# Isofraxidin biosynthesis in Chloranthus: genomic insights into metabolic evolution of an early angiosperm phytoalexin

## TL;DR

This study explores the biosynthesis of isofraxidin, a coumarin in Chloranthus, by analyzing its genome and metabolism, revealing insights into early angiosperm chemical defenses.

## Contribution

The paper provides the first detailed genomic and metabolomic analysis of isofraxidin biosynthesis in an early angiosperm.

## Key findings

- A high-quality genome of Chloranthus spicatus was assembled, revealing an ancient whole-genome duplication.
- 267 candidate genes across 9 enzyme families were identified as involved in isofraxidin biosynthesis.
- Amplified COSY genes and specific CYP450s and O-methyltransferases were linked to key steps in coumarin production.

## Abstract

As an early-diverging angiosperm lineage, Chloranthaceae produces specialized coumarins with documented antimicrobial and anti-inflammatory activities, which contribute to its ecological success. Isofraxidin, the most representative simple coumarin in this clade, exhibits significant pharmaceutical potential. However, its biosynthetic basis remains uncharacterized. Here, we assembled a high-quality triploid genome of Chloranthus spicatus (8.57 Gb, contig N50 = 8.76 Mb) to explore the evolution of defensive metabolism. Genomic analysis revealed an ancient whole-genome duplication event and expanded gene families associated with pathogen resistance. Metabolomic analysis identified at least 49 coumarin compounds in Chloranthus plants, significantly exceeding previous records. Integrated omics revealed 267 candidate biosynthetic genes across 9 enzyme families governing isofraxidin biosynthesis. Building on the upstream synthesis of the phenylpropanoid backbone, this study identifies amplified coumarin synthase (COSY) genes linked to umbelliferone accumulation, and specific CYP450s and O-methyltransferases catalyzing final structural modifications. This work elucidates the evolution of chemical defenses in early angiosperms and enables the engineering of plant-derived antimicrobials.