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

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.