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Background <p>Aromatic ornamentals are increasingly valued for indoor use because plant-associated volatiles can shape sensory experiences and have been discussed in relation to comfort and well-being, thereby driving demand for compact species with fragrance and controllable flowering. <i>Coleus hadiensis</i> (syn. <i>Plectranthus hadiensis</i>) is considered a promising indoor aromatic ornamental because of its fragrance and compact growth habit. However, genomic resources for <i>Coleus</i> remain limited, and the gene families associated with terpenoid biosynthesis and flowering regulation have not been systematically characterized.</p> Results <p>Here, we present a chromosome-level reference genome of <i>C. hadiensis</i> generated using long-read sequencing together with Hi-C scaffolding and provide genome-wide annotation of repeats, terpene-related gene families, and flowering-associated regulators. The assembled 1.83 Gbp genome exhibited a highly repeat-rich genomic architecture dominated by <i>Copia</i>-type long terminal repeat retrotransposons with insertion-time estimates peaking approximately 1–1.5&#xa0;million years ago. We identified 128 terpene synthase coding sequences distributed among multiple subfamilies, several of which formed tandem clusters. A genome-wide survey of phosphatidylethanolamine-binding protein genes further identified candidates associated with flowering regulation, including an <i>FT</i>-like regulator that exhibited repressor activity in a heterologous system.</p> Conclusions <p>Our analyses of the chromosome-scale genome of <i>C. hadiensis</i> provide new insights into genomic features associated with fragrance and flowering traits and establish a foundation for understanding fragrance- and flowering-related characteristics and for advancing genomics-assisted breeding in <i>C. hadiensis</i>.</p>

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A chromosome-scale genome assembly of the aromatic ornamental Coleus hadiensis reveals terpene synthase clusters and a Lamiaceae-conserved floral repressor candidate

  • 期刊论文

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  • 发表日期：

    2026年7月23日

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  • Yoshikazu Furuta,
  • Hiroki Sugimoto,
  • Ritsuko Kitagawa-Yogo,
  • Hinano Mizuno,
  • Akari Nakasone,
  • Hidenori Tanaka,
  • Nobuhiko Muramoto

摘要

Background

Aromatic ornamentals are increasingly valued for indoor use because plant-associated volatiles can shape sensory experiences and have been discussed in relation to comfort and well-being, thereby driving demand for compact species with fragrance and controllable flowering. Coleus hadiensis (syn. Plectranthus hadiensis) is considered a promising indoor aromatic ornamental because of its fragrance and compact growth habit. However, genomic resources for Coleus remain limited, and the gene families associated with terpenoid biosynthesis and flowering regulation have not been systematically characterized.

Results

Here, we present a chromosome-level reference genome of C. hadiensis generated using long-read sequencing together with Hi-C scaffolding and provide genome-wide annotation of repeats, terpene-related gene families, and flowering-associated regulators. The assembled 1.83 Gbp genome exhibited a highly repeat-rich genomic architecture dominated by Copia-type long terminal repeat retrotransposons with insertion-time estimates peaking approximately 1–1.5 million years ago. We identified 128 terpene synthase coding sequences distributed among multiple subfamilies, several of which formed tandem clusters. A genome-wide survey of phosphatidylethanolamine-binding protein genes further identified candidates associated with flowering regulation, including an FT-like regulator that exhibited repressor activity in a heterologous system.

Conclusions

Our analyses of the chromosome-scale genome of C. hadiensis provide new insights into genomic features associated with fragrance and flowering traits and establish a foundation for understanding fragrance- and flowering-related characteristics and for advancing genomics-assisted breeding in C. hadiensis.