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2. Epidemiological insights into water and soil-mediatedtransmission of tomato mottle mosaic virusAna Vučurović, Jakob Brodarič, Irena Bajde, Miha Kitek, Nataša Mehle, 2026, original scientific article Abstract: Tomato mottle mosaic virus (ToMMV) poses a growing threat to tomato and pepper crops, yet its epidemiology remains largelyunexplored. This study aimed to investigate water- and soil-mediated transmission of ToMMV under controlled conditions. Theexperiment involved mechanical inoculation of tomato plants, which demonstrated that infectious ToMMV particles remainedviable in water up to 27 weeks at a 10−2 dilution. In hydroponic systems, ToMMV present in the nutrient solution caused systemicinfection in bait plants within 5–17 weeks, depending on the severity of root injury, while infection was not observed in plantswith intact roots even after 38 weeks of exposure. The transmission of the pathogen via irrigation was also confirmed in an ex-periment where seedlings and seed-derived plants grown in substrate (roots were not deliberately injured) were irrigated withToMMV-contaminated water, resulting in infection 6 and 10 weeks after the start of exposure, respectively. The soil-mediatedtransmission process was further verified by planting healthy seedlings and seeds into previously contaminated substrate, re-sulting in infection within a period of 3–18 weeks. These findings emphasise the need for upgrading integrated managementstrategies, including water quality monitoring and reliable, rapid diagnostics, to mitigate the spread of ToMMV in greenhouseproduction systems. To support the development of effective monitoring strategies, the study also assessed the performance oftwo isothermal amplification assays for potential on-site detection of ToMMV in water. A recombinase-polymerase amplification(RPA) assay exhibited sensitivity comparable to that of reverse transcription-quantitative PCR and reliably detected ToMMV incrude water samples without RNA extraction.
Keywords: RPA assay, RT- qPCR, survival, tomato, tomato mottle mosaic virus, water-linked epidemiology
Published in DiRROS: 22.01.2026; Views: 461; Downloads: 317
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3. Vertical transmission of tomato virusesNataša Mehle, Adrian Fox, Antonio Tiberini, Heiko Ziebell, 2025, independent scientific component part or a chapter in a monograph Abstract: The vertical transmission of tomato viruses through seeds and pollen is a significant yet often overlooked pathway for the persistence and global spread of these pathogens. This review provides a comprehensive synthesis of current knowledge on the mechanisms, epidemiological implications, and management strategies of vertically transmitted tomato viruses. While recent advances in diagnostic techniques such as high-throughput sequencing (HTS), have improved virus detection, key research gaps remain in understanding the molecular and ecological dynamics of seed and pollen transmission. The interaction between vertical and horizontal transmission modes complicates virus epidemiology, necessitating an integrated management approach that includes rigorous seed health testing, genetic resistance breeding, and biosecurity measures. Emerging threats, such as resistance-breaking virus strains and the impact of climate change on vector distribution, underscore the need for enhanced surveillance and stronger international regulatory cooperation. This review highlights the need for interdisciplinary research and collaboration to develop sustainable virus mitigation strategies. Future research priorities include optimizing detection methods, exploring next-generation breeding technologies, and strengthening international biosecurity frameworks to safeguard global tomato production against the growing threat of vertically transmitted viruses.
Keywords: Solanum lycopersicum, tomato, vertical virus transmission, high economic impact, seed-transmitted viruses, plant diseases, virology, biology
Published in DiRROS: 26.09.2025; Views: 822; Downloads: 413
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4. Tomato spotted wilt virus in tomato from Croatia, Montenegro and Slovenia: genetic diversity and evolutionDijana Škorić, Jelena Zindović, Dorotea Grbin, Patrik Pul, Vladan Božović, Paolo Margaria, Nataša Mehle, Anja Pecman, Zala Kogej Zwitter, Denis Kutnjak, Ana Vučurović, 2025, original scientific article Abstract: Tomato spotted wilt orthotospovirus (TSWV) is a major plant pathogen causing significant economic losses in tomato production worldwide. Understanding its genetic diversity and evolutionary mechanisms is crucial for effective disease management. This study analyzed TSWV isolates from symptomatic tomato plants collected across Croatia, Montenegro and Slovenia between 2020 and 2024. High-throughput sequencing (HTS) was employed to obtain whole-genome sequences, followed by phylogenetic analyses to assess genetic variability and relationships among isolates from these three countries and other isolates of worldwide geographic origin. Phylogenetic analyses placed all studied isolates within the L1-M3-S3 genotype, commonly associated with solanaceous crops in Europe. While Croatian and Slovenian isolates exhibited high genetic similarity, Montenegrin isolates clustered in a distinct subgroup, showing closer relationships to Asian and Mediterranean accessions. Despite the severe disease symptoms observed, no substitutions in the NSm protein associated with resistance-breaking (RB) phenotypes were detected. These findings suggest that additional virome components, environmental factors or so far unknown mechanism(s) may contribute to infection and disease severity in tomato and strongly support the need of continuous surveillance of TSWV genetic diversity in order to inform breeding programs and develop sustainable management strategies to mitigate future outbreaks.
Keywords: tomato, HTS, phylogeny, TSWV, plant virus
Published in DiRROS: 16.09.2025; Views: 703; Downloads: 368
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5. Chloroplast vesiculation and induced chloroplast vesiculation and senescence-associated gene 12 expression during tomato flower pedicel abscissionMagda Tušek-Žnidarič, Maja Zagorščak, Živa Ramšak, Katja Stare, Marko Chersicola, Maruša Pompe Novak, Aleš Kladnik, Marina Dermastia, 2025, original scientific article Abstract: Abscission is a tightly regulated process in which plants shed unnecessary, infected, damaged, or aging organs, as well as ripe fruits, through predetermined abscission zones in response to developmental, hormonal, and environmental signals. Despite its importance, the underlying mechanisms remain incompletely understood. This study highlights the deleterious effects of abscission on chloroplast ultrastructure in the cells of the tomato flower pedicel abscission zone, revealing spatiotemporal differential gene expression and key transcriptional networks involved in chloroplast vesiculation during abscission. Significant changes in chloroplast structure and vesicle formation were observed 8 and 14 h after abscission induction, coinciding with the differential expression of vesiculation-related genes, particularly with upregulation of Senescence-Associated Gene 12 (SAG12) and Chloroplast Vesiculation (CV). This suggests a possible vesicle transport of chloroplast degrading material for recycling by autophagy-independent senescence-associated vacuoles (SAVs) and CV-containing vesicles (CCVs). Ethylene signaling appears to be involved in the regulation of these processes, as treatment with a competitive inhibitor of ethylene action, 1-methylcyclopropene, delayed vesiculation, reduced the expression of SAG12, and increased expression of Curvature Thylakoid 1A (CURT1A). In addition, chloroplast vesiculation during abscission was associated with differential expression of photosynthesis-related genes, particularly those involved in light reactions, underscoring the possible functional impact of the observed structural changes. This work provides new insights into the molecular and ultrastructural mechanisms underlying abscission and offers potential new targets for agricultural or biotechnological applications.
Keywords: abscission, chloroplast vesiculation, CURT1A, CV-containing vesicle, senescence-associated vacuole, ethylene, gene expression, tomato flower pedicel
Published in DiRROS: 10.01.2025; Views: 1321; Downloads: 840
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6. 1-aminocyclopropane-1-carboxylate oxidase induction in tomato flower pedicel phloem and abscission related processes are differentially sensitive to ethyleneMarko Chersicola, Aleš Kladnik, Magda Tušek-Žnidarič, Tanja Mrak, Kristina Gruden, Marina Dermastia, 2017, original scientific article Abstract: Ethylene has impact on several physiological plant processes, including abscission, during which plants shed both their vegetative and reproductive organs. Cell separation and programmed cell death are involved in abscission, and these have also been correlated with ethylene action. However, the detailed spatiotemporal pattern of the molecular events during abscission remains unknown. We examined the expression of two tomato ACO genes, LeACO1, and LeACO4 that encode the last enzyme in ethylene biosynthesis, 1-aminocyclopropane-1-carboxylate oxidase (ACO), together with the expression of other abscission-associated genes involved in cell separation and programmed cell death, during a period of 0–12 h after abscission induction in the tomato flower pedicel abscission zone and nearby tissues. In addition, we determined their localization in specific cell layers of the flower pedicel abscission zone and nearby tissues obtained by laser microdissection before and 8 h after abscission induction. The expression of both ACO genes was localized to the vascular tissues in the pedicel. While LeACO4 was more uniformly expressed in all examined cell layers, the main expression site of LeACO1 was in cell layers just outside the abscission zone in its proximal and distal part. We showed that after abscission induction, ACO1 protein was synthesized in phloem companion cells, in which it was localized mainly in the cytoplasm. Samples were additionally treated with 1-methylcyclopropene (1-MCP), a competitive inhibitor of ethylene actions, and analyzed 8 h after abscission induction. Cell-layer-specific changes in gene expression were observed together with the specific localization and ethylene sensitivity of the hallmarks of cell separation and programmed cell death. While treatment with 1-MCP prevented separation of cells through inhibition of the expression of polygalacturonases, which are the key enzymes involved in degradation of the middle lamella, this had less impact on the occurrence of different kinds of membrane vesicles and abscission-related programmed cell death. In the flower pedicel abscission zone, the physical progressions of cell separation and programmed cell death are perpendicular to each other and start in the vascular tissues.
Keywords: abscission, ACO, cell separation, ethylene, laser microdissection, programmed cell death, tomato, ultrastructure
Published in DiRROS: 24.07.2024; Views: 1250; Downloads: 1132
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7. High-throughput sequencing facilitates characterisation of a ʺforgottenʺ plant virus : the case of a henbane mosaic virus infecting tomatoAnja Pecman, Denis Kutnjak, Nataša Mehle, Magda Tušek-Žnidarič, Ion Gutiérrez-Aguirre, Patricija Pirnat, Ian Adams, Neil Boonham, Maja Ravnikar, 2018, original scientific article Abstract: High-throughput sequencing has dramatically broadened the possibilities for plant virus research and diagnostics, enabling discovery of new or obscure viruses, and virus strains and rapid sequencing of their genomes. In this research, we employed high-throughput sequencing to discover a new virus infecting tomato, Henbane mosaic virus (Potyvirus, Potyviridae), which was first discovered at the beginning of 20th century in the United Kingdom in cultivated henbane. A field tomato plant with severe necrotic symptoms of unknown etiology was sampled in Slovenia and high-throughput sequencing analysis using small RNA and ribosomal RNA depleted total RNA approaches revealed a mixed infection with Potato virus M (Carlavirus, Betaflexiviridae), Southern tomato virus (Amalgavirus, Amalgamaviridae) and henbane mosaic virus in the sample. The complete genomic sequence of henbane mosaic virus was assembled from the sequencing reads. By re-inoculation of the infected material on selected test plants, henbane mosaic virus was isolated and a host range analysis was performed, demonstrating the virus was pathogenic on several plant species. Due to limited metadata in public repositories, the taxonomic identification of the virus isolate was initially putative. Thus, in the next step, we used small RNA sequencing to determine genomic sequences of four historic isolates of the virus, obtained from different virus collections. Phylogenetic analyses performed using this new sequence information enabled us to taxonomically position Henbane mosaic virus as a member of the Potyvirus genus within the chili veinal mottle virus phylogenetic cluster and define the relationship of the new tomato isolate with the historic ones, indicating the existence of at least four putative strains of the virus. The first detection of henbane mosaic virus in tomato and demonstration of its pathogenicity on this host is important for plant protection and commercial tomato production. Since the virus was initially present in a mixed infection, and its whole genome was not sequenced, it has probably been overlooked in routine diagnostics. This study confirms the applicability of a combination of high-throughput sequencing and classic plant virus characterization methods for identification and phylogenetic classification of obscure viruses and historical viral isolates, for which no or limited genome sequence data is available.
Keywords: henbane mosaic virus, Tomato, high-throughput sequencing, host range analysis, phylogeny, Potyvirus
Published in DiRROS: 24.07.2024; Views: 1833; Downloads: 908
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8. Detection of four new tomato viruses in Serbia using post hoc high-throughput sequencing analysis of samples from a large-scale field surveyAna Vučurović, Denis Kutnjak, Nataša Mehle, Ivana Stanković, Anja Pecman, Aleksandra Bulajić, Branka Krstić, Maja Ravnikar, 2021, original scientific article Abstract: Tomato production worldwide is affected by numerous plant virus species. The early and accurate detection of viruses is a critical step for disease control. However, the simultaneous detection of the most known tomato viruses can be difficult because of the high number and diversity of tomato-infecting viruses. Here, we have identified four new viruses in Serbia by applying target-independent small RNA high-throughput sequencing (HTS). HTS was applied on pools of samples and separate samples, in total comprising 30 tomato samples that exhibited (severe) virus-like symptoms and were collected in Serbia during three annual surveys (2011 to 2013). These samples had previously tested negative for the presence of 16 tomato viruses using targeted detection methods. Three divergent complete genome sequences of Physostegia chlorotic mottled virus were obtained from different localities, indicating for the first time that this virus is widespread in Serbia and might represent an emergent viral pathogen of tomato. The tomato torrado virus was detected at one locality with devastating yield losses. The southern tomato virus was detected at two localities, and the spinach latent virus was detected at one locality. In addition, we detected the presence of one already-known virus in Serbia, the tomato spotted wilt orthotospovirus. All the HTS results were subsequently confirmed by targeted detection methods. In this study, the successful application of post hoc HTS testing of a limited number of pooled samples resulted in the discovery of new viruses. Thus, our results encourage the use of HTS in research and diagnostic laboratories, including laboratories that have limited resources to resolve disease etiology.
Keywords: viruses, tomato, detection, identification
Published in DiRROS: 19.07.2024; Views: 1462; Downloads: 922
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9. Development and validation of a one-step reverse transcription real-time PCR assay for simultaneous detection and identification of tomato mottle mosaic virus and tomato brown rugose fruit virusAntonio Tiberini, Ariana Manglli, Anna Taglienti, Ana Vučurović, Jakob Brodarič, Luca Ferretti, Marta Luigi, Andrea Gentili, Nataša Mehle, 2022, original scientific article Abstract: Tobamovirus species represent a threat to solanaceous crops worldwide, due to their extreme stability and because they are seed borne. In particular, recent outbreaks of tomato brown rugose fruit virus in tomato and pepper crops led to the establishment of prompt control measures, and the need for reliable diagnosis was urged. Another member of the genus, tomato mottle mosaic virus, has recently gained attention due to reports in different continents and its common features with tomato brown rugose fruit virus. In this study, a new real-time RT-PCR detection system was developed for tomato brown rugose fruit virus and tomato mottle mosaic virus on tomato leaves and seeds using TaqMan chemistry. This test was designed to detect tomato mottle mosaic virus by amplifying the movement protein gene in a duplex assay with the tomato brown rugose fruit virus target on the CP-3’NTR region, which was previously validated as a single assay. The performance of this test was evaluated, displaying analytical sensitivity 10−5–10−6-fold dilution for seeds and leaves, respectively, and good analytical specificity, repeatability, and reproducibility. Using the newly developed and validated test, tomato brown rugose fruit virus detection was 100% concordant with previously performed analyses on 106 official samples collected in 2021 from different continents.
Keywords: real-time PCR, tomato mottle mosaic virus, tomato brown rugose fruit virus, leaves detection, seeds detections, performance criteria
Published in DiRROS: 16.07.2024; Views: 1819; Downloads: 830
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10. Transcriptional and epigenetic changes during tomato yellow leaf curl virus infection in tomatoBeatriz Romero-Rodríguez, Marko Petek, Chen Jiao, Maja Križnik, Maja Zagorščak, Zhangjun Fei, Eduardo Rodríguez Bejarano, Kristina Gruden, Araceli G. Castillo, 2023, original scientific article Abstract: Background Geminiviruses are DNA plant viruses that cause highly damaging diseases affecting crops worldwide. During the infection, geminiviruses hijack cellular processes, suppress plant defenses, and cause a massive reprogramming of the infected cells leading to major changes in the whole plant homeostasis. The advances in sequencing technologies allow the simultaneous analysis of multiple aspects of viral infection at a large scale, generating new insights into the molecular mechanisms underlying plant-virus interactions. However, an integrative study of the changes in the host transcriptome, small RNA profile and methylome during a geminivirus infection has not been performed yet. Using a time-scale approach, we aim to decipher the gene regulation in tomato in response to the infection with the geminivirus, tomato yellow leaf curl virus (TYLCV). Results We showed that tomato undergoes substantial transcriptional and post-transcriptional changes upon TYLCV infection and identified the main altered regulatory pathways. Interestingly, although the principal plant defense-related processes, gene silencing and the immune response were induced, this cannot prevent the establishment of the infection. Moreover, we identified extra- and intracellular immune receptors as targets for the deregulated microRNAs (miRNAs) and established a network for those that also produced phased secondary small interfering RNAs (phasiRNAs). On the other hand, there were no significant genome-wide changes in tomato methylome at 14 days post infection, the time point at which the symptoms were general, and the amount of viral DNA had reached its maximum level, but we were able to identify differentially methylated regions that could be involved in the transcriptional regulation of some of the differentially expressed genes. Conclusion We have conducted a comprehensive and reliable study on the changes at transcriptional, post-transcriptional and epigenetic levels in tomato throughout TYLCV infection. The generated genomic information is substantial for understanding the genetic, molecular and physiological changes caused by TYLCV infection in tomato.
Keywords: geminivirus, TYLCV, tomato, transcriptome, miRNA
Published in DiRROS: 15.07.2024; Views: 1342; Downloads: 771
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