Accessing the biosynthetic gene repertoire of medicinal plants


Ultra-long nanopore sequencing reads offer the exciting opportunity to routinely resolve even large and highly repetitive plant genomes. Highly continuous and complete genome sequences provide scientists with direct access to the enormous biosynthetic gene repertoire of plants. Deciphering the biosynthetic pathways of drug candidates is crucial for an efficient production in heterologous systems. To demonstrate the power of this approach, we sequenced the genomes of medicinal plants and unravelled biosynthesis pathways leading to active compounds. Stinging nettle (Urtica dioica), medicinal plant of the year 2022, was investigated to find all genes for the biosynthesis of rutin and cyanin, two health promoting substances. Red foxglove (Digitalis purpurea) was studied with respect to the biosynthesis of digoxin and digitoxin, powerful cardiotonics. Nasturtium (Tropaeolum majus) forms the basis of commercially available phytochemicals, thus its genome sequence gives insights into multiple biosynthesis pathways with pharmaceutical relevance. To facilitate the automatic identification of all relevant biosynthetic genes in a pathway of interest, we developed computational tools. These complement the existing workflows for sequencing and basecalling with automatic downstream data analysis. Making these tools freely accessible to the community will support the utilization of long-read genomic data for the discovery of novel drug candidates.


Ronja Friedhoff is a biology student at TU Braunschweig in Germany. Her interdisciplinary research in the Pucker lab focuses on synthetic biology and plant genomics. Ronja’s expertise spans wet-lab and dry-lab activities encompassing high-quality DNA extraction, nanopore sequencing, and bioinformatical analyses of the produced data. With these skills, she has sequenced the genomes of several plants with biomedical significance. Beyond research, Ronja organizes and supervises practical courses and recently contributed to the Data Literacy in Genome Research course developed by Prof. Boas Pucker and Katharina Wolff.

Authors: Ronja Friedhoff