How huo xiang makes its medicinal aroma: Genome analysis reveals key biosynthetic gene cluster
image: Evolutionary origin of the pulegone BGC. (A) Original hypothesis of BGC formation based on S. tenuifolia genome assembly. (B) Observation of the A. rugosa BGC and consequences for the hypothesis. (C) Revised hypothesis of BGC formation with new data considered.
Credit: Horticulture Research
Monoterpenoids are important plant-derived compounds widely used in fragrances, nutraceuticals, and medicinal applications. Agastache rugosa, a member of the mint family, produces pulegone and isomenthone, key components contributing to its aromatic and therapeutic properties. In this study, researchers generated a haplotype-resolved chromosome-scale genome of A. rugosa to uncover the genetic basis underlying monoterpenoid biosynthesis. The analysis revealed a biosynthetic gene cluster responsible for pulegone formation, along with evidence of gene duplications and evolutionary divergence compared to closely related species. These findings provide new insight into how specialized metabolic pathways evolve in plants and offer a valuable genomic resource for future metabolic engineering and breeding strategies.
Members of the Lamiaceae family are well known for producing diverse monoterpenoids that contribute to plant defense, aroma, and human health benefits. In Agastache rugosa, two major chemotypes exist: a monoterpenoid-rich pulegone type and a phenylpropanoid-dominant estragole type. Understanding how different biosynthetic pathways are encoded and regulated at the genomic level is critical for explaining chemical diversity across chemotypes. Biosynthetic gene clusters (BGCs) represent an important mechanism for pathway coordination, yet their evolutionary origin and structural rearrangements remain unclear in many medicinal plants. Due to these knowledge gaps, it is necessary to conduct a detailed genomic investigation into monoterpenoid biosynthesis in A. rugosa.
A research team from Nanjing University of Chinese Medicine and the University of York reported a haplotype-resolved genome of Agastache rugosa, published (DOI: 10.1093/hr/uhaf034) on May 1, 2025, in Horticulture Research. The study identified a monoterpenoid biosynthetic gene cluster linked to pulegone production and compared its organization with that of closely related mint species, providing new evolutionary and functional insights into chemical metabolism in aromatic medicinal herbs.
Using PacBio HiFi long-read sequencing combined with Hi-C chromatin conformation analysis, the researchers assembled a high-quality genome with chromosome-level resolution. They identified a biosynthetic gene cluster containing duplicated copies of LS (limonene synthase), L3OH (limonene 3-hydroxylase), and IPR (isopiperitenone reductase), as well as the downstream oxidation enzyme ISPD. This cluster exhibited synteny with a previously characterized pulegone cluster in Schizonepeta tenuifolia, suggesting that the cluster originated in a shared ancestor and later diverged through structural rearrangement. Additionally, a tandem gene array encoding PR (pulegone reductase) was located on a different chromosome. Hi-C interaction profiling revealed potential three-dimensional contact between the gene cluster and the PR array, indicating spatial coordination in metabolic regulation. Both regions were enriched in retrotransposons, supporting the hypothesis that transposable elements contribute to gene cluster formation and expansion in plant specialized metabolism.
The researchers emphasized that this work not only provides a complete and high-resolution genomic foundation for studying A. rugosa, but also contributes to a broader understanding of how metabolic diversity evolves in medicinal plants. They noted that the discovery of gene clustering, duplication events, and long-range chromatin interactions highlights the complex regulatory architecture underlying terpene biosynthesis, offering a framework for future comparative and functional studies across the mint family.
The availability of a haplotype-resolved genome enables targeted genetic improvement of A. rugosa for enhanced essential oil quality and yield. The identified biosynthetic gene cluster offers clear targets for metabolic engineering and synthetic biology applications aimed at producing monoterpenoids more efficiently. Furthermore, insights into 3D genome organization may help optimize pathway flux through regulatory rewiring. Beyond this species, the comparative evolutionary framework established in this study will support natural product discovery and trait enhancement in other aromatic and pharmaceutical plants.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhaf034
Funding information
This research was supported by the National Natural Science Foundation of China (grant nos. 82373978, 81973435), the National Natural Science Foundation for Young Scientists of China (grant no. 81903756), the Natural Science Foundation of Jiangsu Province (grant no. BK20231307), the Open Project of Chinese Materia Medica First-Class Discipline of Nanjing University of Chinese Medicine (grant no. ZYXYL2024-002) and High-Level University 2024 Key Cultivation Project -Research Leadership Program (grant no. RC202411). B.R.L. and S.J.S were funded by the BBSRC (BB/V006452/1). B.R.L acknowledges UKRI fellowship funding (MR/S01862X/1 and MR/X010260/1) and the Royal Society (IEC\NSFC\233491).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.