viruses.Instituto de Patología VegetalFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentin
Novel bird’s-foot trefoil RNA viruses provide insights into a clade of legume-associated enamoviruses and rhabdoviruses
No full textHere, we report the identification and characterization of two novel viruses associated with bird’s-foot trefoil. Virus sequences related to those of enamoviruses (ssRNA (+); Luteoviridae; Enamovirus) and nucleorhabdoviruses (ssRNA (-); Rhabdoviridae; Nucleorhabdovirus) were detected in Lotus corniculatus transcriptome data. The genome of the tentatively named “bird’s-foot trefoil-associated virus 1” (BFTV-1) is a 13,626-nt-long negative-sense ssRNA. BFTV-1 encodes six predicted gene products in the antigenome orientation in the canonical order 3′-N-P-P3-M-G-L-5′. The genome of the proposed “bird’s-foot trefoil-associated virus 2” (BFTV-2) is 5,736 nt long with a typical 5΄-PO-P1-2-IGS-P3-P5-3′ enamovirus genome structure. Phylogenetic analysis indicated that BFTV-1 is closely related to datura yellow vein nucleorhabdovirus and that BFTV-2 clusters into a monophyletic lineage of legume-associated enamoviruses. This subclade of highly related and co-divergent legume-associated viruses provides insights into the evolutionary history of the enamoviruses.Instituto de Patología VegetalFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin
Biological, Molecular and Phiysiological Characterization of Four Soybean mosaic virus Isolates Present in Argentine Soybean Crops
Full text linkSoybean mosaic virus (SMV) causes systemic infections in soybean plants, leading to chlorotic mosaic and producing significant yield losses. The virus is widely distributed in all soybean production areas in the world. In Argentina, three geographical isolates were identified: Marcos Juárez (MJ), Manfredi (M), and North Western Argentina (NOA), and another isolate named “Planta Vinosa” (PV), which causes severe necrosis symptoms in some cultivars. Here, the biological, molecular and physiological characterization of these isolates was performed for the first time. Three of the four isolates showed a low genetic divergence in the evaluated genes (P1, CI and CP). Although SMV-NOA and SMV-PV had high homology at the sequence level, they showed wide differences in pathogenicity, seed mottling and the ability of transmission by seeds or aphids, as well as in physiological effects. SMV-NOA caused early alterations (before symptom appearance, BS) in ΦPSII and MDA content in leaves with respect to the other isolates. After the appearance of macroscopic symptoms (late symptoms, LS), SMV-M caused a significant increase in the content of MDA, total soluble sugars, and starch with respect to the other isolates. Thus, early alterations of ΦPSII and soluble sugars might have an impact on late viral symptoms. Likewise, SMV-MJ developed more severe symptoms in the susceptible Davis cultivar than in DM 4800. Therefore, our results show differences in genome, biological properties and physiological effects among SMV isolates as well as different interactions of SMV-MJ with two soybean cultivars.Instituto de Patología VegetalFil: Maugeri Suarez, M. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales (FCEFyN); ArgentinaFil: Rodriguez, Marianela. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Fisiología y Recursos Genéticos Vegetales; ArgentinaFil: Rodriguez, Marianela. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Estudios Agropecuarios (UDEA) ; ArgentinaFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Laguna, Irma Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Laguna, Irma Graciela. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Rodriguez Pardina, Patricia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Rodriguez Pardina, Patricia. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentin
ICTV Virus Taxonomy Profile: Rhabdoviridae 2022
Full text linkThe family Rhabdoviridae comprises viruses with negative-sense (−) RNA genomes of 10–16 kb. Virions are typically enveloped with bullet-shaped or bacilliform morphology but can also be non-enveloped filaments. Rhabdoviruses infect plants or animals, including mammals, birds, reptiles, amphibians or fish, as well as arthropods, which serve as single hosts or act as biological vectors for transmission to animals or plants. Rhabdoviruses include important pathogens of humans, livestock, fish or agricultural crops. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Rhabdoviridae, which is available at ictv.global/report/rhabdoviridae.Instituto de Patología VegetalFil: Walker, Peter J. University of Queensland. School of Chemistry and Molecular Biosciences; AustraliaFil: Freitas-Astúa, Juliana. Brazilian Agricultural Research Corporation; BrasilFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Blasdell, Kim R. CSIRO Health and Biosecurity; AustraliaFil: Breyta, Rachel. University of Washington; Estados UnidosFil: Dietzgen, Ralf G. University of Queensland. Queensland Alliance for Agriculture and Food Innovation; AustraliaFil: Fooks, Anthony R. Animal and Plant Health Agency Addlestone; Reino UnidoFil: Kondo, Hideki. Okayama University. Institute of Plant Science and Resources; JapónFil: Kurath, Gael. Western Fisheries Research Center; Estados UnidosFil: Kuzmin, Ivan V. University of Texas Medical Branch; Estados UnidosFil: Whitfield, Anna E. North Carolina State University. Department of Entomology and Plant Pathology; Estados Unido
Grapevine holobiome metatranscriptomics provides a glimpse into the wood mycovirome
No full textGiven the agronomic and economic importance of viticulture, grapevine has been shown to host the largest number of viruses among plants to date. Nevertheless, studies assessing the grapevine-associated holobiont remain scarce. In this context, the viral component of this ecological niche is understudied. In this work, through metatranscriptomics of wood samples from individual grapevines that were either healthy or exhibited symptoms of grapevine trunk disease from Argentina, we provide a glimpse into the wood linked virome. Virus discovery from high-throughput sequencing data resulted in the identification and reconstruction of 123 novel virus sequences. Genetic and phylogenetic insights suggest that these sequences correspond to 78 novel virus species. Structural and functional annotation of the viruses showed a great diversity of genomic organizations, with the presence of dsRNA, ssRNA( ) and ssRNA(+) viruses belonging to more than 15 virus families. Some highly divergent viruses resembling narnaviruses, ophioviruses, deltaflexiviruses and bunyaviruses could be accommodated within new genera or even new virus families. The differential detection and variable RNA levels across samples suggest complex dynamics and prevalence patterns of those novel viruses. The viral profile described here provides a first insight into the multifaceted South American grapevine wood holobiont mycovirome.Instituto de Patología VegetalFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Paolinelli, Marcos. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Escoriaza, Maria Georgina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Garcia Lampasona, Sandra Claudia.Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Garcia Lampasona, Sandra Claudia. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza (IBAM); Argentina. Consejo Nacional de Investigaciones Científicas y Técnica. Instituto de Biología Agrícola de Mendoza (IBAM); ArgentinaFil: Gomez Talquenca, Gonzalo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentin
2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
Full text linkIn March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.Instituto de Patología VegetalFil: Kuhn, Jens H. National Institute of Allergy and Infectious Diseases. National Institutes of Health. Integrated Research Facility at Fort Detrick; Estados UnidosFil: Adkins, Scott. US Horticultural Research Laboratory. United States Department of Agriculture. Agricultural Research Service; Estados UnidosFil: Alkhovsky, Sergey V. Ministry of Health of Russian Federation. National Center on Epidemiology and Microbiology .D.I. Ivanovsky Institute of Virology of N.F. Gamaleya; RusiaFil: Avšič-Županc, Tatjana. University of Ljubljana. Faculty of Medicine. Institute of Microbiology and Immunology; EsloveniaFil: Ayllón, María A. Universidad Politécnica de Madrid. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria.Centro de Biotecnología y Genómica de Plantas; EspañaFil: Ayllón, María A. Universidad Politécnica de Madrid. Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas. Departamento de Biotecnología-Biología Vegetal; EspañaFil: Bahl, Justin. University of Georgia. Center for Ecology of Infectious Diseases. Insitute of Bioinformatics. Department of Infectious Diseases. Department of Epidemiology and Biostatistics; Estados UnidosFil: Balkema-Buschmann, Anne. Friedrich-Loeffler-Institut. Institute of Novel and Emerging Infectious Diseases; AlemaniaFil: Ballinger, Matthew J. Mississippi State University. Department of Biological Sciences; Estados UnidosFil: Bandte, Martina. Humboldt-Universität zu Berlin. Faculty of Life Sciences. Division Phytomedicine; AlemaniaFil: Beer, Martin. Friedrich-Loeffler-Institut. Institute of Diagnostic Virology; AlemaniaFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Lodden Økland, Arnfnn. Pharmaq Analytiq; Norueg
Exploring species composition and population dynamics of thrips (Thysanoptera: Thripidae) in peanut crops in Argentina
No full textThrips (Thysanoptera: Thripidae) are major pests of peanut (Arachis hypogaea L.). They cause feeding damage and indirect injuries transmitting plant viruses. In Argentina, peanut is commonly affected by thrips. The crop also is infected by groundnut ringspot orthotospovirus, a virus transmitted by thrips vectors. However, in the country, information about thrips in peanut is very scarce. A 3-yr study was conducted to characterize the species composition and thrips population dynamics in the main peanut-producing area in Argentina. Frankliniella schultzei (Trybom), followed by Caliothrips phaseoli (Hood) were the most abundant species. Together the two species accounted for ~ 95-99 % of the total adult thrips captured in each season. Significant different abundances were observed among these two thrips species throughout each peanut growing season. Nevertheless, the temporal dynamics of F. schultzei and C. phaseoli showed a similar trend in the three study years. In general, the colonization by F. schultzei started in late December and their population increased from the second half of January peaking around the first half of February. The highest densities of F. schultzei occurred simultaneously in foliage and flowers during the warmer months of the year.Instituto de Patología VegetalFil: De Breuil, Soledad. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: De Breuil, Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Giudici, Albano Cesar. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Microbiología y Zoología Agrícola; ArgentinaFil: La Rossa, Francisco Ruben. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Microbiología y Zoología Agrícola; ArgentinaFil: Baldessari, Jorge Javier. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; ArgentinaFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Bejerman, Nicolas Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Giolitti, Fabian. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Giolitti, Fabian. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Lenardon, Sergio Luis. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Lenardon, Sergio Luis. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria. Departamento de Biología Agrícola; Argentin
- …
