{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T22:38:09Z","timestamp":1792708689685,"version":"4.5.0"},"reference-count":87,"publisher":"Springer Science and Business Media LLC","license":[{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Centromeres are essential for faithful chromosome segregation during cell division. Yet despite their conserved function, many centromeres contain highly variable but internally remarkably homogenized tandem-repeat arrays\n                    <jats:sup>1\u20135<\/jats:sup>\n                    whose evolutionary dynamics remain poorly understood. Here, using replicated genome assemblies of mutation accumulation lines, we define the centromere-specific mutation spectrum in\n                    <jats:italic>Arabidopsis thaliana<\/jats:italic>\n                    . We find that kilobase-sized insertion\u2013deletion mutations (indels) occur frequently and consistently preserve tandem-repeat arrays by adding or removing only complete repeat units. Point mutations accumulate at an almost tenfold higher rate than elsewhere in the genome, probably driven by non-allelic gene conversion between closely linked repeat units. These findings suggest a central role for homology-directed DNA repair in centromere evolution, further supported by the accumulation of more frequent and longer tandem-repeat-preserving indels in\n                    <jats:italic>Arabidopsis<\/jats:italic>\n                    lines that are deficient in the anti-recombinase helicase RTEL1. Forward-in-time simulations parameterized with the observed mutation spectrum show that kilobase-sized indels and point mutations alone are sufficient to generate the megabase-sized homogenized repeat blocks characteristic of natural centromeres. Together, our results show that centromere evolution is driven by a distinct mutational spectrum shaped by homology-directed DNA repair, providing a quantitative framework for understanding how mutational processes generate and maintain the large-scale architecture of centromeric DNA.\n                  <\/jats:p>","DOI":"10.1038\/s41586-026-11046-w","type":"journal-article","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T15:06:05Z","timestamp":1790175965000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The mutational dynamics of the Arabidopsis centromeres"],"prefix":"10.1038","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6120-1330","authenticated-orcid":false,"given":"Xiao","family":"Dong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8355-2959","authenticated-orcid":false,"given":"Wen-Biao","family":"Jiao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lara","family":"Goldkuhle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1538-9752","authenticated-orcid":false,"given":"Fernando","family":"Rabanal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7811-1614","authenticated-orcid":false,"given":"Samija","family":"Amar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew T.","family":"Parker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6018-5698","authenticated-orcid":false,"given":"Jos\u00e9 A.","family":"Campoy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9375-1617","authenticated-orcid":false,"given":"Yueqi","family":"Tao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7165-1714","authenticated-orcid":false,"given":"Bruno","family":"Huettel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8512-2802","authenticated-orcid":false,"given":"Jurriaan","family":"Ton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2364-8187","authenticated-orcid":false,"given":"Lisa M.","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1073-8546","authenticated-orcid":false,"given":"Holger","family":"Puchta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2114-7963","authenticated-orcid":false,"given":"Detlef","family":"Weigel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5512-0443","authenticated-orcid":false,"given":"Korbinian","family":"Schneeberger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,23]]},"reference":[{"key":"11046_CR1","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1038\/s41586-023-06062-z","volume":"618","author":"P Wlodzimierz","year":"2023","unstructured":"Wlodzimierz, P. et al. Cycles of satellite and transposon evolution in Arabidopsis centromeres. Nature 618, 557\u2013565 (2023).","journal-title":"Nature"},{"key":"11046_CR2","doi-asserted-by":"publisher","first-page":"1098","DOI":"10.1126\/science.1062939","volume":"293","author":"S Henikoff","year":"2001","unstructured":"Henikoff, S., Ahmad, K. & Malik, H. S. The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293, 1098\u20131102 (2001).","journal-title":"Science"},{"key":"11046_CR3","doi-asserted-by":"publisher","first-page":"111895","DOI":"10.1016\/j.yexcr.2020.111895","volume":"389","author":"PB Talbert","year":"2020","unstructured":"Talbert, P. B. & Henikoff, S. What makes a centromere?\u00a0Exp. Cell. Res. 389, 111895 (2020).","journal-title":"Exp. Cell. Res."},{"key":"11046_CR4","doi-asserted-by":"publisher","DOI":"10.1126\/science.abl4178","volume":"376","author":"N Altemose","year":"2022","unstructured":"Altemose, N. et al. Complete genomic and epigenetic maps of human centromeres. Science 376, eabl4178 (2022).","journal-title":"Science"},{"key":"11046_CR5","doi-asserted-by":"publisher","DOI":"10.1126\/science.abi7489","volume":"374","author":"M Naish","year":"2021","unstructured":"Naish, M. et al. The genetic and epigenetic landscape of the Arabidopsis centromeres. Science 374, eabi7489 (2021).","journal-title":"Science"},{"key":"11046_CR6","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2013-14-1-r10","volume":"14","author":"DP Melters","year":"2013","unstructured":"Melters, D. P. et al. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol. 14, R10 (2013).","journal-title":"Genome Biol."},{"key":"11046_CR7","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1101\/gr.278409.123","volume":"34","author":"M Naish","year":"2024","unstructured":"Naish, M. & Henderson, I. R. The structure, function, and evolution of plant centromeres. Genome Res. 34, 161\u2013178 (2024).","journal-title":"Genome Res."},{"key":"11046_CR8","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1016\/j.gpb.2021.08.003","volume":"20","author":"B Wang","year":"2022","unstructured":"Wang, B. et al. High-quality Arabidopsis thaliana genome assembly with nanopore and HiFi long reads. Genomics Proteomics Bioinformatics 20, 4\u201313 (2022).","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"11046_CR9","doi-asserted-by":"publisher","first-page":"12309","DOI":"10.1093\/nar\/gkac1115","volume":"50","author":"FA Rabanal","year":"2022","unstructured":"Rabanal, F. A. et al. Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes. Nucleic Acids Res. 50, 12309\u201312327 (2022).","journal-title":"Nucleic Acids Res."},{"key":"11046_CR10","doi-asserted-by":"publisher","first-page":"1247","DOI":"10.1016\/j.molp.2022.05.014","volume":"15","author":"X Hou","year":"2022","unstructured":"Hou, X., Wang, D., Cheng, Z., Wang, Y. & Jiao, Y. A near-complete assembly of an Arabidopsis thaliana genome. Mol. Plant 15, 1247\u20131250 (2022).","journal-title":"Mol. Plant"},{"key":"11046_CR11","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1038\/s41586-024-07278-3","volume":"629","author":"GA Logsdon","year":"2024","unstructured":"Logsdon, G. A. et al. The variation and evolution of complete human centromeres. Nature 629, 136\u2013145 (2024).","journal-title":"Nature"},{"key":"11046_CR12","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1038\/299111a0","volume":"299","author":"G Dover","year":"1982","unstructured":"Dover, G. Molecular drive: a cohesive mode of species evolution. Nature 299, 111\u2013117 (1982).","journal-title":"Nature"},{"key":"11046_CR13","doi-asserted-by":"crossref","unstructured":"Smith, G. P. Unequal crossover and the evolution of multigene families. In Cold Spring Harbor Symposia on Quantitative Biology Vol. 38 507\u2013513 (Cold Spring Harbor Laboratory Press, 1974).","DOI":"10.1101\/SQB.1974.038.01.055"},{"key":"11046_CR14","doi-asserted-by":"publisher","first-page":"487","DOI":"10.1093\/genetics\/116.3.487","volume":"116","author":"J Dvo\u0159\u00e1k","year":"1987","unstructured":"Dvo\u0159\u00e1k, J., Jue, D. & Lassner, M. Homogenization of tandemly repeated nucleotide sequences by distance-dependent nucleotide sequence conversion. Genetics 116, 487\u2013498 (1987).","journal-title":"Genetics"},{"key":"11046_CR15","doi-asserted-by":"publisher","first-page":"1715","DOI":"10.1002\/j.1460-2075.1996.tb00517.x","volume":"15","author":"S Gangloff","year":"1996","unstructured":"Gangloff, S., Zou, H. & Rothstein, R. Gene conversion plays the major role in controlling the stability of large tandem repeats in yeast. EMBO J. 15, 1715\u20131725 (1996).","journal-title":"EMBO J."},{"key":"11046_CR16","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1101\/gr.593403","volume":"13","author":"SE Hall","year":"2003","unstructured":"Hall, S. E., Kettler, G. & Preuss, D. Centromere satellites from Arabidopsis populations: maintenance of conserved and variable domains. Genome Res. 13, 195\u2013205 (2003).","journal-title":"Genome Res."},{"key":"11046_CR17","doi-asserted-by":"publisher","first-page":"1913","DOI":"10.1534\/genetics.104.038208","volume":"170","author":"SE Hall","year":"2005","unstructured":"Hall, S. E., Luo, S., Hall, A. E. & Preuss, D. Differential rates of local and global homogenization in centromere satellites from Arabidopsis relatives. Genetics 170, 1913\u20131927 (2005).","journal-title":"Genetics"},{"key":"11046_CR18","doi-asserted-by":"publisher","first-page":"5955","DOI":"10.1093\/emboj\/cdf612","volume":"21","author":"\u00d0 Ugarkovi\u0107","year":"2002","unstructured":"Ugarkovi\u0107, \u00d0 & Plohl, M. Variation in satellite DNA profiles\u2014causes and effects. EMBO J. 21, 5955\u20135959 (2002).","journal-title":"EMBO J."},{"key":"11046_CR19","doi-asserted-by":"publisher","first-page":"eadj4509","DOI":"10.1126\/sciadv.adj4509","volume":"9","author":"D Fultz","year":"2023","unstructured":"Fultz, D., McKinlay, A., Enganti, R. & Pikaard, C. S. Sequence and epigenetic landscapes of active and silent nucleolus organizer regions in Arabidopsis. Sci. Adv. 9, eadj4509 (2023).","journal-title":"Sci. Adv."},{"key":"11046_CR20","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1126\/science.1180677","volume":"327","author":"S Ossowski","year":"2010","unstructured":"Ossowski, S. et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327, 92\u201394 (2010).","journal-title":"Science"},{"key":"11046_CR21","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1534\/genetics.118.301721","volume":"211","author":"M-L Weng","year":"2019","unstructured":"Weng, M.-L. et al. Fine-grained analysis of spontaneous mutation spectrum and frequency in Arabidopsis thaliana. Genetics 211, 703\u2013714 (2019).","journal-title":"Genetics"},{"key":"11046_CR22","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1038\/hdy.2009.67","volume":"103","author":"TN Marriage","year":"2009","unstructured":"Marriage, T. N. et al. Direct estimation of the mutation rate at dinucleotide microsatellite loci in Arabidopsis thaliana (Brassicaceae). Heredity 103, 310\u2013317 (2009).","journal-title":"Heredity"},{"key":"11046_CR23","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/s41586-021-04269-6","volume":"602","author":"JG Monroe","year":"2022","unstructured":"Monroe, J. G. et al. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature 602, 101\u2013105 (2022).","journal-title":"Nature"},{"key":"11046_CR24","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.01426","volume":"2","author":"E Wijnker","year":"2013","unstructured":"Wijnker, E. et al. The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana. eLife 2, e01426 (2013).","journal-title":"eLife"},{"key":"11046_CR25","doi-asserted-by":"publisher","first-page":"e1007155","DOI":"10.1371\/journal.pgen.1007155","volume":"14","author":"M Exposito-Alonso","year":"2018","unstructured":"Exposito-Alonso, M. et al. The rate and potential relevance of new mutations in a colonizing plant lineage. PLoS Genet. 14, e1007155 (2018).","journal-title":"PLoS Genet."},{"key":"11046_CR26","doi-asserted-by":"publisher","first-page":"5328","DOI":"10.1093\/molbev\/msab268","volume":"38","author":"G Shirsekar","year":"2021","unstructured":"Shirsekar, G. et al. Multiple sources of introduction of North American Arabidopsis thaliana from across Eurasia. Mol. Biol. Evol. 38, 5328\u20135344 (2021).","journal-title":"Mol. Biol. Evol."},{"key":"11046_CR27","doi-asserted-by":"publisher","first-page":"e1000843","DOI":"10.1371\/journal.pgen.1000843","volume":"6","author":"A Platt","year":"2010","unstructured":"Platt, A. et al. The scale of population structure in Arabidopsis thaliana. PLoS Genet. 6, e1000843 (2010).","journal-title":"PLoS Genet."},{"key":"11046_CR28","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.20777","volume":"5","author":"T Stuart","year":"2016","unstructured":"Stuart, T. et al. Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation. eLife 5, e20777 (2016).","journal-title":"eLife"},{"key":"11046_CR29","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1038\/nature08351","volume":"461","author":"S Tsukahara","year":"2009","unstructured":"Tsukahara, S. et al. Bursts of retrotransposition reproduced in Arabidopsis. Nature 461, 423\u2013426 (2009).","journal-title":"Nature"},{"key":"11046_CR30","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1002\/jcp.25053","volume":"231","author":"K Rodgers","year":"2016","unstructured":"Rodgers, K. & McVey, M. Error-prone repair of DNA double-strand breaks. J. Cell. Physiol. 231, 15\u201324 (2016).","journal-title":"J. Cell. Physiol."},{"key":"11046_CR31","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/j.tcb.2023.07.002","volume":"34","author":"N Hourvitz","year":"2024","unstructured":"Hourvitz, N., Awad, A. & Tzfati, Y. The many faces of the helicase RTEL1 at telomeres and beyond. Trends Cell Biol. 34, 109\u2013121 (2024).","journal-title":"Trends Cell Biol."},{"key":"11046_CR32","doi-asserted-by":"publisher","first-page":"4889","DOI":"10.1105\/tpc.114.132472","volume":"26","author":"J Recker","year":"2014","unstructured":"Recker, J., Knoll, A. & Puchta, H. The Arabidopsis thaliana homolog of the helicase RTEL1 plays multiple roles in preserving genome stability. Plant Cell 26, 4889\u20134902 (2014).","journal-title":"Plant Cell"},{"key":"11046_CR33","doi-asserted-by":"publisher","first-page":"e1006394","DOI":"10.1371\/journal.pgen.1006394","volume":"12","author":"S R\u00f6hrig","year":"2016","unstructured":"R\u00f6hrig, S., Schr\u00f6pfer, S., Knoll, A. & Puchta, H. The RTR complex partner RMI2 and the DNA helicase RTEL1 are both independently involved in preserving the stability of 45S rDNA repeats in Arabidopsis thaliana. PLoS Genet. 12, e1006394 (2016).","journal-title":"PLoS Genet."},{"key":"11046_CR34","doi-asserted-by":"publisher","first-page":"982","DOI":"10.1038\/s41588-024-01715-9","volume":"56","author":"Q Lian","year":"2024","unstructured":"Lian, Q. et al. A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range. Nat. Genet. 56, 982\u2013991 (2024).","journal-title":"Nat. Genet."},{"key":"11046_CR35","doi-asserted-by":"publisher","first-page":"5213","DOI":"10.1073\/pnas.1616736114","volume":"114","author":"A Durvasula","year":"2017","unstructured":"Durvasula, A. et al. African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 114, 5213\u20135218 (2017).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"11046_CR36","doi-asserted-by":"publisher","first-page":"1711","DOI":"10.1016\/j.molp.2023.08.012","volume":"16","author":"L Wang","year":"2023","unstructured":"Wang, L. et al. A telomere-to-telomere gap-free assembly of soybean genome. Mol. Plant 16, 1711\u20131714 (2023).","journal-title":"Mol. Plant"},{"key":"11046_CR37","doi-asserted-by":"publisher","first-page":"e1000326","DOI":"10.1371\/journal.pbio.1000326","volume":"8","author":"PB Talbert","year":"2010","unstructured":"Talbert, P. B. & Henikoff, S. Centromeres convert but don\u2019t cross. PLoS Biol. 8, e1000326 (2010).","journal-title":"PLoS Biol."},{"key":"11046_CR38","doi-asserted-by":"publisher","first-page":"e1000327","DOI":"10.1371\/journal.pbio.1000327","volume":"8","author":"J Shi","year":"2010","unstructured":"Shi, J. et al. Widespread gene conversion in centromere cores. PLoS Biol. 8, e1000327 (2010).","journal-title":"PLoS Biol."},{"key":"11046_CR39","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1016\/j.cell.2008.10.003","volume":"135","author":"AM Villeneuve","year":"2008","unstructured":"Villeneuve, A. M. Ensuring an exit strategy: RTEL1 restricts rogue recombination. Cell 135, 213\u2013215 (2008).","journal-title":"Cell"},{"key":"11046_CR40","doi-asserted-by":"publisher","first-page":"e70903","DOI":"10.1111\/tpj.70903","volume":"126","author":"L Goldkuhle","year":"2026","unstructured":"Goldkuhle, L., Lechner, L., Capdeville, N., Dorn, A. & Puchta, H. The DNA helicase RTEL1 is involved in the repair of replicative DNA damage independently of the alternative end joining and the DNA\u2013protein cross-link repair pathways in Arabidopsis. Plant J. 126, e70903 (2026).","journal-title":"Plant J."},{"key":"11046_CR41","doi-asserted-by":"publisher","first-page":"113851","DOI":"10.1016\/j.celrep.2024.113851","volume":"43","author":"S Showman","year":"2024","unstructured":"Showman, S., Talbert, P. B., Xu, Y., Adeyemi, R. O. & Henikoff, S. Expansion of human centromeric arrays in cells undergoing break-induced replication. Cell Rep. 43, 113851 (2024).","journal-title":"Cell Rep."},{"key":"11046_CR42","doi-asserted-by":"publisher","first-page":"859","DOI":"10.4161\/cc.7.7.5613","volume":"7","author":"B Llorente","year":"2008","unstructured":"Llorente, B., Smith, C. E. & Symington, L. S. Break-induced replication: what is it and what is it for?\u00a0Cell Cycle 7, 859\u2013864 (2008).","journal-title":"Cell Cycle"},{"key":"11046_CR43","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1038\/nature05723","volume":"447","author":"CE Smith","year":"2007","unstructured":"Smith, C. E., Llorente, B. & Symington, L. S. Template switching during break-induced replication. Nature 447, 102\u2013105 (2007).","journal-title":"Nature"},{"key":"11046_CR44","doi-asserted-by":"publisher","unstructured":"Rice, W. Why do centromeres evolve so fast: BIR replication, hypermutation, transposition, and molecular-drive. Preprint at https:\/\/doi.org\/10.20944\/preprints202012.0669.v1 (2020).","DOI":"10.20944\/preprints202012.0669.v1"},{"key":"11046_CR45","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1105\/tpc.001727","volume":"14","author":"R Siebert","year":"2002","unstructured":"Siebert, R. & Puchta, H. Efficient repair of genomic double-strand breaks by homologous recombination between directly repeated sequences in the plant genome. Plant Cell 14, 1121\u20131131 (2002).","journal-title":"Plant Cell"},{"key":"11046_CR46","doi-asserted-by":"publisher","first-page":"1418","DOI":"10.1111\/tpj.16863","volume":"119","author":"E Dvo\u0159\u00e1k Toma\u0161t\u00edkov\u00e1","year":"2024","unstructured":"Dvo\u0159\u00e1k Toma\u0161t\u00edkov\u00e1, E. et al. The interplay of homology-directed repair pathways in the repair of zebularine-induced DNA\u2013protein crosslinks in Arabidopsis. Plant J. 119, 1418\u20131432 (2024).","journal-title":"Plant J."},{"key":"11046_CR47","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1207\/s15327000em0101_4","volume":"1","author":"J Goldstein","year":"1999","unstructured":"Goldstein, J. Emergence as a construct: history and issues. Emergence 1, 49\u201372 (1999).","journal-title":"Emergence"},{"key":"11046_CR48","doi-asserted-by":"publisher","first-page":"e1000641","DOI":"10.1371\/journal.pgen.1000641","volume":"5","author":"VA Shepelev","year":"2009","unstructured":"Shepelev, V. A., Alexandrov, A. A., Yurov, Y. B. & Alexandrov, I. A. The evolutionary origin of man can be traced in the layers of defunct ancestral alpha satellites flanking the active centromeres of human chromosomes. PLoS Genet. 5, e1000641 (2009).","journal-title":"PLoS Genet."},{"key":"11046_CR49","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1101\/gr.3810906","volume":"16","author":"MK Rudd","year":"2006","unstructured":"Rudd, M. K., Wray, G. A. & Willard, H. F. The evolutionary dynamics of \u03b1-satellite. Genome Res. 16, 88\u201396 (2006).","journal-title":"Genome Res."},{"key":"11046_CR50","doi-asserted-by":"publisher","first-page":"308","DOI":"10.3389\/fpls.2016.00308","volume":"7","author":"TK Wolfgruber","year":"2016","unstructured":"Wolfgruber, T. K. et al. High quality maize centromere 10 sequence reveals evidence of frequent recombination events. Front. Plant Sci. 7, 308 (2016).","journal-title":"Front. Plant Sci."},{"key":"11046_CR51","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1016\/0022-2836(90)90383-W","volume":"216","author":"SJ Durfy","year":"1990","unstructured":"Durfy, S. J. & Willard, H. F. Concerted evolution of primate alpha satellite DNA. J. Mol. Biol. 216, 555\u2013566 (1990).","journal-title":"J. Mol. Biol."},{"key":"11046_CR52","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1016\/0022-2836(89)90332-X","volume":"210","author":"B Chatterjee","year":"1989","unstructured":"Chatterjee, B. & Lo, C. W. Chromosomal recombination and breakage associated with instability in mouse centromeric satellite DNA. J. Mol. Biol. 210, 303\u2013312 (1989).","journal-title":"J. Mol. Biol."},{"key":"11046_CR53","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1007\/s002390010166","volume":"52","author":"IJ Nijman","year":"2001","unstructured":"Nijman, I. J. & Lenstra, J. A. Mutation and recombination in cattle satellite DNA: a feedback model for the evolution of satellite DNA repeats. J. Mol. Evol. 52, 361\u2013371 (2001).","journal-title":"J. Mol. Evol."},{"key":"11046_CR54","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02381-4","volume":"22","author":"Z Lu","year":"2021","unstructured":"Lu, Z. et al. Genome-wide DNA mutations in Arabidopsis plants after multigenerational exposure to high temperatures. Genome Biol. 22, 160 (2021).","journal-title":"Genome Biol."},{"key":"11046_CR55","doi-asserted-by":"publisher","first-page":"638","DOI":"10.1101\/gad.191049.112","volume":"26","author":"JA Birchler","year":"2012","unstructured":"Birchler, J. A. & Presting, G. G. Retrotransposon insertion targeting: a mechanism for homogenization of centromere sequences on nonhomologous chromosomes. Genes Dev. 26, 638\u2013640 (2012).","journal-title":"Genes Dev."},{"key":"11046_CR56","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1101\/gr.214619.116","volume":"27","author":"S Maheshwari","year":"2017","unstructured":"Maheshwari, S., Ishii, T., Brown, C. T., Houben, A. & Comai, L. Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence. Genome Res. 27, 471\u2013478 (2017).","journal-title":"Genome Res."},{"key":"11046_CR57","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1093\/genetics\/155.1.369","volume":"155","author":"RG Shaw","year":"2000","unstructured":"Shaw, R. G., Byers, D. L. & Darmo, E. Spontaneous mutational effects on reproductive traits of Arabidopsis thaliana. Genetics 155, 369\u2013378 (2000).","journal-title":"Genetics"},{"key":"11046_CR58","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).","journal-title":"GigaScience"},{"key":"11046_CR59","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","volume":"18","author":"H Cheng","year":"2021","unstructured":"Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170\u2013175 (2021).","journal-title":"Nat. Methods"},{"key":"11046_CR60","doi-asserted-by":"publisher","first-page":"1291","DOI":"10.1101\/gr.263566.120","volume":"30","author":"S Nurk","year":"2020","unstructured":"Nurk, S. et al. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Res. 30, 1291\u20131305 (2020).","journal-title":"Genome Res."},{"key":"11046_CR61","doi-asserted-by":"publisher","first-page":"D1202","DOI":"10.1093\/nar\/gkr1090","volume":"40","author":"P Lamesch","year":"2012","unstructured":"Lamesch, P. et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 40, D1202\u2013D1210 (2012).","journal-title":"Nucleic Acids Res."},{"key":"11046_CR62","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02823-7","volume":"23","author":"M Alonge","year":"2022","unstructured":"Alonge, M. et al. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol. 23, 258 (2022).","journal-title":"Genome Biol."},{"key":"11046_CR63","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-026-10105-6","author":"H Cheng","year":"2026","unstructured":"Cheng, H. et al. Efficient near-telomere-to-telomere assembly of nanopore simplex reads. Nature https:\/\/doi.org\/10.1038\/s41586-026-10105-6 (2026).","journal-title":"Nature"},{"key":"11046_CR64","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1093\/bioinformatics\/btx699","volume":"34","author":"BS Pedersen","year":"2018","unstructured":"Pedersen, B. S. & Quinlan, A. R. Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics 34, 867\u2013868 (2018).","journal-title":"Bioinformatics"},{"key":"11046_CR65","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","volume":"31","author":"FA Sim\u00e3o","year":"2015","unstructured":"Sim\u00e3o, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210\u20133212 (2015).","journal-title":"Bioinformatics"},{"key":"11046_CR66","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02134-9","volume":"21","author":"A Rhie","year":"2020","unstructured":"Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21, 245 (2020).","journal-title":"Genome Biol."},{"key":"11046_CR67","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094\u20133100 (2018).","journal-title":"Bioinformatics"},{"key":"11046_CR68","doi-asserted-by":"publisher","first-page":"btad308","DOI":"10.1093\/bioinformatics\/btad308","volume":"39","author":"P Wlodzimierz","year":"2023","unstructured":"Wlodzimierz, P., Hong, M. & Henderson, I. R. TRASH: Tandem Repeat Annotation and Structural Hierarchy. Bioinformatics 39, btad308 (2023).","journal-title":"Bioinformatics"},{"key":"11046_CR69","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841\u2013842 (2010).","journal-title":"Bioinformatics"},{"key":"11046_CR70","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","volume":"17","author":"M Martin","year":"2011","unstructured":"Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10\u201312 (2011).","journal-title":"EMBnet. J."},{"key":"11046_CR71","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"11046_CR72","doi-asserted-by":"publisher","first-page":"W160","DOI":"10.1093\/nar\/gkw257","volume":"44","author":"F Ram\u00edrez","year":"2016","unstructured":"Ram\u00edrez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160 (2016).","journal-title":"Nucleic Acids Res."},{"key":"11046_CR73","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1911-0","volume":"20","author":"M Goel","year":"2019","unstructured":"Goel, M., Sun, H., Jiao, W.-B. & Schneeberger, K. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 20, 277 (2019).","journal-title":"Genome Biol."},{"key":"11046_CR74","unstructured":"Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https:\/\/doi.org\/10.48550\/arxiv.1303.3997 (2013)."},{"key":"11046_CR75","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nbt.1754","volume":"29","author":"JT Robinson","year":"2011","unstructured":"Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24\u201326 (2011).","journal-title":"Nat. Biotechnol."},{"key":"11046_CR76","doi-asserted-by":"publisher","first-page":"e1005944","DOI":"10.1371\/journal.pcbi.1005944","volume":"14","author":"G Mar\u00e7ais","year":"2018","unstructured":"Mar\u00e7ais, G. et al. MUMmer4: A fast and versatile genome alignment system. PLoS Comput. Biol. 14, e1005944 (2018).","journal-title":"PLoS Comput. Biol."},{"key":"11046_CR77","doi-asserted-by":"publisher","first-page":"3088","DOI":"10.1093\/bioinformatics\/btx346","volume":"33","author":"B Gel","year":"2017","unstructured":"Gel, B. & Serra, E. karyoploteR: an R\/Bioconductor package to plot customizable genomes displaying arbitrary data. Bioinformatics 33, 3088\u20133090 (2017).","journal-title":"Bioinformatics"},{"key":"11046_CR78","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1905-y","volume":"20","author":"S Ou","year":"2019","unstructured":"Ou, S. et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. 20, 275 (2019).","journal-title":"Genome Biol."},{"key":"11046_CR79","doi-asserted-by":"publisher","unstructured":"Bousios, A. & Primetis, E. ATHILAfinder: a tool to detect ATHILA LTR retrotransposons in plant genomes. Preprint at bioRxiv https:\/\/doi.org\/10.64898\/2026.03.20.713144 (2026).","DOI":"10.64898\/2026.03.20.713144"},{"key":"11046_CR80","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh, K. & Standley, D. M. MAFFT Multiple Sequence Alignment Software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772\u2013780 (2013).","journal-title":"Mol. Biol. Evol."},{"key":"11046_CR81","doi-asserted-by":"publisher","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","volume":"5","author":"MN Price","year":"2010","unstructured":"Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2\u2013approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).","journal-title":"PLoS ONE"},{"key":"11046_CR82","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","volume":"49","author":"I Letunic","year":"2021","unstructured":"Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293\u2013W296 (2021).","journal-title":"Nucleic Acids Res."},{"key":"11046_CR83","doi-asserted-by":"publisher","unstructured":"Qi, J. et al. De novo annotation of centromere with centroAnno. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2025.02.19.639205 (2025).","DOI":"10.1101\/2025.02.19.639205"},{"key":"11046_CR84","doi-asserted-by":"publisher","first-page":"btae493","DOI":"10.1093\/bioinformatics\/btae493","volume":"40","author":"AP Sweeten","year":"2024","unstructured":"Sweeten, A. P., Schatz, M. C. & Phillippy, A. M. ModDotPlot\u2014rapid and interactive visualization of tandem repeats. Bioinformatics 40, btae493 (2024).","journal-title":"Bioinformatics"},{"key":"11046_CR85","first-page":"10","volume":"2006","author":"S Tomar","year":"2006","unstructured":"Tomar, S. Converting video formats with FFmpeg. Linux J. 2006, 10 (2006).","journal-title":"Linux J."},{"key":"11046_CR86","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-024-03388-3","volume":"25","author":"Y Tao","year":"2024","unstructured":"Tao, Y. et al. Atlas of telomeric repeat diversity in Arabidopsis thaliana. Genome Biol. 25, 244 (2024).","journal-title":"Genome Biol."},{"key":"11046_CR87","doi-asserted-by":"publisher","unstructured":"Dong, X. & Schneeberger, K. The mutational dynamics of the Arabidopsis centromeres. Figshare https:\/\/doi.org\/10.6084\/m9.figshare.32135497 (2026).","DOI":"10.6084\/m9.figshare.32135497"}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-026-11046-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-026-11046-w","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-026-11046-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T22:02:25Z","timestamp":1792706545000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-026-11046-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,23]]},"references-count":87,"alternative-id":["11046"],"URL":"https:\/\/doi.org\/10.1038\/s41586-026-11046-w","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,23]]},"assertion":[{"value":"2 June 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 August 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 September 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}]}}