The first run of MinION-Mk1D in our lab using cDNA PCR barcoding kit. It looks promising - approx. 1 million reads in 3 hours!
#ONT #Sequencing #Diagnostics #virus #viroid #HTS #Bioinformatics

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

#EProbe design via MiFi enabled fast, sensitive detection of #hop #viruses and #viroids directly from unassembled #HTS data, with 40-nt probes offering optimal sensitivity and specificity in both in silico and in vitro validations 🧬🌿🔍
📄 https://doi.org/10.1094/PHYTOFR-09-24-0106-FI
👤 EVBC: Ali Pasha

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 ...

Pleased to share our paper on investigating the German hop virome 🍺😊
We have also identified other plant associated microorganisms, some of which infect hop, in the RNA-seq data 👨🏻‍💻🧬
doi.org/10.1371/jour...
#virome #hop #bioinformatics #virology

Another part of my PhD dissertation is out :)
doi.org/10.1111/ppa....

Highly Curated and Reliable E-Probes for Detection of Viral Pathogens in Unassembled HTS Datasets from Hops | PhytoFrontiers™ Implementing high-throughput sequencing (HTS) in virus detection has recently become widespread. Bioinformatics expertise, programming skills, and access to high-capacity computers are essential for H...

A new US-Germany lab’s collaboration developing a novel HTS detection of viruses & viroids infecting Hops based on electronic probes & EDNA. Great pleasure for Dr. A. Espindola & I working this out with GRA Ali Pasha & Dr. Heiko Ziebel. A vailable on First Look apsjournals.apsnet.org/doi/10.1094/...