BackgroundMurraya paniculata(L.) Jack, commonly called orange jessamine in the family Rutaceae, is an important ornamental plant in tropical and subtropical regions which is famous for its strong fragrance. Although genome assemblies have been reported for many Rutaceae species, mainly in the genusCitrus, full genomic information has not been reported forM. paniculata, which is a prerequisite for in-depth genetic studies onMurrayaand manipulation using genetic engineering techniques. Here, we report a high-quality chromosome-level genome assembly ofM. paniculataand aim to provide insights on the molecular mechanisms of flower volatile biosynthesis.ResultsThe genome assembly with a contig N50 of 18.25 Mb consists of 9 pseudomolecules and has a total length of 216.86 Mb. Phylogenetic analysis revealed thatM. paniculatadiverged from the common ancestor approximately 25 million years ago and has not undergone any species-specific whole genome duplication events. Genome structural annotation and comparative genomics analysis revealed that there are obvious differences in transposon contents among the genomes ofM. paniculataandCitrusspecies, especially in the upstream regions of genes. Research on the flower volatiles ofM. paniculataandC. maximaat three flowering stages revealed significant differences in volatile composition with the flowers ofC. maximalacking benzaldehyde and phenylacetaldehyde. Notably, there are transposons inserted in the upstream region of thephenylacetaldehyde synthase(PAAS) genesCg1g029630andCg1g029640inC. maxima, but not in the upstream region of threePAASgenesMe2G_2379,Me2G_2381, andMe2G_2382inM. paniculata. Our results indicated that compared to the low expression levels ofPAASgenes inC. maxima, the higher expression levels of the threePAASgenes inM. paniculataare the main factor affecting the phenylacetaldehyde biosynthesis and causing the content difference of phenylacetaldehyde. The phenylacetaldehyde synthetic activities of the enzymes encoded byM. paniculata PAASgenes were validated by in vitro analyses.ConclusionsOur study provides useful genomic resources ofM. paniculatafor further research on Rutaceae plants, identifies newPAASgenes, and provides insights into how transposons contribute to variations in flower volatiles amongMurrayaandCitrusplants.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12915-023-01639-6.