Integrative multi-omics data provide insights into the biosynthesis of furanocoumarins and mechanisms regulating their accumulation in Angelica dahurica

Jiaojiao Ji; Xiaoxu Han; Lanlan Zang; Yushan Li; Liqun Lin; Donghua Hu; Shichao Sun; Yonglin Ren; Garth Maker; Zefu Lu; Li Wang

doi:10.1038/s42003-025-08076-x

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Integrative multi-omics data provide insights into the biosynthesis of furanocoumarins and mechanisms regulating their accumulation in Angelica dahurica

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Integrative multi-omics data provide insights into the biosynthesis of furanocoumarins and mechanisms regulating their accumulation in Angelica dahurica

Jiaojiao Ji, Xiaoxu Han, Lanlan Zang, Yushan Li, Liqun Lin, Donghua Hu, Shichao Sun, Yonglin Ren, Garth Maker, Zefu Lu, …

Communications biology, Vol.8(1), 649

2025

DOI: https://doi.org/10.1038/s42003-025-08076-x

PMID: 40269101

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Abstract

Angelica - genetics

Angelica - growth & development

Angelica - metabolism

Biosynthetic Pathways

Cytochrome P-450 Enzyme System - genetics

Cytochrome P-450 Enzyme System - metabolism

Furocoumarins - biosynthesis

Furocoumarins - metabolism

Gene Expression Regulation, Plant

Multiomics

Plant Proteins - genetics

Plant Proteins - metabolism

Plant Roots - genetics

Plant Roots - growth & development

Plant Roots - metabolism

Furocoumarins (FCs), important natural compounds with biodefense roles and pharmacological activities, are notably abundant in medicinal plant Angelica dahurica. However, its accumulation patterns over development stages in FC-enriched tissue, biosynthetic pathways, and regulatory mechanisms in A. dahurica remain elusive. Here, we quantified the concentration dynamics of 17 coumarins across six developmental stages of root and found a gradual decrease in FC concentration as the roots develop. Using a de-novo assembled chromosome-level genome for A. dahurica, we conducted integrative multi-omics analyses to screen out candidate genes to fill in the sole missing step in the biosynthesis of imperatorin and isoimperatorin. This revealed that CYP71AZ18 catalyzes hydroxylation at the C-5 position of psoralen to generate bergaptol, while CYP71AZ19 and CYP83F95 catalyze hydroxylation at the C-8 position to produce xanthotoxol, notably indicating that a single step is catalyzed by two genes from distinct CYP450 subfamilies in this species. CYP71AZ19 originated from a proximal duplication event of CYP71AZ18, specific to A. dahurica, and subsequently underwent neofunctionalization. Accessible chromatin regions (ACRs), especially proximal ACRs, correlated with high gene expression levels, and the three validated genes exhibited strong signals of ACRs, showing the importance of chromosomal accessibility in regulating metabolite biosynthesis.

Details

Title: Integrative multi-omics data provide insights into the biosynthesis of furanocoumarins and mechanisms regulating their accumulation in Angelica dahurica
Authors/Creators: Jiaojiao Ji - Agricultural Genomics Institute at Shenzhen
Xiaoxu Han - Agricultural Genomics Institute at Shenzhen
Lanlan Zang - Agricultural Genomics Institute at Shenzhen
Yushan Li - Institute of Crop Sciences
Liqun Lin - Agricultural Genomics Institute at Shenzhen
Donghua Hu - Agricultural Genomics Institute at Shenzhen
Shichao Sun - Agricultural Genomics Institute at Shenzhen
Yonglin Ren - Murdoch University, Centre for Biosecurity and One Health
Garth Maker - Murdoch University, Centre for Computational and Systems Medicine
Zefu Lu - Institute of Crop Sciences
Li Wang - Agricultural Genomics Institute at Shenzhen
Publication Details: Communications biology, Vol.8(1), 649
Publisher: Springer Nature; BERLIN
Number of pages: 15
Grant note: 32300223, 32070242, and 82373837 / National Natural Science Foundation of China (National Science Foundation of China)
Identifiers: 991005765128807891
Murdoch Affiliation: Centre for Biosecurity and One Health; School of Medical, Molecular and Forensic Sciences; College of Environmental and Life Sciences; Centre for Computational and Systems Medicine
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.16 Phytochemicals; 3.16.1717 Bioactive Coumarins
Web Of Science research areas: Biology
ESI research areas: Biology & Biochemistry