Search Results (85)

Saffron (Crocus sativus L.) is a vegetatively propagated crop of high economic and cultural value, potentially affected by viral infections that may impact its productivity. Despite Iran’s dominance in global saffron production, knowledge of its virome remains limited. In this study, we conducted the first nationwide virome survey of saffron in Iran employing a high-throughput sequencing (HTS) approach on pooled samples obtained from eleven provinces in Iran and one location in Afghanistan. Members of three virus families were detected—Potyviridae (Potyvirus), Solemoviridae (Polerovirus), and Geminiviridae (Mastrevirus)—as well as one satellite from the family Alphasatellitidae (Clecrusatellite). A novel Potyvirus, tentatively named saffron Iran virus (SaIRV) and detected in three provinces, shares less than 68% nucleotide identity with known Potyvirus species, thus meeting the ICTV criteria for designation as a new species. Genetic diversity analyses revealed substantial intrapopulation SNP variation but no clear geographical clustering. Among the two wild Crocus species sampled, only Crocus speciosus harbored turnip mosaic virus. Virome network and phylogenetic analyses confirmed widespread viral circulation likely driven by corm-mediated propagation. Our findings highlight the need for targeted certification programs and biological characterization of key viruses to mitigate potential impacts on saffron yield and quality. Full article

Tomato yellow leaf curl disease poses one of the most severe threats to tomato production worldwide. This disease is associated with a group of closely related tomato yellow leaf curl viruses. These viruses can be transmitted by the sweet potato whitefly (Bemisia tabaci) in a persistent-circulative mode. Virus particles can infect the midgut and filter chamber of whiteflies feeding on infected plants, circulate in the hemolymph, and eventually infect the primary salivary gland (PSG) of whiteflies. Later, the whiteflies feed on healthy plants, and viral particles are introduced into the plants through their saliva. Virus–vector interactions play a crucial role in the efficiency and dynamics of virus transmission. In this study, we assessed the effects of the acquisition time and viral load of source plants on infections of two tomato begomoviruses, tomato yellow leaf curl Thailand virus (TYLCTHV) and tomato leaf curl Taiwan virus (ToLCTV), in B. tabaci Middle East–Asia Minor 1. We found that more viruses were acquired and accumulated in the whitefly midgut and PSG before reaching a plateau when the acquisition time increased and when the source plant had a higher viral load. The midgut and PSG acquired and accumulated more TYLCTHV than ToLCTV with the same acquisition time and regardless of the viral loads in coinfected source plants. These results not only help us to understand virus–vector interactions but also help in developing integrated disease management strategies. Full article

Tomato yellow leaf curl virus (TYLCV), tomato leaf curl New Delhi virus (ToLCNDV), and tomato chlorosis virus (ToCV) are emerging viruses that cause significant damage to tomato (Solanum lycopersicum). TYLCV and ToLCNDV are single-stranded DNA viruses from the genus Begomovirus, family Geminiviridae, while ToCV is an RNA virus from the genus Crinivirus (family Closteroviridae). These viruses share overlapping geographic ranges, vectors (the whitefly Bemisia tabaci), and host plants, making mixed infections common. This study investigated interactions between TYLCV and ToLCNDV and between ToLCNDV and ToCV in mixed infections of susceptible and TYLCV-resistant tomato genotypes. We evaluated infection, disease development, trans-replication of genome components, and genetic exchange. Our results showed no significant synergistic or antagonistic interactions, complementation, or interference between the viruses. TYLCV resistance in tomato genotypes remained stable. The DNA-B component of ToLCNDV exhibited impaired functionality and was not complemented by TYLCV. No evidence was found that the crinivirus tomato chlorosis virus (ToCV) enhances ToLCNDV infection, suggesting limited interactions despite shared vectors. Genetic exchange was detected in defective DNA (def-DNA) molecules using high-throughput sequencing (HTS), indicating potential genetic interactions between these viruses. These findings suggest that mixed infections do not pose immediate concerns for increased pathogenicity but highlight the ecological implications of genetic exchange, warranting further study of the evolutionary consequences of such interactions in mixed-virus environments. Full article

Cotton leaf curl Kokhran virus-Burewala (CLCuKoV-Bur) has a circular single-stranded ssDNA genome of 2759 nucleotides in length and belongs to the genus Begomovirus (family, Geminiviridae). CLCuKoV-Bur causes cotton leaf curl disease (CLCuD) and is transmitted by the whitefly Bemisis tabaci cryptic species. Monopartite begomoviruses encode five open reading frames (ORFs). CLCuKoV-Bur replicates through a dsDNA intermediate. Five open reading frames (ORFs) are organized in the small circular, single-stranded (ss)-DNA genome of CLCuKoV-Bur (2759 bases). RNA interference (RNAi) is a naturally occurring process that has revolutionized the targeting of gene regulation in eukaryotic organisms to combat virus infection. The aim of this study was to elucidate the potential binding attractions of cotton-genome-encoded microRNAs (Gossypium hirsutum-microRNAs, ghr-miRNAs) on CLCuKoV-Bur ssDNA-encoded mRNAs using online bioinformatics target prediction tools, RNA22, psRNATarget, RNAhybrid, and TAPIR. Using this suite of robust algorithms, the predicted repertoire of the cotton microRNA-binding landscape was determined for a CLCuKoV-Bur consensus genome sequence. Previously experimentally validated cotton (Gossypium hirsutum L.) miRNAs (n = 80) were selected from a public repository miRNA registry miRBase (v22) and hybridized in silico into the CLCuKoV-Bur genome (AM421522) coding and non-coding sequences. Of the 80 ghr-miRNAs interrogated, 18 ghr-miRNAs were identified by two to four algorithms evaluated. Among them, the ghr-miR399d (accession no. MIMAT0014350), located at coordinate 1747 in the CLCuKoV-Bur genome, was predicted by a consensus or “union” of all four algorithms and represents an optimal target for designing an artificial microRNA (amiRNA) silencing construct for in planta expression. Based on all robust predictions, an in silico ghr-miRNA-regulatory network was developed for CLCuKoV-Bur ORFs using Circos software version 0.6. These results represent the first predictions of ghr-miRNAs with the therapeutic potential for developing CLCuD resistance in upland cotton plants. Full article

Single-stranded DNA (ssDNA) viruses are a diverse group of pathogens with broad host range, including bacteria, archaea, protists, fungi, plants, invertebrates, and vertebrates. Their small compact genomes have evolved to encode multiple proteins. This review focuses on the structure and functional diversity of the icosahedral capsids across the ssDNA viruses. To date, X-ray crystallography and cryo-electron microscopy structural studies have provided detailed capsid architectures for 8 of the 35 ssDNA virus families, illustrating variations in assembly mechanisms, symmetry, and structural adaptations of the capsid. However, common features include the conserved jelly-roll motif of the capsid protein and strategies for genome packaging, also showing evolutionary convergence. The ever-increasing availability of genomic sequences of ssDNA viruses and predictive protein modeling programs, such as using AlphaFold, allows for the extension of structural insights to the less-characterized families. Therefore, this review is a comparative analysis of the icosahedral ssDNA virus families and how the capsid proteins are arranged with different tessellations to form icosahedral spheres. It summarizes the current knowledge, emphasizing gaps in the structural characterization of the ssDNA capsidome, and it underscores the importance of continued exploration to understand the molecular underpinnings of capsid function and evolution. These insights have implications for virology, molecular biology, and therapeutic applications. Full article

Grapevine red blotch is an emerging disease that threatens vineyard productions in North America. Grapevine red blotch virus (GRBV, species Grablovirus vitis, genus Grablovirus, family Geminiviridae), the causal agent of red blotch disease, is transmitted by Spissistilus festinus (Hemiptera: Membracidae) in a circulative, non-propagative mode. To gain new insight into GRBV-S. festinus interactions, we delved into vertical transmission and documented a lack of transovarial transmission. In addition, we investigated S. festinus sex differences in the horizontal transmission of GRBV by creating small arenas with 30 detached trifoliates of common snap bean, an experimental host of GRBV, and a preferred feeding host of S. festinus. Tracking the movement of viruliferous males, females, or a combination of the two sexes over two weeks in replicated experiments demonstrated that male S. festinus dispersed more than females with specimens of both sexes predominantly grouping together on trifoliates spatially surrounding the trifoliate onto which they were released. These behaviors resulted in a greater rate of GRBV transmission by S. festinus males (17%, 20 of 120) than females (4%, 5 of 120) or mixed-sex cohorts (9%, 17 of 180). In arenas with aviruliferous S. festinus and one (single) or four (hotspot) GRBV-infected trifoliates out of 30 total trifoliates, a higher GRBV transmission rate by males was confirmed in both single infection (50%, 30 of 60) and hotspot infection (83%, 50 of 60) arenas than by females in single infection (35%, 21 of 60) and hotspot infection (67%, 40 of 60) arenas. These findings highlighted sex-associated differences in the transmission of GRBV by S. festinus and a positive correlation between the initial virus prevalence and the rate of transmission. Finally, the secondary spread of GRBV resulted primarily from S. festinus dispersal by walking or jumping. Together, these unique GRBV transmission features support the need to characterize dispersal behaviors of S. festinus in vineyard ecosystems. Full article

Geminiviridae are ssDNA plant viruses whose control has both economical and agricultural importance. Their capsids assemble into two distinct architectural forms: (i) a T = 1 icosahedral and (ii) a unique twinned quasi-isometric capsid. Described here are the high-resolution structures of both forms of the maize streak virus using cryo-EM. A comparison of these two forms provides details of the coat protein (CP) and CP–CP and CP–genome interactions that govern the assembly of the architecture of the capsids. Comparative analysis of other representative members of Geminiviridae reveals structural conservation of 60–95% compared to a sequence similarity of 21–30%. This study provides a structural atlas of these plant pathogens and suggests possible antiviral-targetable regions of these capsids. Full article

Sida mottle virus (SiMoV) and Sida micrantha mosaic virus (SiMMV) are major Brazilian begomoviruses (Geminiviridae). However, the range of DNA–A identity of isolates of these viruses (81–100%) is not in agreement with the current criteria for Begomovirus species demarcation (<91%). To clarify this putative classification problem, we performed a comprehensive set of molecular analyses with all 53 publicly available isolates (with complete DNA–A genomes) designated as either SiMoV or SiMMV (including novel isolates obtained herein from nationwide metagenomics-based studies). Two well-defined phylogenetic clusters were identified. The SiMMV complex (n = 47) comprises a wide range of strains (with a continuum variation of 88.8–100% identity) infecting members of five botanical families (Malvaceae, Solanaceae, Fabaceae, Oxalidaceae, and Passifloraceae). The SiMoV group now comprises eight isolates (90–100% identity) restricted to Malvaceae hosts, including one former reference SiMMV isolate (gb|NC_077711) and SP77 (gb|FN557522; erroneously named as “true SiMMV”). Iteron analyses of metagenomics-derived information allowed for the discovery of the missing DNA–B cognate of SiMoV (93.5% intergenic region identity), confirming its bipartite nature. Henceforth, the correct identification of SiMoV and SiMMV isolates will be a crucial element for effective classical and biotech resistance breeding of the viral host species. Full article

Beet curly top virus (BCTV, curtovirus, geminiviridae) causes one of the most economically significant viral diseases in crops in the Western United States and is transmitted only by the beet leafhopper (Circulifer tenellus) in a non-propagative circulative manner. A better understanding of how this virus overcomes insect vector cellular barriers is essential to understanding virus–vector interactions. The distribution of BCTV in its beet leafhopper vector was investigated using immunofluorescence confocal laser scanning microscope analysis (iCLSM) on the whole-mount-dissected organs of leafhoppers. BCTV was localized in several lobes of the principal salivary glands, filter chamber, anterior midgut, and mid midgut, suggesting the occurrence of midgut and salivary gland barriers to BCTV transmission in its vector C. tenellus. This study also investigated the distribution of the chaperon GroEL homolog protein produced by primary endosymbiotic bacteria within the beet leafhopper, which is believed to indirectly affect viral transmission by enhancing insect immunity and resistance to viruses. GroEL was identified in leafhopper salivary glands lobes, the stylet, salivary canal, the filter chamber, and the Malpighian tubule. This is the first work to visualize the localization of a curtovirus within its beet leafhopper vector. Together, these results can help understand ssDNA virus–vector relationships, including cellular transmission barriers and other vector protein components. Full article

Mulberry crinkle leaf virus (MCLV), identified in mulberry plants (Morus alba L.), is a member of the genus Mulcrilevirus in the family Geminiviridae. The functions of the V2 protein encoded by MCLV remain unclear. Here, Agrobacterium-mediated infectious clones of a wild-type MCLV vII (MCLV^WT) and two V2 mutant MCLV vIIs, including MCLV^mV2 (with a mutation of the start codon of the V2 ORF) and MCLV^dV2 (5′-end partial deletion of the V2 ORF sequence), were constructed to investigate the roles of V2 both in planta and at the cellular level. Although all three constructs (pCA-1.1MCLV^WT, pCA-MCLV^mV2, and pCA-MCLV^dV2) were able to infect both natural host mulberry plants and experimental tomato plants systematically, the replication of the MCLV^mV2 and MCLV^dV2 genomes in these hosts was significantly reduced compared to that of MCLV^WT. Similarly, the accumulation of MCLV^mV2 and MCLV^dV2 in protoplasts of Nicotiana benthamiana plants was significantly lower than that of MCLV^WT either 24 h or 48 h post-transfection. A complementation experiment further confirmed that the decreased accumulation of MCLV in the protoplasts was due to the absence of V2 expression. These results revealed that MCLV-encoded V2 greatly enhances the level of MCLV DNA accumulation and is designated the replication enhancer protein of MCLV. Full article

Begomoviruses, transmitted by the whitefly Bemisia tabaci, pose significant threats to global agriculture due to their severe impact on various crops. Among the satellite molecules associated with begomoviruses, betasatellites play a crucial role in enhancing disease severity and yield losses. The spread and association of these molecules with helper viruses in host plants are thus matters of concern. Here, we focus on the propagation of betasatellites and, more specifically, on their transfer between different helper viruses and hosts through vector transmission. Our results show that the cotton leaf curl Gezira betasatellite (CLCuGeB), initially acquired with its helper virus cotton leaf curl Gezira virus (CLCuGeV) from an okra plant, can be transmitted and assisted by a different helper virus, tomato yellow leaf curl virus (TYLCV), in a different host plant (tomato plant). The new association can be formed whether TYLCV and CLCuGeB encounter each other in a host plant previously infected with TYLCV or in whiteflies having acquired the different components separately. Our findings reveal two pathways by which betasatellites can be transferred between helper viruses and host plants and highlight the ability of betasatellites to spread in begomovirus-infected environments. Full article

Wheat dwarf virus (WDV, genus Mastrevirus, family Geminiviridae) is one of the causal agents of wheat viral disease, which severely impacts wheat production in most wheat-growing regions in the world. Currently, there is little information about natural resistance against WDV in common wheat germplasms. CRISPR/Cas9 technology is being utilized to manufacture transgenic plants resistant to different diseases. In the present study, we used the CRISPR/Cas9 system targeting overlapping regions of coat protein (CP) and movement protein (MP) (referred to as CP/MP) or large intergenic region (LIR) in the wheat variety ‘Fielder’ to develop resistance against WDV. WDV-inoculated T₁ progenies expressing Cas9 and sgRNA for CP/MP and LIR showed complete resistance against WDV and no accumulation of viral DNA compared with control plants. Mutation analysis revealed that the CP/MP and LIR targeting sites have small indels in the corresponding Cas9-positive plants. Additionally, virus inhibition and indel mutations occurred in T₂ homozygous lines. Together, our work gives efficient results of the engineering of CRISPR/Cas9-mediated WDV resistance in common wheat plants, and the specific sgRNAs identified in this study can be extended to utilize the CRISPR/Cas9 system to confer resistance to WDV in other cereal crops such as barley, oats, and rye. Full article

The diversity of Geminiviridae and Alphasatellitidae species in tomatoes was assessed via high-throughput sequencing of 154 symptomatic foliar samples collected from 2002 to 2017 across seven Brazilian biomes. The first pool (BP1) comprised 73 samples from the North (13), Northeast (36), and South (24) regions. Sixteen begomoviruses and one Topilevirus were detected in BP1. Four begomovirus-like contigs were identified as putative novel species (NS). NS#1 was reported in the semi-arid (Northeast) region and NS#2 and NS#4 in mild subtropical climates (South region), whereas NS#3 was detected in the warm and humid (North) region. The second pool (BP2) comprised 81 samples from Southeast (39) and Central–West (42) regions. Fourteen viruses and subviral agents were detected in BP2, including two topileviruses, a putative novel begomovirus (NS#5), and two alphasatellites occurring in continental highland areas. The five putative novel begomoviruses displayed strict endemic distributions. Conversely, tomato mottle leaf curl virus (a monopartite species) displayed the most widespread distribution occurring across the seven sampled biomes. The overall diversity and frequency of mixed infections were higher in susceptible (16 viruses + alphasatellites) in comparison to tolerant (carrying the Ty–1 or Ty–3 introgressions) samples, which displayed 9 viruses. This complex panorama reinforces the notion that the tomato-associated Geminiviridae diversity is yet underestimated in Neotropical regions. Full article

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. Full article

Plants can respond to insect infestation and virus infection by inducing plant defenses, generally mediated by phytohormones. Moreover, plant defenses alter host quality for insect vectors with consequences for the spread of viruses. In agricultural settings, other organisms commonly interact with plants, thereby inducing plant defenses that could affect plant–virus–vector interactions. For example, plant defenses induced by omnivorous insects can modulate insect behavior. This study focused on tomato yellow leaf curl virus (TYLCV), a plant virus of the family Geminiviridae and genus Begomovirus. It is transmitted in a persistent circulative manner by the whitefly Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae), posing a global threat to tomato production. Mirids (Hemiptera: Miridae) are effective biological control agents of B. tabaci, but there is a possibility that their omnivorous nature could also interfere with the process of virus transmission. To test this hypothesis, this study first addressed to what extent the mirid bug Dicyphus hesperus Knight induces plant defenses in tomato. Subsequently, the impact of this plant–omnivore interaction on the transmission of TYLCV was evaluated. Controlled cage experiments were performed in a greenhouse setting to evaluate the impact of mirids on virus transmission and vector acquisition by B. tabaci. While we observed a reduced number of whiteflies settling on plants exposed to D. hesperus, the plant defenses induced by the mirid bug did not affect TYLCV transmission and accumulation. Additionally, whiteflies were able to acquire comparable amounts of TYLCV on mirid-exposed plants and control plants. Overall, the induction of plant defenses by D. hesperus did not influence TYLCV transmission by whiteflies on tomato. Full article