Pan‐Genome of Jasminum sambac Reveals the Genetic Diversity of Different Petal Morphology and Aroma‐Related Genes

ABSTRACT Jasmine ( Jasminum sambac ) is globally renowned for its distinct fragrance and ornamental appeal, existing primarily in three floral morphologies: single‐petal, double‐petal and multi‐petal. De novo sequencing and chromosome‐level genome assembly were performed on two distinct jasmine varieties: ‘Yuanye’ double‐petal and ‘Bijian’ multi‐petal jasmines. These assemblies, along with three previously published genomes, were integrated to construct a pan‐genome framework that comprehensively encompasses both the core and variable genomic components of jasmine. A substantial number of structural variations (SVs) and single nucleotide polymorphisms (SNPs) had been identified, of which 89.5% were insertions/deletions (size ≥ 50 bp), whereas gene families also exhibited significant contractions and expansions, revealing the high complexity and dynamics of the jasmine genomes. Comparative genomic approaches further revealed multiple transcription factor families associated with aromatic biosynthesis, floral organogenesis and environmental adaptability. Key genes involved in the formation of jasmine scent, with a particular focus on the variation in copy number and expression levels of critical enzyme genes responsible for the production of four major volatile terpenoids and benzyl acetate, thereby elucidating the genetic basis of jasmine aroma diversity. Additionally, within the MADS‐box gene family, the PI and AP3 subfamilies are hypothesized to play crucial roles in the development of floral organs. Through the integration of these comprehensive data, a pan‐genome website for jasmine was developed to facilitate data download and visualise genomic variations via a genome browser ( https://www.pan‐jasmine.cn/ ). In summary, this work provides valuable genomic resources for the genetic enhancement and marker‐assisted breeding of jasmine.