#PlantViromics

Metagenomics Study of the Commercial Tomato Virome Focused on Virus Species of Epidemiological Interest Plant viruses have detrimental effects on commercial tomato cultivation leading to severe economic consequences. Viral metagenomics studies provide the opportunity to examine in depth the virome composition of a sample set without any pre-existing knowledge of the viral species that are present. In the present study, 101 plant samples were collected from commercial greenhouses in 13 countries in Europe, Africa, Asia, and North America between 2017 and 2024. All samples were processed with the VLP enrichment protocol NetoVIR and the obtained data were analyzed with the ViPER pipeline. Forty-three eukaryotic viral species were identified, with a median identification of 2 species per sample. The most prevalent viral species were pepino mosaic virus (PepMV), tomato brown rugose fruit virus (ToBRFV), and southern tomato virus (STV). The obtained genome sequences were used to study the diversity and phylogeny of these viruses. The three genotypes identified for PepMV showed low diversity within each genotype (96.2–99.0% nucleotide identity). Low isolate diversity was also found for ToBRFV and STV. No significant association could be found between STV identification and the presence of symptoms, questioning the pathogenic potential of STV. Three other pathogenic viral species of particular interest due to their effects on tomato cultivation or recent emergence, namely tomato torrado virus (ToTV), tomato fruit blotch virus (ToFBV), and cucumber mosaic virus (CMV), were part of the virome with low prevalence. Our study provided a comprehensive overview of the analyzed samples’ virome, as well as the possibility to inspect the genetic diversity of the identified viral genomes and to look into their potential role in symptom development.

Metagenomic analysis of 101 tomato samples from 13 countries revealed 43 viral species, including PepMV, ToBRFV, and STV, showcasing the global complexity of the commercial tomato virome. #PlantViromics #HTS 🍅🧬
📄 https://doi.org/10.3390/v17101334
👤 EVBC members: Nikolas Basler, Jelle Matthijnssens

Wild and globally traded ornamental aquatic plants harbor diverse plant viruses, including notable crop pathogens - Environmental Microbiome Background Aquatic plants play key roles in ecosystems, serving as primary producers and providing habitat for other aquatic life. While many are ecologically important, some invasive species, often i...

Globally traded ornamental aquatic plants host a diverse array of plant viruses, including pathogens relevant to crops, highlighting the hidden risk of virus spread via trade. #PlantViromics #Biosecurity 🌿🦠
📄 doi.org/10.1186/s407...
👤 EVBC member: Denis Kutnjak

Virus and viroid diversity in hops, investigating the German hop virome Germany is worldwide one of the largest hop (Humulus lupulus L.) producers, an essential crop for the brewing industry. However, infections caused by viruses and viroids can severely impact hop yield and quality. In 2019, citrus bark cracking viroid (CBCVd) – a highly aggressive pathogen in hop – was first reported in Germany, raising concerns about its spread and prompting a broader investigation of the German hop virome.To investigate the viro-diversity in German hops, we started with a pilot study in 2021 targeting three hopyards in the Hallertau region (Bavaria), where CBCVd was previously detected. This study was expanded in 2022 and 2023 to include other main hop growing regions of Tettnang (Baden-Wuerttemberg) and Elbe-Saale (Saxony, Saxony-Anhalt, Thuringia). Leaf samples were collected from hop as well as non-hop plants inside and outside the hopyard, pooled, and proceeded for double-stranded RNAs extraction. High-throughput sequencing (HTS) was used as a diagnostic tool, followed by RT-PCR confirmation. Our analysis identified four viruses infecting hops; hop latent virus (HpLV), hop mosaic virus (HpMV), apple mosaic virus (ApMV), arabis mosaic virus (ArMV) – and two viroids; hop latent viroid (HLVd) and CBCVd. HpLV, HpMV, and HLVd were consistently found across all targeted hopyards, while CBCVd was confined to the Hallertau region. ArMV was only detected in one hopyard at one sampling timepoint. ApMV was the only virus detected in both hop and non-hop plants. Additional analysis of hop pool datasets revealed the presence of other potential hop pathogens, i.e., fungi and bacteria. The results showed a low diversity of viruses and viroids infecting hops. However, this study provides a comprehensive overview on the major viruses and viroids in German hopyards. The results may serve as a useful resource for the development of disease management strategies in hop cultivation and highlight the valuable implementation of HTS in plant pathogen surveillance.

A nationwide #HTS survey of German hopyards identified HpLV, HpMV, ApMV, ArMV and viroids HLVd and CBCVd (CBCVd confined to Hallertau), highlighting HTS as a powerful tool for #PlantPathogenSurveillance and management #PlantViromics 🧬🌾🔬
📄https://doi.org/10.1371/journal.pone.0329289
👤EVBC: Ali Pasha