Medicinal plants have long served as important sources of traditional remedies and modern drug discovery, yet the genetic and biochemical foundations of many ethnomedicinal species remain insufficiently understood. Clinacanthus nutans, commonly known as “ezuihua” in Chinese, is a member of the Acanthaceae family and has been used in Thailand, Malaysia, Indonesia, and China for treating inflammation, viral infections, metabolic disorders, and tumor-related symptoms. Although previous phytochemical studies have reported flavonoids, triterpenoids, sulfur-containing glycosides, and chlorophyll derivatives in this plant, its genome-level regulatory mechanisms and organ-specific accumulation patterns remain unclear. Based on these challenges, an in-depth investigation of the genome, biosynthetic pathways, and organ-specific metabolic regulation of C. nutans is urgently needed.
In a study published (DOI: 10.1093/hr/uhag037) on February 23, 2026, in Horticulture Research, researchers from Fujian Agriculture and Forestry University and collaborating institutions reported the first chromosome-scale genome assembly of C. nutans. The study combines PacBio high-fidelity sequencing, chromosome conformation capture sequencing, Illumina sequencing, transcriptomic profiling, and metabolomic analysis to explore the evolutionary history and tissue-specific medicinal basis of this ethnomedicinal plant.
The researchers assembled a 731.61 Mbp chromosome-scale genome of C. nutans, with 93.76% of the assembled sequences anchored to 18 pseudochromosomes. Genome annotation identified 32,943 high-confidence protein-coding genes, while repetitive elements accounted for 69.05% of the genome, mainly long terminal repeat retrotransposons. Comparative genomic analyses revealed a Lamiales-wide whole-genome duplication event, followed by extensive chromosomal rearrangements, suggesting that ancient genome duplication and subsequent gene diversification may have contributed to the evolution of specialized medicinal traits.
To understand how different organs contribute to the plant’s medicinal potential, the team analyzed transcriptomes and metabolomes from five tissues: root, stem, young leaf, mature leaf, and flower. Transcriptomic analysis revealed pronounced differences between underground and aboveground organs, especially between roots and leaves. Metabolomic profiling detected 487 metabolites, with flavonoids and phenolic acids being the most abundant classes. Flavonoids, including kaempferol, luteolin, and apigenin derivatives, were mainly enriched in leaves and flowers, while triterpenoids and related compounds were more abundant in roots.
The study further identified 54 enzyme-encoding genes related to flavonoid biosynthesis and 53 enzyme-encoding genes related to triterpenoid biosynthesis. Gene family expansion in these pathways was mainly driven by segmental and dispersed duplications. Candidate genes such as CHS, CHI, 4CL, MVK, and OSC showed organ-biased expression patterns consistent with metabolite accumulation. Weighted gene co-expression network analysis also highlighted candidate transcription factor families, including MYB, bHLH, WRKY, AP2/ERF, and C2H2, that may participate in regulating these biosynthetic pathways. Importantly, these regulatory relationships are inferred from co-expression patterns and should be regarded as testable hypotheses rather than experimentally confirmed mechanisms.
The study provides a molecular framework for interpreting the traditional use of different C. nutans organs. Instead of viewing the plant as a single medicinal material, the findings show that roots, leaves, flowers, and stems have distinct biosynthetic profiles and may contribute differently to its therapeutic potential. This genome-enabled perspective helps bridge ethnomedicinal knowledge and modern plant science, offering a clearer route for identifying useful compounds, improving medicinal quality evaluation, and guiding the rational utilization of specific plant organs.
This work establishes a foundational genomic and multiomics platform for C. nutans. The chromosome-scale genome, transcriptomic profiles, and metabolomic datasets will support future studies on functional gene validation, metabolic engineering, and molecular breeding. In practical terms, the findings may help develop more precise quality control standards for medicinal materials and promote organ-targeted utilization of this species. More broadly, the integrative strategy used in this study offers a transferable framework for investigating other ethnomedicinal plants whose traditional applications depend on different plant parts but whose molecular mechanisms remain largely unexplored.
###
References
DOI
10.1093/hr/uhag037
Original Source URL
https://doi.org/10.1093/hr/uhag037
Funding information
This work was supported by the National Key R&D Program of China (2023YFA0913500) and the National Natural Science Foundation of China (32270366 and 32460062).
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.