Research

Specialized Metabolism

Plants produce a plethora of specialized metabolites to cope with numerous environmental challenges. Examples are terpenoids, flavonoids, and betalains. We are particularly interested in flavonoids which are responsible for the pigmentation of many blue or red flowers. Flavonoids can be separated into several subgroups including flavonols, anthocyanins, proanthocyanidins, and flavones. There are multiple reasons why working on the flavonoid biosynthesis is promising. [Details about flavonoid biosynthesis]

Generally, we are interested in the discovery of promising biosynthesis pathways for biotechnological applications. This is not restricted to the flavonoid biosynthesis, but instead using this model system to develop new genome mining approaches. Different methods for the identification biosynthetic pathways are combined including screens and comparisons of plant genome sequences. Currently, we explore the withanolide biosynthesis in collaboration with the Franke lab (Leibniz University Hannover). [Details about withanolide biosynthesis]

Biosynthetic networks are controlled by transcription factors. One of the largest transcription factor families in plants is the MYBs, which are involved in controlling a variety of plant-specific processes. [Details about MYBs]

Plant Genomics & Long Read Sequencing

Plant genome sequences contain the blue print for all proteins (enzymes). Sequencing and investigating genomes is an effective approach to reveal the biochemical potential of plants. Especially the correlation of genomic data (DNA) with transcriptomic (RNA) and metabolomic (chemical compounds) data sets allows the identification of biosynthesis pathways. Rapid developments of long read sequencing technologies allow the cost-effective analysis of large plant genomes. Sequencers distributed by Oxford Nanopore Technologies (ONT) are portable and can even be operated in the field. This so called nanopore sequencing approach analysis individual DNA strands. We use this technology to resolve the genome sequences of of important plant species. This is also a great opportunity for students to contribute to a genome sequencing project. [Details about our genome sequencing projects]

Applied Bioinformatics

Specific biological questions require the development of dedicated tools. We write such tools mostly in Python and R. The developed tools are freely available on github (bpucker). Some tools are available on our web server. The following tools are examples of active developments.

• KIPEs (A): Knowledge-based Identification of Pathway Enzymes allows the automatic annotation of the proteins involved in the core steps of the flavonoid biosynthesis. This supports the identification of molecular mechanisms underlying color differences between cultivars of the same species. In addition, rapid annotation of flavonoid biosynthesis genes in novel/uncharacterized species becomes convenient.
• MGSE (B): Mapping-based Genome Size Estimation is a novel approach to infer the true genome size of a species based on sequence reads. This approach harnesses the equal representation of all regions (even repeats) in the read set. The average number of sequence reads (coverage) is estimated based on single copy regions in a reference genome sequence. Dividing the combined coverage of all positions in an assembly by this sequencing depth results in the genome size estimation.
• NAVIP (C): Neighborhood-Aware Variant Impact Predictor enables the prediction of functional consequences arising from sequence variants between a sequenced sample and a reference. In contrast to many established tools, NAVIP considers all variants in one gene at the same time when predicting the potential effect of sequence variants.
• MYB_annotator (D): This tool enables the automatic identification and annotation of MYBs in a novel transcriptome/genome sequence assembly of a plant species. The identified candidates are functionally annotated based on orthology to previously characterized sequences.
• bHLH_annotator (E): This tool enables the automatic identification and annotation of bHLHs in a novel transcriptome/genome sequence assembly of a plant species. The identified candidates are functionally annotated based on orthology to previously characterized sequences.