{"doi":"10.64898/2026.01.17.700053","title":"Pangenome analysis reveals the evolutionary dynamics of repeat-based holocentromeres","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>\n                  Centromeres are essential for chromosome segregation, yet their organisation and evolution remain poorly understood in holocentric species, where kinetochore activity is distributed along entire chromosomes\n                  <jats:sup>1,2</jats:sup>\n                  . While monocentric centromeres are often structured by megabase-sized satellite arrays\n                  <jats:sup>3–5</jats:sup>\n                  , the role of repetitive DNA in holocentric systems remains enigmatic. Here, we analyse the dynamics of centromeric\n                  <jats:italic>Tyba</jats:italic>\n                  satellite DNA repeats and transposable elements across a chromosome-scale pangenome comprising 56 long-read haplotype assemblies from 20\n                  <jats:italic>Rhynchospora</jats:italic>\n                  species\n                  <jats:sup>6,7</jats:sup>\n                  , a plant genus with repeat-based holocentromeres\n                  <jats:sup>8,9</jats:sup>\n                  . We identify over 4.6 million monomers of the\n                  <jats:italic>Tyba</jats:italic>\n                  satellite repeat, arranged into 43,400 discrete arrays that span all chromosomes. CENH3 ChIP-seq reveals that, unexpectedly, the same\n                  <jats:italic>Tyba</jats:italic>\n                  satellite defines holocentromere across the entire genus, demonstrating deep conservation of centromeric DNA over over 40 million years despite extensive karyotype evolution and centromere array turnover. We show that\n                  <jats:italic>Tyba</jats:italic>\n                  arrays function as modular centromeric units whose number and spacing, but not size, scale with chromosome length.\n                  <jats:italic>Tyba</jats:italic>\n                  sequence diversity recapitulates species phylogeny, while higher-order repeat formation and antagonism with transposable elements shape array turnover. A novel synteny-aware algorithm reveals rapid gain, loss, and rearrangement of arrays across homologous chromosomes. Using cytogenetics and polymer simulations, we demonstrate that inter-array spacing governs chromatin loop length and chromatid thickness, linking repeat-based holocentromere organisation directly to chromosome mechanics. Our findings uncover a scalable, modular logic for holocentromere function and establish a framework for understanding the plasticity of repeat-based centromere evolution and genome architecture in eukaryotes.\n                </jats:p>","journal":null,"year":null,"id":641239,"datarank":0.16479184330021646,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.0,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1667043,"name":"Estela Perez-Roman","orcid":"0000-0001-5659-7860","position":1,"is_corresponding":false},{"id":1667044,"name":"Amanda Souza Câmara","orcid":"0000-0002-3136-6633","position":2,"is_corresponding":false},{"id":1667046,"name":"Laura A. Robledillo","orcid":"0000-0002-7617-2613","position":3,"is_corresponding":false},{"id":1667048,"name":"Gokilavani Thangavel","orcid":"0000-0001-7985-310X","position":4,"is_corresponding":false},{"id":1279984,"name":"Meng Zhang","orcid":"0000-0002-1800-0928","position":5,"is_corresponding":false},{"id":1667049,"name":"Jacob González Isa","orcid":"0009-0008-7266-7812","position":6,"is_corresponding":false},{"id":1667050,"name":"Letícia Maria Parteka","orcid":"0000-0002-2174-9067","position":7,"is_corresponding":false},{"id":1667051,"name":"Marco Castellani","orcid":"0000-0002-5809-9387","position":8,"is_corresponding":false},{"id":995189,"name":"Bruno Hüettel","orcid":"0000-0001-7165-1714","position":9,"is_corresponding":false},{"id":1667052,"name":"André L. L. Vanzela","orcid":"0000-0002-2442-2211","position":10,"is_corresponding":false},{"id":616075,"name":"Ian R. Henderson","orcid":"0000-0001-5066-1489","position":11,"is_corresponding":false},{"id":616074,"name":"Alexandros Bousios","orcid":"0000-0002-8005-6949","position":12,"is_corresponding":false},{"id":1667053,"name":"André Marques","orcid":"0000-0002-9567-2576","position":13,"is_corresponding":false},{"id":616065,"name":"Piotr Włodzimierz","orcid":"0000-0003-1040-7878","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-08-07T16:48:07.140248Z","pmid":null,"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":[]}