Faculty of Natural Sciences, University of Sarajevo, Bosnia and Herzegovina.
Bioinformatics. 2011 Jul 1;27(13):i257-65. doi: 10.1093/bioinformatics/btr224.
Ancestral genomes provide a better way to understand the structural evolution of genomes than the simple comparison of extant genomes. Most ancestral genome reconstruction methods rely on universal markers, that is, homologous families of DNA segments present in exactly one exemplar in every considered species. Complex histories of genes or other markers, undergoing duplications and losses, are rarely taken into account. It follows that some ancestors are inaccessible by these methods, such as the proto-monocotyledon whose evolution involved massive gene loss following a whole genome duplication.
We propose a mapping approach based on the combinatorial notion of 'sandwich consecutive ones matrix', which explicitly takes gene losses into account. We introduce combinatorial optimization problems related to this concept, and propose a heuristic solver and a lower bound on the optimal solution. We use these results to propose a configuration for the proto-chromosomes of the monocot ancestor, and study the accuracy of this configuration. We also use our method to reconstruct the ancestral boreoeutherian genomes, which illustrates that the framework we propose is not specific to plant paleogenomics but is adapted to reconstruct any ancestral genome from extant genomes with heterogeneous marker content.
Upon request to the authors.
与简单比较现存基因组相比，祖先基因组为理解基因组的结构演化提供了更好的方法。大多数祖先基因组重建方法依赖于通用标记，即存在于每个被考虑物种的一个范例中的 DNA 片段的同源家族。很少考虑基因或其他标记的复杂历史，经历过复制和丢失。因此，这些方法无法访问某些祖先，例如原单子叶植物的祖先，其演化涉及到在整个基因组复制后大量基因丢失。
我们提出了一种基于“夹心连续一矩阵”组合概念的映射方法，该方法明确考虑了基因的丢失。我们引入了与这一概念相关的组合优化问题，并提出了一种启发式求解器和最优解的下界。我们使用这些结果来提出单子叶植物祖先原染色体的配置，并研究该配置的准确性。我们还使用我们的方法来重建原始有胎盘哺乳动物的祖先基因组，这表明我们提出的框架不仅适用于植物古基因组学，而且适用于从具有异质标记内容的现存基因组中重建任何祖先基因组。
请向作者索取。
