The haplotype-resolved telomere-to-telomere genome and OMICS analyses reveal the genetic responses of tapping in rubber tree

The haplotype-resolved telomere-to-telomere genome and OMICS analyses reveal the genetic responses of tapping in rubber tree | 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 The haplotype-resolved telomere-to-telomere genome and OMICS analyses reveal the genetic responses of tapping in rubber tree Han Cheng, Chaochao Li, Yuan Yuan, Zhiyuan Wang, Zhiyi Nie, Tingkai Wu, and 14 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4798254/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 07 Jul, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Rubber tree (Hevea brasiliensis), as the primary source of natural rubber (NR), holds a significant economic significance. The high-quality genome has been long pursued to understand the rubber production process, genomic structure, and genomics-assisted breeding. Here, we assemble the first haplotype-resolved telomere-to-telomere (T2T), gap-free reference genome for rubber tree (CATAS 7-33-97). Two haplotypes (both 1.56 Gb) reveal all telomere and most centromeric regions. A dramatic amount of variations exist between the two haplotypes, including a 32.71 Mb inversion (sv33M) on chromosome 8. Complete assemblies of all 36 chromosomes enabled the exhaustive identification of rubber biosynthesis genes and the revealing of consistent allele specific expression (ASE) profiles. The reconstruction of the natural rubber biosynthesis pathway through transcriptomic and metabolomic profiling unraveled that mevalonate and its derivatives serve as the major carbon reservoir for quick latex replenishment during tapping. Jasmonic acid (JA) was crucial for the consecutive tapping-dependent rubber yield increment by responding to mechanic injuries, and by elevating rubber biosynthesis activity. Finally, we proposed a model of rubber tree's response to tapping, in which JA levels increased after mechanical damage. Subsequently, MYC2 in the JA signaling pathway stimulated the expression of MVK1 gene and the synthesis of mevalonic acid (MVA), enhancing rubber biosynthesis. The assembly of the haplotype-resolved T2T genome is a major step forward to understanding the complexity of the rubber biosynthesis mechanism in latex-producing plants, accelerating rubber tree genetic improvement. Biological sciences/Computational biology and bioinformatics/Data mining Biological sciences/Genetics/Gene regulation Biological sciences/Plant sciences/Plant physiology Biological sciences/Molecular biology/Transcriptomics Biological sciences/Genetics/Sequencing/Sequence annotation Hevea brasiliensis natural rubber T2T genome rubber biosynthesis rubber tapping Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryMaterial.pdf Cite Share Download PDF Status: Published Journal Publication published 07 Jul, 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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The high-quality genome has been long pursued to understand the rubber production process, genomic structure, and genomics-assisted breeding. Here, we assemble the first haplotype-resolved telomere-to-telomere (T2T), gap-free reference genome for rubber tree (CATAS 7-33-97). Two haplotypes (both 1.56 Gb) reveal all telomere and most centromeric regions. A dramatic amount of variations exist between the two haplotypes, including a 32.71 Mb inversion (sv33M) on chromosome 8. Complete assemblies of all 36 chromosomes enabled the exhaustive identification of rubber biosynthesis genes and the revealing of consistent allele specific expression (ASE) profiles. The reconstruction of the natural rubber biosynthesis pathway through transcriptomic and metabolomic profiling unraveled that mevalonate and its derivatives serve as the major carbon reservoir for quick latex replenishment during tapping. Jasmonic acid (JA) was crucial for the consecutive tapping-dependent rubber yield increment by responding to mechanic injuries, and by elevating rubber biosynthesis activity. Finally, we proposed a model of rubber tree's response to tapping, in which JA levels increased after mechanical damage. Subsequently, MYC2 in the JA signaling pathway stimulated the expression of MVK1 gene and the synthesis of mevalonic acid (MVA), enhancing rubber biosynthesis. 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