A chromosome-scale genome of the Korean cultivar Sesamum indicumvar. Goenbaek provides insight into its oil-seed quality and health-promoting gene repertoire

Abstract Sesamum indicum seeds are omnipresent in Korean dietary habits as food decorations, and the oil is used in traditional medicine due to its natural antioxidant content. Although genomic resources are available mainly from Chinese and Indian genotypes, the lack of Korean genomic resources hampers the design of novel genotypes with valuable agronomic importance as well as food and health-enhancing properties. This study aimed to generate a high-quality chromosome-level genome of the Korean cultivar Goenbaek, which is rich in oil, sesamin, and sesamolin. The combination of short- and long-reads and chromosome conformation capture data helped to assemble the genome into 13 chromosomes spanning 262.5 Mbp with an N50 value of 19.9 Mbp. A total of 23,539 protein-coding genes were predicted. Phylogenetic analysis placed Goenbaek on a distinct branch, suggesting geographical or adaptive patterns leading to genetic diversity. Goenbaek exhibited a set of 1,171 species-specific gene families enriched in lipid metabolism and biosynthesis, fatty acid metabolism, and phenylpropanoid biosynthesis, which confirmed its rich oil content. In addition, health-beneficial genes related to sphingolipid and selenocompound metabolism were also identified. The new reference-grade genome will serve as a reference for the Korean genomics-assisted sesame breeding program for the improvement of agronomic traits and for the investigation of oil and specialized metabolites.