Enhanced Pore-C with C-Phasing Enables Chromosomal-Scale, Haplotype-Resolved Assembly of Ultra-Complex Genomes

Enhanced Pore-C with C-Phasing Enables Chromosomal-Scale, Haplotype-Resolved Assembly of Ultra-Complex Genomes | 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 Enhanced Pore-C with C-Phasing Enables Chromosomal-Scale, Haplotype-Resolved Assembly of Ultra-Complex Genomes Xingtan Zhang, Yibin Wang, Ping Zhao, Xiaofei Zeng, Jiaxin Yu, and 12 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7343323/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Ultra-complex, repeat-rich polyploids and hybrid genomes with extensive identical-by-descent regions pose a formidable challenge for chromosome-scale, haplotype-resolved assembly, since short-read scaffolding approaches such as Hi-C struggle to disambiguate their highly similar sequences. Long-read chromatin conformation capture technology (Pore-C) provides potential to overcome this by generating multi-kilobase fragments, high-order concatemers and native 5-methylcytosine (5mC) signals. Here, we first optimized the Pore-C to ePore-C (enhanced Pore-C) protocol for plant tissues, which markedly boosts sequencing yield and reduces the cost per gigabase. We then present C-Phasing, a comprehensive assembly pipeline that integrates ePore-C long reads, high-order concatemers and native 5mC methylation profiles to resolve and scaffold even the most challenging regions. By leveraging methylation-based anchoring and improved statistical modeling, C-Phasing effectively rescues collapsed contigs and corrects chimeras, and boosts both completeness and continuity of chromosome-scale assemblies. Fully compatible with both Pore-C and Hi-C data, C-Phasing outperforms existing tools across diverse polyploid genomes, including a modern cultivated sugarcane genome (aneuploid, 2n=9-12x=114), where it markedly enhances assembly quality and completeness over a previous reference. Biological sciences/Computational biology and bioinformatics/Genome informatics Biological sciences/Genetics/Genome polyploid ultra-complex genome genome assembly haplotype-resolved scaffolding Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryMaterials.pdf Supplementary Information FigS15.pdf Supplementary Figure 15 FigS17.pdf Supplementary Figure 17 FigS19.pdf Supplementary Figure 19 FigS24.pdf Supplementary Figure 24 Cite Share Download PDF Status: Under Review 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. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7343323","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":527548519,"identity":"216a0128-27d4-46fd-81d0-8a4c52aa455b","order_by":0,"name":"Xingtan 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