Bioinformatics for the polyploidization-fractionation cycle in angiosperms

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Over the scale of millions of years, biological evolution entails not only mutations in individual genes, but also the rearrangement of the order of the genes on the chromosomes compared to other species descended from their common ancestor. In addition, and especially in plant genomes, the entire genome may be doubled, and the excess genes deleted in a seemingly unpredictable way. We model all these processes mathematically and develop combinatorial algorithms and statistical analyses to understand the rearrangement of gene order within and between chromosomes. This is applied to understand the evolution of genomes, particularly of crops and other flowering plants. Focusing on combinatorial algorithms, probability modeling and extensive collaborative analysis of flowering plant genomes, we propose to provide a comprehensive formal understanding of a wide range of phenomena connected to the evolution of chromosomes, specifically at the level of gene order. This development of a battery of formal combinatorial, mathematical and statistical tools will be thoroughly integrated with our work on the genomes of a large number of individual species. Our approaches should directly impact thinking within computational biology and should lead to useful ideas for biological research, as well as new discoveries about the genomes of many flowering plants.