{"doi":"10.1016/j.cell.2022.12.039","title":"Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs","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.","journal":"Cell","year":2023,"id":316701,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":94,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9139,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":709899,"name":"Uri Neri","orcid":"0000-0003-0894-2484","position":1,"is_corresponding":false},{"id":106775,"name":"Simon Roux","orcid":"0000-0002-5831-5895","position":2,"is_corresponding":false},{"id":107326,"name":"Yuri I. Wolf","orcid":"0000-0002-0247-8708","position":3,"is_corresponding":false},{"id":840127,"name":"Antônio Pedro Camargo","orcid":"0000-0003-3913-2484","position":4,"is_corresponding":false},{"id":109878,"name":"Mart Krupovìč","orcid":"0000-0001-5486-0098","position":5,"is_corresponding":false},{"id":106094,"name":"Peter Simmonds","orcid":"0000-0002-7964-4700","position":6,"is_corresponding":false},{"id":19851,"name":"Nikos C. Kyrpides","orcid":"0000-0002-6131-0462","position":7,"is_corresponding":false},{"id":525766,"name":"Uri Gophna","orcid":"0000-0001-5129-5652","position":8,"is_corresponding":false},{"id":109877,"name":"Valerian V. Dolja","orcid":"0000-0002-8148-4670","position":9,"is_corresponding":false},{"id":17837,"name":"Eugene V. Koonin","orcid":"0000-0003-3943-8299","position":10,"is_corresponding":false},{"id":63487,"name":"Benjamin D. Lee","orcid":"0000-0002-7133-8397","position":0,"is_corresponding":true}],"reference_count":107,"raw_metadata":null,"created_at":"2026-07-19T01:06:44.698773Z","pmid":"36696902","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}