Cattle T2T X Chromosome: Insights into Natural Neocentromere Evolution

Cattle T2T X Chromosome: Insights into Natural Neocentromere Evolution | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Cattle T2T X Chromosome: Insights into Natural Neocentromere Evolution Wai Low, Paulene Pineda, Callum Macphillamy, Yan Ren, Tong Chen, and 10 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6068440/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 28 Nov, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract The cattle genome is crucial for understanding ruminant biology, but it remains incomplete. The first telomere-to-telomere haplotype-resolved X chromosome and four autosomes of cattle are presented in a near-complete assembly that is 431 Mb (16%) longer than the current reference genome. The UOA_Wagyu_1 assembly identified 738 new protein-coding genes and supported characterization of centromeric repeats and transposable elements while revealing 49,610 structural variants. The cattle X centromere is a natural neocentromere with highly identical inverted repeats, no bovine satellite repeats, low CENP-A signal, low methylation, and low CpG content, in contrast to the autosomal centromeres that are comprised of typical bovine satellite repeats and epigenetic features. It likely formed from transposable element expansion and CpG deamination, suggesting dynamic evolution. Eighteen X-pseudoautosomal region genes have conserved testes expression between cattle and apes. All cattle X neocentromere protein-coding genes are expressed in testes, which suggest they potentially play a role in reproduction. Biological sciences/Genetics/Genomics Biological sciences/Computational biology and bioinformatics/Genome informatics Full Text Additional Declarations There is NO Competing Interest. Supplementary Files Extendeddatafig1.tif Extended data figure 1 Extendeddatafig2.tif Extended data figure 2 Extendeddatafig3.tif Extended data figure 3 Extendeddatafig4.tif Extended data figure 4 Extendeddatafig5.tif Extended data figure 5 Extendeddatafig6.tif Extended data figure 6 Extendeddatafig7.tif Extended data figure 7 ExtendedDataFigurelegends.docx Extended data figure legends Supplementaryinformation20250218.docx Supplementary Information WagyuSupplementaryTable20250218.xlsx Supplementary Table Cite Share Download PDF Status: Published Journal Publication published 28 Nov, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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