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

RNA Virus Discovery Consortium

Research output: Contribution to journalArticlepeer-review

19 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)646-661.e4
JournalCell
Volume186
Issue number3
DOIs
StatePublished - 2 Feb 2023

Funding

FundersFunder number
Edmond J. Safra Center for Bioinformatics
NCBI
US Department of Energy Joint Genome Institute
National Institutes of Health
U.S. Department of EnergyDE-AC02-05CH11231
U.S. Department of Energy
U.S. National Library of Medicine
Office of Science
European Research CouncilERC-AdG 787514
European Research Council
Agence Nationale de la RechercheANR-20-CE20-009-02, ANR-21-CE11-0001-01
Agence Nationale de la Recherche
Tel Aviv University

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