Haplotype-resolved genome assembly provides insights into the floral scent of Rosa rugosa

Abstract Rose is an important aromatic plant and produces flowers that are used in medicine and food. We herein present a haplotype-resolved genome for Rosa rugosa cultivar Hanxiang. Analyses of allele-specific expression identified a potential mechanism underlying floral scent biosynthesis. Population genomic analyses involving 133 Rosa accessions elucidated evolutionary histories and a single R. rugosa domestication event. Pathways mediating the synthesis of scent-related metabolites were enriched according to the analyses of the transcriptomes, haplotype variations, and allelic imbalances during the flower development stages of Hanxiang and Guomeigui ( R. rugosa accessions with diverse fragrances). The enzyme-encoding ASE genes RrHX1G119800 and RrHX1G204700 (primary amine oxidases) and RrHX2G284700 (L-tryptophan decarboxylase) in the phenylethylamine pathway were tentatively designated as core genes useful for improving 2-phenylethanol production in rose flowers. Our results provide molecular insights into the formation of R. rugosa floral fragrances and genome-level data that are useful for enhancing rose traits via genetic engineering.