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A notable family of such replicons is Obelisks, ~1 kilobase (kb) cccRNAs encoding a protein with a unique fold, Oblin-1, and detected in diverse metatranscriptomes. To identify potential cccRNAs in a sequence similarity\u2013independent manner, we adopt the Fragmented and primer-Ligated DsRNA Sequencing (FLDS) method to selectively sequence double-stranded (ds) RNAs, replicative intermediates of RNA replicons. We focus on candidates with predicted extensive intramolecular base-pairing, a hallmark of viroid-like elements. Using FLDS, we explore metatranscriptomes from acidic hot springs in Japan and discover a distinct family of Obelisks apparently associated with thermoacidophilic bacteria (Hot spring Obelisks, HsObs). Despite lacking sequence similarity to known Oblins, HsObs share key features, including ~1\u2009kb genome size, rod-like RNA secondary structure, and the predicted fold of the encoded protein, HsOblin. A comprehensive metatranscriptome search for Oblin-1 and HsOblin homologs expands Obelisk diversity about two-fold, revealing multiple subfamilies sharing the same core fold,. some of which are also predicted to encode additional small proteins with simple alpha-helical folds. These findings highlight Obelisks as widespread and overlooked components of microbial ecosystems, expanding understanding of viroid-like RNA replicon diversity and evolution.<\/jats:p>","DOI":"10.1038\/s41467-026-71096-6","type":"journal-article","created":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T09:03:40Z","timestamp":1776675820000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Identification of hot spring Obelisk-like RNA replicons and expanded diversity of the Obelisk superfamily"],"prefix":"10.1038","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5318-9212","authenticated-orcid":false,"given":"Syun-ichi","family":"Urayama","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8924-1035","authenticated-orcid":false,"given":"Akihito","family":"Fukudome","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0430-2095","authenticated-orcid":false,"given":"Pascal","family":"Mutz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1325-3125","authenticated-orcid":false,"given":"Yosuke","family":"Matsushita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1247-4946","authenticated-orcid":false,"given":"Yoshihiro","family":"Takaki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8028-3228","authenticated-orcid":false,"given":"Yosuke","family":"Nishimura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7841-0814","authenticated-orcid":false,"given":"Sofia","family":"Medvedeva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5486-0098","authenticated-orcid":false,"given":"Mart","family":"Krupovic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3943-8299","authenticated-orcid":false,"given":"Eugene V.","family":"Koonin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2323-0880","authenticated-orcid":false,"given":"Takuro","family":"Nunoura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,4,20]]},"reference":[{"key":"71096_CR1","doi-asserted-by":"publisher","first-page":"1829","DOI":"10.1261\/rna.047126.114","volume":"20","author":"E Lasda","year":"2014","unstructured":"Lasda, E. & Parker, R. 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