{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T10:48:20Z","timestamp":1792061300865,"version":"4.4.0"},"reference-count":126,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:00:00Z","timestamp":1792022400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:00:00Z","timestamp":1792022400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["acsess.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Plant Genome"],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The olive tree (\n                    <jats:italic>Olea europaea<\/jats:italic>\n                    L. subsp.\n                    <jats:italic>europaea<\/jats:italic>\n                    ) is one of the most representative perennial crops of the Mediterranean Basin, yet the genomic processes underlying its domestication and diversification remain poorly understood. Here, we investigated repeatome variation across 20 accessions, including 11 wild oleasters and nine cultivated varieties, using comparative clustering of high\u2010throughput sequencing data, complemented by structural analyses of transposable elements (TEs) and tandem repeats (TRs). Repetitive DNA accounts for about 54% of the olive genomes and is composed primarily of long terminal repeat retrotransposons (LTR\u2010REs) and TRs. Comparative analyses revealed lineage\u2010specific differences in LTR\u2010REs between wild and cultivated genotypes, while TRs exhibited higher abundances and greater variability in oleasters for some families (e.g., Oe\u201080 and Oe\u2010178), reinforcing the view that TRs evolve rapidly and largely independently in olive. We also identified a new TR (Oe\u2010155) and confirmed its distinct monomer sequence and chromosomal organization, suggesting that this subfamily is differentiating from TRs Oe\u2010218 and Oe\u201080. To refine TE dynamics, we surveyed full\u2010length elements in two reference assemblies (cv. Leccino and a wild\n                    <jats:italic>sylvestris<\/jats:italic>\n                    genotype). Leccino is enriched in intact LTR\u2010REs, whereas\n                    <jats:italic>sylvestris<\/jats:italic>\n                    harbored more full\u2010length Class II DNA transposons. Additionally, the patterns of TE\u2010gene proximity vary significantly between them. Dating of full\u2010length LTR\u2010RE insertions revealed that most RE activity predates domestication, with only a small fraction of very recent insertions. These results highlight repetitive DNA as a major contributor to genome diversification in olive and provide a foundation for integrating repeatome variation with demographic history, introgression, and clonal propagation.\n                  <\/jats:p>","DOI":"10.1002\/tpg2.70323","type":"journal-article","created":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T10:14:39Z","timestamp":1792059279000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome evolution of Mediterranean olives following DNA repeats diversification"],"prefix":"10.1002","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9747-8040","authenticated-orcid":false,"given":"Flavia","family":"Mascagni","sequence":"first","affiliation":[{"name":"Department of Agriculture, Food and Environment University of Pisa  Pisa Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel","family":"Simoni","sequence":"additional","affiliation":[{"name":"Department of Agriculture, Food and Environment University of Pisa  Pisa Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriele","family":"Usai","sequence":"additional","affiliation":[{"name":"Department of Agriculture, Food and Environment University of Pisa  Pisa Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-4740-6506","authenticated-orcid":false,"given":"Alexis","family":"Ryo","sequence":"additional","affiliation":[{"name":"Centre de Recherche sur la Biodiversit\u00e9 et l'Environnement (CRBE) Universit\u00e9 de Toulouse, CNRS, IRD, Toulouse INP, Universit\u00e9 Toulouse 3\u2013Paul Sabatier (UT3)  Toulouse France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Castellacci","sequence":"additional","affiliation":[{"name":"Department of Agriculture, Food and Environment University of Pisa  Pisa Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0819-7054","authenticated-orcid":false,"given":"Ugo","family":"Rogo","sequence":"additional","affiliation":[{"name":"Department of Agriculture, Food and Environment University of Pisa  Pisa Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marilena","family":"Ceccarelli","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Biology and Biotechnology University of Perugia  Perugia Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luciana","family":"Baldoni","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Biology and Biotechnology University of Perugia  Perugia Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tommaso","family":"Giordani","sequence":"additional","affiliation":[{"name":"Department of Agriculture, Food and Environment University of Pisa  Pisa Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucia","family":"Natali","sequence":"additional","affiliation":[{"name":"Department of Agriculture, Food and Environment University of Pisa  Pisa Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Cavallini","sequence":"additional","affiliation":[{"name":"Department of Agriculture, Food and Environment University of Pisa  Pisa Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2275-6012","authenticated-orcid":false,"given":"Guillaume","family":"Besnard","sequence":"additional","affiliation":[{"name":"Centre de Recherche sur la Biodiversit\u00e9 et l'Environnement (CRBE) Universit\u00e9 de Toulouse, CNRS, IRD, Toulouse INP, Universit\u00e9 Toulouse 3\u2013Paul Sabatier (UT3)  Toulouse France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,15]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022\u20102836(05)80360\u20102"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/aob\/mcq235"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365\u2010313X.2007.03242.x"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.14489"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.20.10.3434\u20103441.2000"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evu058"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/dnares\/dsu042"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1186\/BF03500883"},{"issue":"1","key":"e_1_2_10_10_1","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1080\/23818107.2023.2248234","article-title":"On the taxonomic subdivision of the Brown Olive from Africa and Asia through the reinstatement of Olea europaea subsp. africana (Mill.) 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