The following project descriptions should give an impression of the ongoing and planned research projects. If you are interested, please contact the named person. It is often possible to add wet lab work to a bioinformatics project. We offer the opportunity to start with a data analysis that generates hypotheses followed by validation experiments. Obviously, it is also possible to select only a bioinformatics or molecular biology project. The list of available projects is incomplete and we offer more projects upon request. A presentation of your own ideas for research projects is encouraged if it is connected to the research going on the group. Please contact Boas Pucker.
If you contact us about a project, please provide some brief explanations (bullet points are fine):
Latest update of projects: 1st June 2023
Background: Sequencing plant genomes is turning into a routine task. We perform this regularly with our MinIONs. Large data sets are available that allow the investigation of various properties of the sequenced plant species. Specific pathways or gene families can be studied based on highly continuous genome sequences. We have several long read data sets and derived genome sequences available that require downstream analyses prior to publication.
Objective: Perform bioinformatic analyses to understand the biology of a plant species based on the genome sequence. The results of these analyses should form the basis of a publication about the genome sequence.
Requirements: This project requires a strong interest in computational work and some previous experience with Linux and terminals. The modules GE33, GE31, or 'Data Literacy in Genomics' would provide a strong basis for this project.
Contact: Boas Pucker
Background: Specialized metabolites are produced by plants to survive under challenging conditions. The biosynthesis of these compounds is often induced by environmental conditions i.e. biotic or abiotic stresses. Many different classes of specialized metabolites are already known and well studied. Examples are terpenes, alkaloids, flavonoids, or betalains. However, specialized metabolites could also be derived from completely different precursors. Such compounds have not been studied due to methodological limitations.
Objectives: The objective is the identification of hints for specialized metabolism based on novel precursors. The approach is to screen numerous sequence data sets for gene duplications and neofuctionalization events affecting players of specific biosynthesis pathways. Such gene duplications could reveal the basis of unknown biosynthesis pathways.
Requirements: Strong interest in big data analyses and computational biology is required. Previous experience with Linux and working with command line tools would be helpful. Experience with Python or another script language would be beneficial. Our modules BB34, GE31, and 'Data Literacy in Genome Research' would provide a strong basis.
Contact: Boas Pucker
Background: Equisetum is a fascinating genus. The members are considered morphologically similar to some of the earliest land plants. Many species are characterized by an extremely large genome. Equisetum produces a plethora of specialized metabolites that are likely to resemble an adaptation to the environmental conditions.
Objective: Identification of differentially expressed genes between different species and accessions of Equisetum is the first objective. These genes will be screened for candidates to explain differences in the ability to produce specialized metabolites. Once identified, the validation of these candidates is possible.
Requirements: Interest in molecular biology (RNA extraction), sequencing, and data analysis is required. Any previous experience would be helpful, but is not mandatory.
Contact: Boas Pucker
Background: The flavonoid biosynthesis is a model system for transcriptional regulation, because many genes are involved in the formation of colorful pigments. Since the activity of gene products can be seen easily, these gene could be considered 'reporter genes'. One example is the transcription factor MYB12 that activates genes in the flavonol biosynthesis pathway. Flavonols can be easily visualized in a staining with Naturstoffreagenz A. Although research on the flavonoid biosynthesis revealed many transcription factors and complex interactions between them, there are probably more to find.
Objective: The aim of this project is to apply a sophisticated co-expression analysis to find such novel candidates. This relies on the assumption that transcription factors and their target genes should show similar expression levels across a wide range of tissue types and conditions. The results of this analysis are integrated in the next step and finally subjected to a quality assessment. Validation of candidates in the lab is possible, but not mandatory.
Requirements: You should be interested in eukaryotic transcription factors. Some basic knowledge about a script or programming language (ideally Python or R) would be helpful. The modules BB34 and GE33 provide a strong basis.
Contact: Boas Pucker
Project (BSc/MSc): Finding a needle in a haystack ... with a magnet ('FloColDiff')
Background: Anthocyanins are responsible for the blue to red coloration of many flowers. The formation of anthocyanins is well understood in several model species like petunia. There are numerous flowering plant species which have cultivars with different flower colors. Shifts from red or blue to colorless (white) are frequent, but also shifts from blue to red/orange. The molecular basis of these differences was investigated in several plant species and revealed many possible mechanisms.
Objective: The precise objective and approach are confidential. Details will be discussed in a meeting.
Requirements: Interest in flowers and/or anthocyanins. Running scripts on a Linux system. Experience in using bioinformatic tools would be helpful for some data sets e.g. RNA-Seq.
Contact: Maria
Background: We previously developed KIPEs for the automatic identification of the well characterized core genes of the flavonoid biosynthesis in the genome or transcriptome assembly of a new plant species. The flavonoid biosynthesis is involved in many process thus numerous studies need to look at some flavonoid biosynthesis genes. KIPEs performs a phylogenetic analysis which is superior to a frequently used BLAST-only approach regarding the reliability of the results. Additionally, KIPEs checks candidate sequences for the presence of functionally relevant amino acids e.g. the active center.
Objective: The aim of this project is to add extensions to KIPEs to enable the analysis of various additional reactions and other pathways. There are multiple pathways that can be integrated independently which allows multiple students to work on this topic. Here is a list of opportunities, but own ideas are welcome as well:
(1) identification of isoflavonoid biosynthesis genes: this is a branch of the flavonoid biosynthesis that was not included in the initial KIPEs release
(2) identification of the lignin biosynthesis pathway.
Requirements: You should be interested in the respective pathway or in specialized metabolism in general. Some basic knowledge about running scripts on Linux would be helpful.
Related publications:
(1) Pucker, B.; Reiher, F.; Schilbert, H.M. Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium. Plants 2020;https://doi.org/10.3390/plants9091103
(2) Rempel, A.; Pucker, B. KIPEs3: Automatic annotation of biosynthesis pathways. bioRxiv 2022.06.30.498365; doi: doi.org/10.1101/2022.06.30.498365
Contact: Boas Pucker
There is a possibilty to conduct exciting research on flavonoids in the group of Stefan Martens (Italy). More details are available upon request. Please get in touch if you would like to go abroad for some months. ERASMUS could be a funding source for this opportunity.