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Rosa rugosa , commonly known as rugged rose, is a perennial ornamental shrub. It produces beautiful flowers with a mild fragrance and colorful seed pods. Unlike many other cultivated roses,  R. rugosa  adapts to a wide range of habitat types and harsh environmental conditions such as salinity, alkaline, shade, drought, high humidity, and frigid temperatures. Here, we produced and analyzed a high-quality genome sequence for  R. rugosa  to understand its ecology, floral characteristics and evolution. PacBio HiFi reads were initially used to construct the draft genome of  R. rugosa , and then Hi-C sequencing was applied to assemble the contigs into 7 chromosomes. We obtained a 382.6 Mb genome encoding 39,704 protein-coding genes. The genome of  R. rugosa  appears to be conserved with no additional whole-genome duplication after the gamma whole-genome triplication (WGT), which occurred ~100 million years ago in the ancestor of core eudicots. Based on a comparative analysis of the high-quality genome assembly of  R. rugosa  and other high-quality Rosaceae genomes, we found a unique large inverted segment in the Chinese rose  R. chinensis  and a retroposition in strawberry caused by post-WGT events. We also found that floral development- and stress response signaling-related gene modules were retained after the WGT. Two  MADS-box  genes involved in floral development and the stress-related transcription factors  DREB2A-INTERACTING PROTEIN 2  ( DRIP2 ) and  PEPTIDE TRANSPORTER 3  ( PTR3 ) were found to be positively selected in evolution, which may have contributed to the unique ability of this plant to adapt to harsh environments. In summary, the high-quality genome sequence of  R. rugosa  provides a map for genetic studies and molecular breeding of this plant and enables comparative genomic studies of  Rosa  in the near future.

A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics