Haplotype-resolved genome assembly provides insights into the unique floral scent of Rosa rugosa originated in China

Rosa rugosa is an important aromatic plant and produces flowers that are used in medicine, food, plant essential oils, hydrosols, and other aromatic products. 2-phenylethanol (2-PE) is the main effective substance in the volatile organic compounds of rose fragrance, and its synthesis mechanism in R. rugosa needs to be investigated. We herein present a haplotype-resolved genome of R. rugosa cv. Hanxiang (HX). Pathways mediating the synthesis of scent-related metabolites were deciphered in depth. Allelic imbalances reveal the distinct roles of different haplotyping in shaping the key trait including fragrance during the flower development stages. We deciphered the population structure and genetic composition of rose. Selected and mutated genes in groups of separated aromas including but not limited to one rate-limiting enzymes, primary amine oxidases, is responsible for the high level of 2-PE biosynthesis in R. rugosa, which could provide new genetic resources for enhancing aroma in other species.