How a decaploid plant evolved to fight disease with powerful compounds

Researchers have decoded the chromosome-level genome of Houttuynia cordata, an important East Asian medicinal plant known for its strong flavor and wide pharmacological use. This species was found to be decaploid, containing ten sets of chromosomes, and has undergone multiple genome duplications during evolution. The team identified significantly expanded gene families involved in the biosynthesis of medicinal alkaloids, including STR, DDC, 6OMT, and 4OMT. High expression of these genes in root and rhizome tissues supports their vital role in alkaloid accumulation. This study not only unveils the evolutionary history of H. cordata, but also sets a foundation for its genetic improvement and pharmaceutical exploration.

Houttuynia cordata is a unique plant widely used in traditional Chinese medicine and as a culinary vegetable across Asia. Its therapeutic properties are primarily attributed to alkaloids, a diverse group of bioactive compounds. However, the lack of genomic resources has long limited deeper understanding of its biosynthetic pathways and genetic diversity. Moreover, polyploid plants like H. cordata—with complex genomes and variable chromosome numbers—are difficult to study using conventional genetic tools. Understanding the mechanisms behind its evolution, chromosome structure, and secondary metabolite production is crucial. Due to these challenges, comprehensive research into the genome and alkaloid biosynthesis of H. cordata is urgently needed.

A research team from Hunan Agricultural University and collaborating institutes has published (DOI: 10.1093/hr/uhae203) the first chromosome-level genome of decaploid Houttuynia cordata in Horticulture Research on July 30, 2024. By integrating Illumina, PacBio HiFi, and Hi-C technologies, the scientists assembled 88 pseudochromosomes representing the 90 actual chromosomes of this medicinal plant. The study not only uncovers the plant's complex genome evolution but also identifies key genes driving the biosynthesis of isoquinoline and indole alkaloids, paving the way for improved cultivation and medical applications.
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Using high-fidelity sequencing and chromosome conformation techniques, the researchers constructed a 2.63 Gb genome for H. cordata, resolving its decaploid nature (2n = 10x = 90). Analysis revealed that the species experienced two whole-genome duplication events—approximately 17 and 3.3 million years ago—contributing to extensive gene duplication and evolution. Among 139,087 predicted protein-coding genes, several gene families involved in alkaloid synthesis were remarkably expanded.

Notably, l-amino acid/l-tryptophan decarboxylase (DDC) and strictosidine synthase (STR)—critical for isoquinoline and indole alkaloid biosynthesis—showed high copy numbers and tissue-specific expression, particularly in roots and rhizomes. 6OMT and 4OMT, key enzymes in methylation steps, were also significantly enriched. The study identified nine copies of TTM3, a gene involved in root development, further supporting the plant’s adaptation and high alkaloid content in underground parts. This integrated genomic and transcriptomic approach provides the most comprehensive view of H. cordata's evolution and medicinal potential to date.

“This genome represents a major leap in our understanding of polyploid medicinal plants,” said Dr. Jianguo Zeng, corresponding author of the study. “By dissecting the complex genome structure and linking expanded gene families with alkaloid biosynthesis, we now have genetic targets to explore both evolutionary biology and pharmaceutical enhancement of Houttuynia cordata. The findings highlight the power of modern sequencing tools in resolving intricate genomes and translating them into applied health benefits.”

The insights gained from this decaploid genome provide a valuable foundation for molecular breeding and bioengineering of H. cordata. By targeting the identified gene families, researchers can now develop strategies to enhance alkaloid content for pharmaceutical use or improve agronomic traits such as disease resistance and root growth. Furthermore, this study offers a genomic model for other polyploid medicinal plants, facilitating future comparative and evolutionary studies. The findings hold promise for advancing plant-based drug discovery and could lead to novel therapeutic compounds derived from this traditional medicinal herb.

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References

DOI

10.1093/hr/uhae203

Original Source URL

https://doi.org/10.1093/hr/uhae203

Funding information

This work was supported by the China Agriculture Research System (No. CARS-21).

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.