Genome assembly provided new insights into the Cinnamomum burmannii evolution and D-borneol biosynthesis differences between chemotypes

D-Borneol is a precious monoterpenoid widely used in the pharmaceutical and cosmetic industries. Cinnamomum burmannii (Nees et T.Nees) Blume (C. burmannii) is one of the key resources for D-Borneol. However, only one chemotype of C. burmannii contain high content of D-Borneol in its leaves and stems. Limited by little information from C. burmannii, the D-Borneol biosynthesis mechanisms, as well as the mechanisms underlying the D-Borneol production differences among chemotypes remains elusive. To fill these gaps, we generated a completed genome of a high D-Borneol content chemotype of C. burmannii. Phylogenetic analysis suggests that C. burmannii is sister to a clade containing C. camphora and C. kanehirae while the variations of chromosome structure and LTR-RTs are important factors for differentiation in Cinnamomum. Further comparison of genome sequence demonstrated few genomic sequence differences between two chemotypes of C. burmannii. However, the pathway and transcriptomic profiling analysis revealed the expression differences of the genes in MEP pathway, a main pathway responsible for D-Borneol synthesis, which may be the critical determinant for the D-Borneol production differences between the two chemotypes. Our results also implied epigenetic modulation may participate in this process. Finally, a genome database (CAMD) of Cinnamomum species was constructed for better resources exploration. The present study provided the first high-quality genome and comprehensive genomic resources of C. burmannii. which not only provided new insights into the evolution of Cinnamomum species, but also shed light on the mechanisms of D-Borneol biosynthesis and the molecular signatures characterized high and low D-Borneol chemotypes of C. burmannii.