Bioinformatics for the polyploidization-fractionation cycle in angiosperms

在数百万年的时间里，生物进化不仅需要个体基因的突变，还需要染色体上基因顺序的重新排列，而不是与来自共同祖先的其他物种相比。此外，特别是在植物基因组中，整个基因组可能会翻倍，而多余的基因可能会以一种看似不可预测的方式被删除。我们对所有这些过程进行数学建模，并开发组合算法和统计分析，以了解染色体内和染色体之间基因顺序的重排。这被用于理解基因组的进化，特别是农作物和其他开花植物的基因组进化。****专注于组合算法，概率建模和开花植物基因组的广泛协作分析，我们建议提供与染色体进化相关的广泛现象的全面形式理解，特别是在基因顺序水平上。这一系列正式组合、数学和统计工具的发展将与我们对大量个体物种基因组的研究彻底结合起来。我们的方法应该直接影响计算生物学的思考，并应该为生物学研究带来有用的想法，以及关于许多开花植物基因组的新发现。

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.