Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs

Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins and hijack cellular enzymes for replication. The extent and diversity of viroid-like agents are poorly understood. We developed a computational pipeline to identify viroid-like cccRNAs and applied it to 5,131 metatranscriptomes and 1,344 plant transcriptomes. The search yielded 11,378 viroid-like cccRNAs spanning 4,409 species-level clusters, a 5-fold increase compared to the previously identified viroid-like elements. Within this diverse collection, we discovered numerous putative viroids, satellite RNAs, retrozymes, and ribozy-like viruses. Diverse ribozyme combinations and unusual ribozymes within the cccRNAs were identified. Self-cleaving ribozymes were identified in ambiviruses, some mito-like viruses and capsid-encoding satellite virus-like cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems implies that their host range is far broader than currently known, and matches to CRISPR spacers suggest that some cccRNAs replicate in prokaryotes. [Display omitted] •Metatranscriptome search yields a 5-fold increase in viroid-like circular RNA diversity•Distant relatives of hepatitis delta virus and diverse viroid-like viruses are discovered•Viroid-like circular RNAs are targeted by endogenous CRISPR systems•Diverse ribozymes and ribozyme combinations identified in viroid-like RNAs A large-scale survey of covalently closed circular RNA across ecosystems reveals that viroids infect a wide range of host species, extending beyond plants, and identifies additional types of ribozyme activity as well as functional features in these molecules.