Recent evolution, domestication and metabolism of cyanide compounds in Lima bean

Recent evolution, domestication and metabolism of cyanide compounds in Lima bean | 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 Recent evolution, domestication and metabolism of cyanide compounds in Lima bean Jorge Duitama, Erick Duarte, Tatiana Garcia, Federico Zuñiga, and 16 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5727653/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract The evolution and functional genomics of the biosynthesis of secondary metabolites, including production of hydrogen cyanide (HCN), is a major goal in Lima bean research. This work describes our latest findings in short time evolution, genomics and expression, applied to Lima bean. This includes a chromosome-level assembly for the Andean gene pool and long-read sequencing of wild relatives. Large indels explained by transposable elements affect promoter regions of several genes related to domestication traits. The two major gene pools of P. lunatus diverged within the last million years, but recent insertions of LTRs produced important variations in genome size and composition. A core metabolic network for Phaseolus revealed patterns of variability in RNA expression for genes related to different primary and secondary metabolic processes. The Phaseolus genomes have important differences in the number, location, and expression of genes, which can explain the unique ability of Lima bean across domesticated Phaseolus species for production of HCN. Biological sciences/Plant sciences/Plant domestication Biological sciences/Genetics/Plant genetics Biological sciences/Plant sciences/Natural variation in plants Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryMaterials20241228.pdf Supplementary materials SupplementaryTables.xlsx Supplementary tables SupplementaryFile1orthogroups.txt Supplementary file 1 SupplementaryFile2SVsSVIMAndeanVsMeso.vcf.gz Supplementary file 2 SupplementaryFile3SVsONTAlignments.zip Supplementary file 3 SupplementaryFile4VisualizationsAgronomicGenes.pdf Supplementary file 4 SupplementaryFile5expressionDataPvulgaris.zip Supplementary file 5 SupplementaryFile6LimaAndeanV02.gff3.gz Supplementary file 6 SupplementaryFile7CoreNetworkPhaseolusPvulgarisEnzymes.xml Supplementary file 7 333.pdf Reporting Summary Cite Share Download PDF Status: Posted 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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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-5727653","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":397476883,"identity":"36d1d458-2444-4a18-b30b-6f0c1248d818","order_by":0,"name":"Jorge 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