Detecting footprints of selection at duplicated genes in cultivated and wild flowering plant species using population genetics tools
Plant Genetics and Genomics
Final Report Abstract
Numerous studies revealed that gene duplication plays an important role in the genome evolution of angiosperms (flowering plants). In a previous study of angiosperm genomes, my colleagues and I provided empirical evidence that positive selection is acting far more frequently on duplicated genes compared to single-copy genes. These findings raised further interesting questions concerning the evolution of duplicated genes in angiosperms which we wanted to answer in this project. First, we extended our method to the analysis of large a candidate gene family that is known to play an important role in plant development, immunity, and perception of environmental conditions or stresses. We provided a framework for the difficult task of analysing the evolutionary history of large, complex, and divergent gene families. This sub-project led to a publication in a highly renowned journal and has since become a resource for researchers working on this gene family. Second, we extended our analysis to intraspecific polymorphism data in order to shed light on role of natural selection in the early evolutionary stages of new gene copies. To do this, we developed a pipeline to distinguish alleles and gene copies. Comprehensive analysis to rule out potential biases and fine-tuning all parameters created a compelling data set which will be analysed further using population genetics tools in collaboration with researchers in France and Germany. Third, I started a collaboration with a researcher in Munich to investigate which modes of duplication are primarily responsible for the lineage-specific expansion of gene families in addition to the initial project. I carried out this project in collaboration with Dr Nathalie Chantret of INRA, Montpellier within the ARCAD (Agopolis Resource Center for Crop Conservation, Adaptation, and Diversity) project. The unique structure of this project, which unifies scientists from various fields (bioinformatics, population genetics, comparative genomics among others), gave me the opportunity to establish a broad scientific network that assisted me in the diverse research topics this project encompasses. In addition, I was able to advance my skills on the analysis of large datasets using bioinformatic tools by attending courses provided by the hosting institute and in collaboration with the bioinformatics team. Finally, I was able to build a scientific network in France and reconnected to the german science community by initiating collaborations in Munich. My research is timely as it connects bioinformatics, molecular evolution, and plant genomics. Taken together, this project enabled me to expand my knowledge on plant evolutionary genomics and to establish international collaborations.
Publications
- (2016). Evolutionary dynamics of the Leucine- Rich Repeats Receptor-Like Kinase (LRR-RLK) subfamily in angiosperms. Plant Physiology 170: 1595-1610
Fischer I, Diévart A, Droc G, Dufayard J-F, Chantret N
(See online at https://doi.org/10.1104/pp.15.01470)
