Background
Aromatic ornamentals are increasingly valued for indoor use, where plant-associated volatiles can shape sensory experiences and have been discussed in relation to comfort and well-being, thereby increasing the demand for compact species with fragrance and controllable flowering. Coleus hadiensis (syn. Plectranthus hadiensis) represents a promising candidate for indoor aromatic ornamental use because of its fragrance and compact growth habit. However, genomic resources for Coleus remain limited, and the gene families underlying terpenoid biosynthesis and flowering regulation have not been systematically characterized.
Results
Here we report a chromosome-level reference genome of C. hadiensis generated using long-read sequencing and Hi-C scaffolding and provide a genome-wide annotation of repeats, terpene-related gene families, and flowering-associated regulators. The 1.83 Gbp assembled genome revealed a highly repeat-rich genome architecture dominated by Copia-type long terminal repeat retrotransposons with insertion-time estimates peaking at approximately 1–1.5 million years ago. Terpene synthase genes were comprehensively identified with 128 coding sequences distributed across multiple subfamilies, several of which formed tandem clusters. A genome-wide survey of phosphatidylethanolamine-binding protein genes identified candidates associated with flowering control, including an FT-like regulator with repressor activity in a heterologous system.
Conclusions
Our analyses of the chromosome-scale genome of C. hadiensis provided new insight into genomic features associated with fragrance and flowering and established a foundation for understanding fragrance- and flowering-related traits and for advancing genomics-assisted breeding in C. hadiensis.