Ramie (Boehmeria nivea) has been cultivated for thousands of years and is valued for strong bast fibers, nutritious green fodder, and bioactive compounds. chlorogenic acid (CGA), a phenylpropanoid metabolite with antioxidant and antimicrobial properties, is especially abundant in ramie tissues and contributes to the crop’s potential in food, feed, and plant-based products. Yet previous ramie genome assemblies remained fragmented, limiting the analysis of chromosome ends, centromeres, structural variation, and duplicated genes. The molecular basis of CGA accumulation was also unclear, including why roots and leaves differ so sharply and which biosynthetic route operates most strongly. Given these challenges, deeper research is needed into ramie’s complete genomic architecture and the molecular mechanisms controlling CGA biosynthesis and tissue-specific accumulation.
Researchers from Yangzhou University, Changsha Medical University, the Institute of Bast Fiber Crops at the Chinese Academy of Agricultural Sciences, and Changsha University published (DOI: 10.1093/hr/uhag144) the study online on 21 April 2026 in Horticulture Research. The team assembled a complete genome for the ramie germplasm “1380” and used it to examine genome evolution, gene-family expansion, and the origin of CGA biosynthesis from algae to higher plants. They then integrated root and leaf molecular profiles with enzyme assays to define the principal CGA-producing route in ramie and identify candidate genes for future improvement.
The researchers combined Pacific Biosciences high-fidelity (HiFi) reads, Oxford Nanopore Technologies (ONT) ultra-long reads, chromosome conformation capture (Hi-C) data, and short-read sequencing. The final Bniv_1380 assembly spans 344.21 megabases across 14 chromosomes, contains all 28 telomeres and 14 centromeres, and has no sequence gaps. It includes 25,853 predicted genes, 90.52% of which received functional annotations; Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis recovered 99.8% of conserved plant genes. Comparative analysis across 21 representative species suggested that key gene families of the core CGA pathway originated in land plants, while ramie showed expansion of several pathway genes, including six cinnamate 4-hydroxylase (C4H) copies. Liquid chromatography–tandem mass spectrometry (LC–MS/MS) detected clear metabolic separation between roots and leaves, with root CGA levels approximately tenfold higher. Ribonucleic acid sequencing (RNA-seq) identified 7,239 differentially expressed genes, including ten genes encoding major CGA-pathway enzymes. Five potential key genes were prioritized by integrating transcript abundance with metabolite patterns. Strong candidates included 4-coumarate–coenzyme A ligase 9 (Bni4CL9), cinnamate 4-hydroxylase (BniC4H), and p-coumarate 3-hydroxylase (BniC3H). Finally, a p-coumarate 3-hydroxylase (C3H) protein activity assay showed that C3H converted coumaroylquinic acid into CGA, supporting route 1 as the main biosynthetic route in ramie.
The authors said the complete genome transforms ramie from a genetically under-resolved crop into a workable system for connecting chromosome evolution with valuable plant chemistry. They said the tenfold difference between roots and leaves provides a clear biological contrast for finding the genes, enzymes, and regulatory networks that shape CGA production. The results also give breeders a more precise starting point than metabolite screening alone, because candidate targets can now be evaluated within a complete chromosomal framework. Future work, they added, should test these targets across broader germplasm collections, developmental stages, and field environments.
The study could accelerate marker-assisted breeding, genomic selection, and carefully designed genetic or metabolic engineering aimed at raising CGA content in ramie. Higher-CGA lines may strengthen the crop’s value for functional feed, plant-derived ingredients, and research on natural antioxidant and antimicrobial compounds, while the complete genome can also support improvement of fiber yield, stem growth, and stress resilience. However, the candidate genes and proposed pathway still require validation through gene editing, overexpression, loss-of-function studies, and multi-location field trials. Breeding programs will also need to determine whether increasing CGA changes fiber quality, forage palatability, plant growth, or other phenylpropanoid products. The resource therefore offers a roadmap rather than a finished commercial solution.
###
References
DOI
10.1093/hr/uhag144
Original Source URL
https://doi.org/10.1093/hr/uhag144
Funding information
This work was supported by grants from the National Natural Science Foundation of China (32472109) and Hunan Provincial Natural Science (2026JJ50437; 2026JJ50400).
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.