Chromosome-level genome assembly of Origanum vulgare subsp. hirtum reveals evolutionary insights and regulatory modules in terpenoid biosynthesis

Abstract

Oregano ( Origanum vulgare ) is a highly valued aromatic herb for culinary, medicinal, and ornamental purposes. Its commercial value is largely from its essential oil (EO), which is rich in key bioactive terpenoids, such as carvacrol and thymol. Greek oregano ( O. vulgare subsp. hirtum ) subspecies is particularly prized for its high EO content. In this study, we generated a high-quality genome assembly of Greek oregano to investigate its evolutionary trajectory and the genetic basis of terpenoid biosynthesis. The assembly spans 709.74 Mb and is anchored to 15 chromosomes, with a scaffold N50 of 46.36 Mb. Comparative genomic analysis revealed a whole-genome duplication event, estimated at ∼59.93 million years ago, which likely contributed to the diversification of terpenoid biosynthesis pathways within the Lamiaceae family. Using a rapid screening approach, we identified Greek oregano mutants with higher EO content. Integrated genomic and transcriptomic analysis of a high-EO mutant highlighted the importance of α -linolenic acid metabolism/jasmonic acid (JA) biosynthesis pathways in EO production. Exogenous JA treatment led to upregulation of key EO biosynthetic genes and higher EO content. Furthermore, a JA-inducible bHLH transcription factor, OvbHLH13, was identified as a central regulator of terpenoid biosynthesis. Through Y1H, transcriptional activation, and EMSA assays, we demonstrated that OvbHLH13 directly bound to and transactivated the promoter of OvSDR1 , which encodes a critical enzyme in thymol and carvacrol production. Collectively, this genomic resource provides valuable insights into the genetic and regulatory network controlling terpenoid biosynthesis and establishes a critical genomic foundation for molecular breeding of Greek oregano.

Acknowledgments

We thank Dr. Yiwei Jiang (Beijing Forestry University), Dr. Kehua Wang (China Agricultural University), and Dr. Hongwei Liu (Nanjing Agricultural University) for their careful editing of the manuscript. This work was supported by the Open Competition Projects of the Key Laboratory of Grassland Ecosystems (Ministry of Education), Gansu Agricultural University (Project No: KLGE-2024-03), and by the National Natural Science Foundation of China (32371778, U23A20218, 32271755).

Author contributions

BX and JZ conceived and designed the study. TY, HG, YZ, YY, HH, XL, JL, CX, YW, HY, LH, YL, SY, and YC conducted the experiments. TY, YW, and JZ analyzed the data. BX and JZ wrote and revised the manuscript.

Data availability

The raw genome sequencing and RNA sequencing data from fluorescence, leaf, root, and shoot samples for genome annotation have been deposited in the China National Center for Bioinformation database under accession number PRJCA038347. The raw RNA sequencing data from HEO1 mutant and WT plants have also been deposited in the China National Center for Bioinformation database under accession number PRJCA047213. Files corresponding to the genome assembly, structural annotations, predicted protein sequences, and transcript sequences have been publicly deposited in Figshare (https://doi.org/10.6084/m9.figshare.30354568). The data supporting the findings of this work are available from the supplementary material or upon request.

Conflicts of interest statement

The authors declare no conflicts of interest.

Supplementary material

Supplementary material is available at Horticulture Research online.

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