For centuries, medicinal plants have been nature's pharmacy, offering healing properties that traditional medicines harnessed across cultures.
Today, modern science is revolutionizing this ancient wisdom through bioinformatics—a powerful interdisciplinary field merging biology, computer science, and data analytics. By decoding the genetic and metabolic secrets of plants, bioinformatics is accelerating the discovery of novel therapeutics, optimizing cultivation, and preserving biodiversity.
Billion USD (2023 Market Value)
Billion USD (2032 Projected Value) 6
Medicinal Plants Sequenced
Bioinformatics enables the sequencing and assembly of medicinal plant genomes, which are often complex due to high heterozygosity, polyploidy, and repetitive sequences.
As of February 2025, 431 medicinal plants across 203 species have been sequenced, though only 11 have achieved telomere-to-telomere (T2T) gapless assemblies .
Bioinformatics tools integrate data from genomics, transcriptomics, proteomics, and metabolomics to map metabolic pathways.
AI-driven platforms like OmicsNet combine multi-omics data to optimize secondary metabolite synthesis networks 4 .
By comparing genomes across species, researchers uncover evolutionary relationships and identify conserved genes involved in secondary metabolism.
Comparative analysis of Scutellaria baicalensis and Scutellaria barbata revealed tandem gene duplications driving flavonoid diversity 7 .
A 2025 study published in Scientific Reports investigated the antioxidant and cytotoxic properties of Psoralea bituminosa, a plant traditionally used for antimicrobial and antihyperglycemic effects 1 .
Aqueous and methanol extracts were prepared from dried leaves.
Total Phenol Content (TPC) and Total Flavonoid Content (TFC) were quantified.
Liquid Chromatography-Mass Spectrometry (LC-MS) identified bioactive compounds.
DPPH Assay measured antioxidant activity (IC₅₀ values).
Cytotoxicity Testing against eight cancer cell lines using cell viability assays.
Cheminformatics: Molecular descriptors and PCA clustering analyzed drug-likeness.
Bioinformatics: Transcriptomic data from cancer cell lines were mined to identify enriched pathways.
| Extract | Total Phenol Content (mg/g) | Total Flavonoid Content (mg/g) | DPPH IC₅₀ (µg/mL) |
|---|---|---|---|
| Aqueous | 81.57 | 39.06 | 330.77 |
| Methanol | 65.23 | 32.14 | 348.27 |
| Cell Line | IC₅₀ (µg/mL) |
|---|---|
| A549 | 27.73 |
| MDA-MB231 | 41.83 |
| PC3 | 53.90 |
| T47D | >150 |
This study demonstrates how integrative approaches—combining phytochemistry, bioassays, and bioinformatics—can decode the mechanistic basis of plant bioactivity. The cheminformatics clustering highlighted structural groups with distinct drug-likeness scores, while transcriptomics offered insights into pathways targeted by the extract 1 .
Only 11 T2T gapless genomes exist for medicinal plants due to challenges like high heterozygosity and repetitive elements .
Future efforts must prioritize complete assemblies to fully characterize biosynthetic gene clusters (BGCs).
AI will play a larger role in predicting biosynthetic pathways and gene-editing targets (e.g., CRISPR-Cas9) for metabolic engineering 4 .
Ethnobotanical studies are declining (only 14% of studies in the Fertile Crescent were field-based) 8 .
Bioinformatics can help document traditional knowledge and identify species at risk (e.g., Teucrium polium).
China leads medicinal plant genomics (69.9% of assemblies), but global initiatives like the Earth BioGenome Project aim to sequence all known species 6 .
Bioinformatics is transforming medicinal plant research from a traditional practice into a data-driven science.
By integrating genomics, AI, and multi-omics, researchers can unravel the complex biosynthetic pathways of therapeutic compounds, accelerate drug discovery, and promote sustainable use of plant resources. However, challenges remain—from improving genome assemblies to preserving ethnobotanical knowledge.
As technology advances, bioinformatics will continue to bridge ancient wisdom with modern innovation, unlocking nature's pharmacy for future generations.
For further reading, explore the Frontiers Research Topic on AI-Assisted Bioinformatics and Functional Genomics Technologies in Medicinal Plants 4 .