Detecting footprints of selection at duplicated genes in cultivated and wild flowering plant species using population genetics tools

• Applicant: Dr. Iris Fischer
• Subject Area: Evolution and Systematics of Plants and Fungi ; Plant Genetics and Genomics
• Term: from 2014 to 2016
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 252524989

Numerous studies revealed that gene duplication and retention play an important role in genome evolution. Some models dealing with duplication and retention dynamics tried to establish a theoretical link between gene duplication and adaptation. Indeed, many cases of positive selection acting at duplicated genes from different plant taxa could be identified using phylogenetic approaches. These approaches give solid evidence for long term and/or recurring positive selection. Applying such an approach to angiosperm (flowering plant) genomes, my colleagues and I provided empirical evidence that positive selection is acting far more frequently on duplicated genes compared to single-copy genes. However, studies searching for recent selection footprints at duplicated genes using population genetic tools are scarce. The main reason for this is that it is very difficult to distinguish alleles from gene copies in genome and especially transcriptome data. However, a reliable classification of alleles and gene duplicates is essential for population genetic analysis. In this project, I first plan to develop a pipeline to distinguish alleles and gene copies. This will be done by developing previous programs which were used to differentiate between duplicated and single-copy genes further. In the next step, I plan to apply suitable population genetic methods to analyse these duplicates. Specifically, I want to analyse the ARCAD dataset which contains transcriptomes of cultivated plants and populations of their wild sister species. This dataset allows identifying genes responsible for adaptation. This work will be carried out in the group of Dr Nathalie Chantret as part of the ARCAD project, which provides the dataset. The ARCAD project has a unique structure as it is conducted in collaboration with many scientists from various fields (e.g. bioinformatics, population genetics, comparative genomics). Therefore, I will be able to establish a broad scientific network which will be helpful for conducting this project. Additionally, I will have the opportunity to improve my programing skills in collaboration with the ARCAD bioinformatics team which will be useful for my future research. This project will undoubtedly help me to develop my knowledge and skills further in order to continue investigating the interesting topic of gene duplication and gene family evolution in plants.

• DFG Programme: Research Fellowships
• International Connection: France
• Host: Dr. Nathalie Chantret