NGS-enabled transcriptomic insights into plant–viroid interactions

Visit the ViroiDoc YouTube channel to watch a featured video lecture on how NGS-enabled transcriptomic insights into plant–viroid interactions and discovery of viroid and viroid-like species by Prof. Jernej Jakše from the Biotechnical Faculty UL.

The emergence of a novel hop disease in Slovenia, characterized by leaf yellowing, curling, and bine cracking, prompted the search for its causal agent. Conventional pathogen detection methods failed to identify the casual agent leading to the application of next-generation sequencing (NGS) and metagenomic approaches.

Using small RNA and total RNA sequencing, Prof. Jakše with his group identified Citrus bark cracking viroid (CBCVd) as the highly aggressive agent associated with hop stunt disease after confirming Koch's postulates. This was the first report of this viroid outside its original citrus hosts. Comparative analyses revealed that hop isolates differ from citrus sequences by five single-nucleotide changes. Subsequent transcriptomic analyses provided comprehensive insights into host–viroid interactions. RNA-seq profiling of hop cv. ‘Celeia’ infected with CBCVd revealed differential expression of many genes. Defense-related genes such as PR-1, chitinase, and thaumatin-like proteins were upregulated, whereas key elements of photosynthesis, primary carbon metabolism, and hormone homeostasis were strongly downregulated. Co-infection with hop latent viroid (HLVd) intensified these responses, suggesting complex coinfection interference.

Prof. Jakše with his group demonstrated that NGS-based sequencing is a powerful tool for diagnosing unknown plant diseases and elucidating the molecular basis of viroid pathogenicity. Integrating small RNA, mRNA, and miRNA data offers a tool to study host reprogramming under viroid infection and provides a foundation for developing molecular diagnostics and breeding strategies for viroid resistance in hop.

Curious to learn more?

Visit the ViroiDoc YouTube channel to watch a featured video lecture by Prof. Jernej Jakše, recorded in September 2025 during the ViroiDoc Days of the EU-funded ViroiDoc project's training activities.

Jernej Jakše is a Full Professor of genetics at the University of Ljubljana (UL), Biotechnical Faculty, Agronomy Department. His work spans both basic and applied research in genetics and biotechnology, where he employs cutting-edge research.

Jernej Jakše also serves as the supervisor for Doctoral Candidate Joao Colaço (DC1) who will work on the individual research project “How Disrupting Viroid Biogenesis Impacts Viroid propagation" at the UL.

Explore more content on viroid research by visiting ViroiDoc YouTube channel.