From Demodification to Sequencing: the Genome of Bacteriophage Carin-5

From Demodification to Sequencing: the Genome of Bacteriophage Carin-5 | 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 From Demodification to Sequencing: the Genome of Bacteriophage Carin-5 Rémi SIESKIND, Sophia MISSOURY, Frédéric BONHOMME, Pauline NOGARET, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7091417/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 05 Dec, 2025 Read the published version in Scientific Reports → Version 1 posted 10 You are reading this latest preprint version Abstract The bacteriophage Carin-5, which infects Cobetia marina, presented significant challenges for genome sequencing due to DNA modifications that hindered efficient amplification of its DNA. Initial attempts using an optimized Illumina library preparation protocol yielded only a partial genome. Among the obtained contigs, the gene encoding the replicative DNA polymerase was identified. This gene was subsequently cloned into an expression vector and the encoded DNA polymerase protein was purified. The purified DNA polymerase was used to replicate the Carin-5 genomic DNA in vitro, effectively bypassing the modification-induced amplification barriers. This approach enabled the amplification of the entire Carin-5 genomic DNA and the use of a standard NGS library preparation protocol and allowed to obtain the complete sequence of the Carin-5 genome. The DNA modifications were characterized by mass spectrometry, and they showed a clear analogy with the oligosaccharide-hypermodified thymidines of bacteriophage SP-15. The annotated genome of Carin-5 carried a gene block encoding enzymes for nucleotide sugar modifications and glycosyltransferases. Biological sciences/Biological techniques Biological sciences/Biotechnology Biological sciences/Genetics Biological sciences/Microbiology Biological sciences/Molecular biology Full Text Additional Declarations No competing interests reported. Supplementary Files Carin5paperSI.pdf Cite Share Download PDF Status: Published Journal Publication published 05 Dec, 2025 Read the published version in Scientific Reports → Version 1 posted Editorial decision: Revision requested 13 Aug, 2025 Reviews received at journal 08 Aug, 2025 Reviewers agreed at journal 31 Jul, 2025 Reviews received at journal 31 Jul, 2025 Reviewers agreed at journal 22 Jul, 2025 Reviewers invited by journal 21 Jul, 2025 Editor invited by journal 15 Jul, 2025 Editor assigned by journal 14 Jul, 2025 Submission checks completed at journal 11 Jul, 2025 First submitted to journal 10 Jul, 2025 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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