Diversity and evolution of viroids and viroid-like RNA agents

Thesis

Viroids are the smallest and simplest known pathogens. Comprised of circular noncoding RNA, these agents can cause fatal diseases in plants. Although other viroid-like agents such as satellite RNAs, ribozyviruses, and retrozymes have been discovered, the evolution and true extent of viroids and viroid-like RNA agents remains poorly understood.

The primary aim of this project was to examine the diversity and evolution of viroids and viroid-like RNA agents. To achieve this goal, a comprehensive database of relevant sequences was curated and a specialized software pipeline for the detection of viroid-like sequences was built. The database provides a value-added resource of sequences, sample metadata, and annotations. The pipeline detects circular sequences from input transcriptomes or metatranscriptomes and then searches against the viroid database and a set of self-cleaving ribozyme profiles. Viroid-like sequences are then clustered into species-level clusters and their secondary structures predicted.

The pipeline was tested on a diverse set of plant transcriptomes to verify its ability to recover known viroid sequences. It was then applied to a large collection of global metatranscriptomes from varied ecosystems. The search yielded a fivefold increase of species-level diversity compared to the set of known viroids and viroid-like sequences. The results also included novel ribozyme content within the viroid-like sequences. Second, new clades of ribozyviruses were identified among the circular RNAs. Third, the search identified the viroid-like nature of two additional types of small RNA viruses, both of which infect fungi and/or protists and lack capsids. Finally, CRISPR spacer matches to viroid-like sequences were detected, suggesting that the host range of viroid-like agents extends to prokaryotes.

This project was the first large-scale metatranscriptomic investigation of viroids and viroid-like agents. The results reveal that their true diversity of these unique agents has been previously understated and opens up new questions into their origin and evolutionary history.

Authors: Lee, BD

• DOI: 10.5287/ora-5j5oa4nrk
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: obelisk; metatranscriptomics; satellite RNA; viroid; ribozyvirus; satRNA; circular RNA
• Subjects: Bioinformatics; Computational biology; Virology; Evolution (Biology)