Genome assembly and multiomic analyses reveal insights into flower and bark colors of Lagerstroemia excelsa.

Lagerstroemia excelsa is a unique plant species from China, holds a significant aesthetic and economic value, and plays a crucial role in landscape architecture and horticulture. Thus far, there is little genetic and genomic information available about this species, which limits its use in development of new cultivars. In this study, a high-quality genome map of L. excelsa was obtained via whole-genome sequencing. Results showed that its genome size is about 330.4 Mb and a scaffold mapping rate is approximately 97.20%, resulting in 24 pseudochromosomes. L. excelsa might have undergone a recent whole-genome triplication event and diverged from the pomegranate about 32.3 million years ago (MYA). Subsequently, the divergence time between L. indica and L. excelsa was around 5.9 MYA. The transcriptomic and metabolomic analyses of L. excelsa and L. indica indicated that the chalcone synthase pathway may play a key role in regulating flower color differentiation between the two species. Additionally, a transcription factor LeMYB103 may be involved in regulating anthocyanin synthesis by interacting with LeMYB66, resulting in the accumulation of anthocyanins in the stem bark. This study is the first step toward genomic analysis of L. excelsa, which may provide a foundation for further molecular investigation of this species and offer valuable insights into the molecular mechanisms underlying the flower and stem bark colors in L. excelsa, two important ornamental traits in Lagerstroemia breeding.