{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T11:10:35Z","timestamp":1784632235073,"version":"3.55.0"},"reference-count":135,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T00:00:00Z","timestamp":1783555200000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["T2425005"],"award-info":[{"award-number":["T2425005"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>RNA editing, a post-transcriptional modification in plant mitochondria and plastids, is essential for environmental adaptation and diverse physiological processes. Despite extensive identification of RNA editing factors, primarily including pentatricopeptide repeat (PPR), multiple organelle RNA editing factor (MORF), organelle RNA recognition motif-containing (ORRM), and organelle zinc finger (OZ) proteins, their evolutionary history remains poorly understood. Here, we perform kingdom-wide evolutionary analyses across 364 high-quality Archaeplastida genomes and find massive PPR gene expansions in early-diverging land plants, predominantly driven by dispersed duplication associated with retroposition. Furthermore, integrative analyses imply that DYW subgroup PPR genes have been horizontally transferred from plants to bdelloid rotifers. MORF proteins, accessory partners of PPRs, possess MORF hallmark domains structurally similar to protein-folding peptidase S8 propeptide\/proteinase inhibitor I9 domains, suggesting a role in protein folding during RNA editing. Considering diverse domain compositions, we reclassify MORF, ORRM, and OZ proteins and uncover prevalent hallmark domain fusions. Together, these findings illuminate the kingdom-wide evolution of plant RNA editing machinery.<\/jats:p>","DOI":"10.1093\/molbev\/msag168","type":"journal-article","created":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T11:49:46Z","timestamp":1783511386000},"source":"Crossref","is-referenced-by-count":0,"title":["Kingdom-wide evolutionary characterization of RNA editing factors in Archaeplastida"],"prefix":"10.1093","volume":"43","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-8567-4625","authenticated-orcid":false,"given":"Ming","family":"Chen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8291-8493","authenticated-orcid":false,"given":"Qingming","family":"Qu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6603-5060","authenticated-orcid":false,"given":"Zhang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,9]]},"reference":[{"key":"2026072106312440500_msag168-B1","doi-asserted-by":"publisher","DOI":"10.26508\/lsa.201900429","article-title":"Detecting sequence signals in targeting peptides using deep learning","volume":"2","author":"Armenteros","year":"2019","journal-title":"Life Sci Alliance."},{"key":"2026072106312440500_msag168-B2","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1146\/annurev-arplant-050213-040159","article-title":"Pentatricopeptide repeat proteins in plants","volume":"65","author":"Barkan","year":"2014","journal-title":"Annu Rev Plant Biol."},{"key":"2026072106312440500_msag168-B3","doi-asserted-by":"publisher","DOI":"10.1016\/j.plantsci.2024.112101","article-title":"Dissecting the molecular puzzle of the editosome core in Arabidopsis organelles","volume":"344","author":"Baudry","year":"2024","journal-title":"Plant Sci."},{"key":"2026072106312440500_msag168-B4","doi-asserted-by":"publisher","first-page":"D444","DOI":"10.1093\/nar\/gkae1082","article-title":"InterPro: the protein sequence classification resource in 2025","volume":"53","author":"Blum","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"2026072106312440500_msag168-B5","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1007\/3-540-35273-2_11","article-title":"Sampling kinetic protein folding pathways using all-atom models","volume":"703","author":"Bolhuis","year":"2006","journal-title":"Lecture Notes Phys"},{"key":"2026072106312440500_msag168-B6","doi-asserted-by":"publisher","first-page":"1090","DOI":"10.1111\/nph.12928","article-title":"The cytidine deaminase signature HxE(x)nCxxC of DYW1 binds zinc and is necessary for RNA editing of ndhD-1","volume":"203","author":"Boussardon","year":"2014","journal-title":"New Phytol."},{"key":"2026072106312440500_msag168-B7","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2026072106312440500_msag168-B8","doi-asserted-by":"publisher","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"2026072106312440500_msag168-B9","doi-asserted-by":"publisher","first-page":"924","DOI":"10.1134\/S0006297911080086","article-title":"RNA editing in plant organelles. 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