1. Program strokovnih nalog s področja zdravstvenega varstva rastlin : naloge zdravstvenega varstva rastlin po javnem pooblastiluNataša Mehle, Manca Pirc, Špela Alič, Irena Bajde, Aleksander Benčič, Aleš Blatnik, Alexandra Bogožalec Košir, Jakob Brodarič, Veronika Bukvič, Marjana Camloh, Ana Dolinar Češarek, Vesna Dukić, Sara Fišer, Vladimir Grujić, Tjaša Jakomin, Denis Kutnjak, Janja Matičič, Anja Pecman, Špela Prijatelj-Novak, Nina Prezelj, Neža Turnšek, Ana Vučurović, Tanja Dreo, 2026, končno poročilo o rezultatih raziskav Ključne besede: diagnostika, virusi, bakterije, fitoplazme, viroidi, varstvo rastlin
Objavljeno v DiRROS: 12.02.2026; Ogledov: 357; Prenosov: 0 |
2. Key insights from nanopore high-throughput sequencing training : 14. 1. 2026, WageningenAnja Pecman, Veronika Bukvič, Ana Vučurović, Denis Kutnjak, Nataša Mehle, 2026, drugo učno gradivo Ključne besede: HTS, workshop, nanopores
Objavljeno v DiRROS: 02.02.2026; Ogledov: 125; Prenosov: 42
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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, izvirni znanstveni članek Povzetek: 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.
Ključne besede: tomato, HTS, phylogeny, TSWV, plant virus
Objavljeno v DiRROS: 16.09.2025; Ogledov: 478; Prenosov: 218
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5. Annual (2024) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)Jens H. Kuhn, Scott Adkins, Sergey V. Alkhovsky, Wenxia An, Tatjana Avšič-Županc, María A. Ayllón, Katarina Bačnik, Justin Bahl, Anne Balkema-Buschmann, Matthew J. Ballinger, Ion Gutiérrez-Aguirre, Denis Kutnjak, Nataša Mehle, Anja Pecman, Maja Ravnikar, Ana Vučurović, 2025, izvirni znanstveni članek Povzetek: In April 2024, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was expanded by 1 new order, 1 new family, 6 new subfamilies, 34 new genera and 270 new species. One class, two orders and six species were renamed. Seven families and 12 genera were moved; ten species were renamed and moved; and nine species were abolished. This article presents the updated taxonomy of Negarnaviricota as currently accepted by the ICTV, providing an essential annual update on the classification of members of this phylum that deepen understandings of their evolution, and supports critical public health measures for virus identification and tracking.
Ključne besede: Aliusviridae, Arenaviridae, articulaviral, Articulavirales, Artoviridae, Aspiviridae, Bornaviridae, bunyaviral, Bunyavirales, Bunyaviricetes, bunyavirus, Crepuscuviridae, Discoviridae, Elliovirales, Filoviridae, Fimoviridae, Goujianvirales, Hantaviridae, Hareavirales, International Committee on Taxonomy of Viruses (ICTV), jingchuviral, Jingchuvirales, Konkoviridae, Lispiviridae, megaclassification, megataxonomy, mononegaviral, Mononegavirales, muviral, Muvirales, Mymonaviridae, Myriaviridae, naedreviral, Naedrevirales, Nairoviridae, Natareviridae, negarnaviricot, Negarnaviricota, Nyamiviridae, Orthomyxoviridae, Orthornavirae, Paramyxoviridae, Peribunyaviridae, Phasmaviridae, Phenuiviridae, Pneumoviridae, Rhabdoviridae, Riboviria, Sunviridae, Tenuivirus, Tosoviridae, Tospoviridae, Tulasviridae, virus classification, virus nomenclature, virus taxonomy, virology
Objavljeno v DiRROS: 24.06.2025; Ogledov: 662; Prenosov: 455
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6. Virome scanning of pear germplasm collections identifies a new Velarivirus and extends thegeographical spread of three other pear virusesNuria Fontdevila Pareta, Carole Gailly, Arnaud G. Blouin, Beatrix Buchmann, Markus Buenter, Thierry Candresse, Nathalie Dubuis, Denis Kutnjak, Marc Lateur, Anja Pecman, Stéphan Steyer, Sébastien Massart, 2025, izvirni znanstveni članek Povzetek: In this study, an extensive virome investigation was performed on a germplasm collection of pear trees (Pyrus communis L.) from the Walloon Agricultural Research Centre (Gembloux, Belgium). In total,128 pear trees samples were analyzed as pools using high-throughput sequencing (HTS) techniques, and/or tested individually for targeted viruses by RT-PCR. During the virome survey, a novel velarivirus was identified in several asymptomatic trees while four known viruses were detected. Bioinformatics tools were used to assemble the genome of the new virus. The pear germplasm collection from Kozjanski Park (Slovenia) and a viral collection from Agroscope (Nyon, Switzerland) were also surveyed for the new pear virus and for three known viruses (CiVA, ARWV-1, and ARWV-2) to study their prevalence and geographic distribution. In Belgium, the new velarivirus was detected by RT-PCR in six of the 99 sampled trees (6%) and citrus virus A (CiVA) in 49 (49%) of them; in Slovenia four of the six trees sampled (67%) were positive for CiVA; and in Switzerland four of the nine trees sampled (44%) were positive for CiVA and 1 (11%) for apple rubbery wood virus 1 and 2 (ARWV-1 and -2). This study, combined pooled HTS analyses to maximize the number of germplasm tested and targeted RT-PCR tests on individual samples for accurate detection. It reports and describes a new velarivirus discovered in pear trees and first detections of CiVA in Belgium, Switzerland and Slovenia, and ARWV-1 and -2 in Switzerland.
Ključne besede: virome, plant virus, pear, velarivirus, high-throughput sequencing, citrus virus A, apple rubbery wood virus 1, apple rubbery wood virus 2, pyrus virus A
Objavljeno v DiRROS: 08.05.2025; Ogledov: 841; Prenosov: 590
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7. First report of watermelon crinkle leaf-associated virus 1 (WCLaV-1) and WCLaV-2 in watermelon in SloveniaAna Vučurović, Irena Bajde, Jakob Brodarič, Anja Pecman, Zala Kogej Zwitter, Veronika Bukvič, Nejc Jakoš, Denis Kutnjak, Mojca Rot, Nataša Mehle, 2025, drugi znanstveni članki Povzetek: In July 2024, a pooled leaf sample (D760/24) was collected from several plants of three watermelon cultivars (Citrullus lanatus cvs. Crimson Sweet, Asahi Miyako Hybrid F1 and Top Gun) grown in an open field (approx. 0.5ha) in Dombrava, Slovenia. The plants which were included in the pooled sample showed virus-like symptoms, such as leaf mosaic, wilting and necrosis (eXtra Supplementary material Fig. S1). The disease incidence was estimated at 10%. DNA and RNA were extracted following Mehle et al. (2013) and RNeasy Plant Mini Kit (Qiagen, Germany) protocols, respectively. The sample was tested positive by reverse-transcription (RT)-PCR for watermelon crinkle leaf-associated virus 1 (WCLaV-1) and WCLaV-2 ( Hernandez et al. 2021) and negative for other viruses (details on viruses tested and primers used are available in eXtra Table S1). The obtained amplicons of expected sizes of WCLaV-1 and WCLaV-2 movement protein (MP) and RNA-dependent RNA polymerase (RdRp) genes (eXtra Fig S2) were then subjected to Sanger sequencing (Eurofins Genomics, Germany) and BLAST analysis. The MP (PQ570004, PQ570006) and the RdRp (PQ570005, PQ570007) sequences exhibited 100% identity with multiple accessions of WCLaV-1, such as PP792977 and PP792976, and WCLaV-2, such as LC636073 and LC636074. Illumina high-throughput sequencing (HTS, Novogene, Germany, NovaSeq X Plus, PE150) identified WCLaV-1 (PV012703-04) and WCLaV-2 (PV012705-06) reads, along with cucumis melo amalgavirus 1 (CmAV1, PV012707) and solanum nigrum ilarvirus 1 reads (insufficient reads to reconstruct genome segments, it may originate from pollen contamination of nearby infected plants in the field (Rivarez et al. 2023)). HTS data were analyzed in CLC Genomics Workbench v. 24 (Qiagen, USA) using the pipeline by (Pecman et al. 2022). Consensus genome sequences were reconstructed by iterative read mapping to the most similar reference sequence of the virus obtained from NCBI GenBank. To check for WCLaVs in watermelon seeds sold in Slovenia, we tested five seed samples from Sugar Baby, Crimstar F1, and Crimson Sweet (three lots) by RT-PCR. We also tested four leaf samples from plants grown from these seeds at 3-5 true leaves stage. Both viruses were found in all seed and leaf extracts. However, mechanical inoculations with the sap of two samples (plants grown from infected seed sample and sample D760/24) on several commonly used indicator plants including Chenopodium quinoa, Capsicum annuum, Nicotiana clevelandii, Nicotiana glutinosa, Nicotiana benthamiana, Nicotiana tabacum cv. White Burley, Nicotiana rustica, Datura stramonium, Cucurbita pepo cv. Bianca di Trieste, and Cucurbita maxima did not result in their infection. Retrospective analyses of our HTS data of two watermelon and 84 other cucurbits samples from previous years showed WCLaV-1 and WCLaV-2 reads in two pooled samples (containing equal amount of RNA of each sample): one from 2018 and another from 2019. RT-PCR confirmed the presence of WCLaVs only in watermelons. The pool from 2018 was sequenced at GATC (Germany, NovaSeq 6000 S2, PE 150) and from 2019 in-house using Oxford Nanopore Technologies (UK, MinION Mk1B device, SQK-PCS108, R9 flow cell). All HTS reads are deposited in the NCBI Short Reads Archive (PRJNA1202089). This is the first report of WCLaV-1 and WCLaV-2 in Slovenia and Europe, the two viruses which were included to the Alert list of the European and Mediterranean Plant Protection Organization, due to limited knowledge about their epidemiology (EPPO 2023). Further research is necessary to determine the incidence of these viruses in Europe, elucidate their epidemiology, symptoms association and their potential impact on the production of watermelons in the region.
Ključne besede: WCLaV-1, WCLaV-2, watermelon, viruses, diagnostics
Objavljeno v DiRROS: 22.04.2025; Ogledov: 882; Prenosov: 394
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8. First report of Tomato brown rugose fruit virus in tomato in SloveniaAna Vučurović, Jakob Brodarič, Tjaša Jakomin, Anja Pecman, Anita Benko-Beloglavec, Nataša Mehle, 2022, drugi znanstveni članki Povzetek: In July 2021, during an official survey for Tomato brown rugose fruit virus (ToBRFV), a sample composed of leaves and fruit was taken from three tomato (Solanum lycopersicum cv. Factor F1) plants growing in a greenhouse producing fresh tomatoes in central Slovenia. The sampled plants were slightly dwarfed and showed deformations such as leaf curling, narrowing and small leaves (Figure 1), while no virus symptoms were observed on the fruit.
Ključne besede: detection, identification, plant virus disease
Objavljeno v DiRROS: 26.02.2025; Ogledov: 902; Prenosov: 790
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9. Program strokovnih nalog s področja zdravstvenega varstva rastlin : naloge zdravstvenega varstva rastlin po javnem pooblastiluNataša Mehle, Manca Pirc, Ana Vučurović, Marjana Camloh, Denis Kutnjak, Anja Pecman, Špela Alič, Aleksander Benčič, Vladimir Grujić, Neža Turnšek, Janja Matičič, Špela Prijatelj-Novak, Aleš Blatnik, Jakob Brodarič, Irena Bajde, Veronika Bukvič, Tjaša Jakomin, Tanja Dreo, 2025, končno poročilo o rezultatih raziskav Ključne besede: diagnostika, virusi, bakterije, fitoplazme, varstvo rastlin
Objavljeno v DiRROS: 03.02.2025; Ogledov: 1047; Prenosov: 0
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10. Detection of plant viruses using nanopore highthroughput sequencing : validation reportAnja Pecman, Veronika Bukvič, Ana Vučurović, Irena Bajde, Jakob Brodarič, Nataša Mehle, Denis Kutnjak, 2023, končno poročilo o rezultatih raziskav Ključne besede: diagnostics, method validation, nanopores, high-throughput sequencing
Objavljeno v DiRROS: 02.09.2024; Ogledov: 1318; Prenosov: 2080
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