The red flower wintersweet genome provides insights into the evolution of magnoliids and the molecular mechanism for tepal color development.

Wintersweet (Chimonanthus praecox) is one of the most important ornamental plants, whose color is mainly determined by the middle tepals. However, the molecular mechanisms underlying the intriguing flower color development among different wintersweet groups are still largely unknown. In addition, wintersweet belongs to magnoliids, and the issue remains as to how to determine the phylogenetic position of magnoliids conclusively. Here, the whole genome of red flower wintersweet, a new wintersweet type, was sequenced and assembled with high-quality. The genome comprised 11 super-scaffolds (chromosomes) with a total size of 737.03 Mb. Based on the analyses of the long branch attraction (LBA), incomplete lineage sorting (ILS), sparse taxon sampling and other factors, we suggest that a bifurcating tree may not fully represent the complex early diversification of the angiosperms, and that magnoliids are most likely to be the sister of the eudicots. The wintersweet genome appears to have undergone two rounds of whole-genome duplication (WGD) events: a younger WGD event representing an independent event specific to the Calycanthaceae species; and an ancient WGD event shared by Laurales. By integrating genomic, transcriptomic, and metabolomic data, CpANS1 and transcription factor CpMYB1 were considered to play key roles in regulating tepal color development, whereas CpMYB1 needs to form a complex with bHLH and WD40 to fully perform its regulatory function. The present study not only provided novel insights into the evolution of magnoliids and the molecular mechanism for flower color development, but also laid the foundation for subsequent functional genomics study and molecular breeding of wintersweet.