CITATION.cff

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title: Viroid-like circRNA discovery and analysis suite
authors:
- family-names: Lee
  given-names: Benjamin D.
- family-names: Neri
  given-names: Uri
- family-names: Roux
  given-names: Simon
- family-names: Wolf
  given-names: Yuri I.
- family-names: Camargo
  given-names: Antonio Pedro
- family-names: Krupovic
  given-names: Mart
- family-names: Simmonds
  given-names: Peter
- family-names: Kyrpides
  given-names: Nikos
- family-names: Gophna
  given-names: Uri
- family-names: Dolja
  given-names: Valerian V.
- family-names: Koonin
  given-names: Eugene V.
preferred-citation:
  type: article
  title: Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs
  authors:
  - family-names: Lee
    given-names: Benjamin D.
  - family-names: Neri
    given-names: Uri
  - family-names: Roux
    given-names: Simon
  - family-names: Wolf
    given-names: Yuri I.
  - family-names: Camargo
    given-names: Antonio Pedro
  - family-names: Krupovic
    given-names: Mart
  - family-names: Simmonds
    given-names: Peter
  - family-names: Kyrpides
    given-names: Nikos
  - family-names: Gophna
    given-names: Uri
  - family-names: Dolja
    given-names: Valerian V.
  - family-names: Koonin
    given-names: Eugene V.
  journal: Cell
  volume: '186'
  issue: '3'
  year: '2023'
  issn: 0092-8674
  doi: 10.1016/j.cell.2022.12.039
  url: https://www.sciencedirect.com/science/article/pii/S0092867422015823
  abstract: Summary 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.
  start: 646-661.e4