Faculdade de Computação - FACOM, Universidade Federal de Mato Grosso do Sul - UFMS, Campo Grande, Brazil.
Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
BMC Genomics. 2020 Apr 16;21(Suppl 2):273. doi: 10.1186/s12864-020-6609-x.
Computationally inferred ancestral genomes play an important role in many areas of genome research. We present an improved workflow for the reconstruction from highly diverged genomes such as those of plants.
Our work relies on an established workflow in the reconstruction of ancestral plants, but improves several steps of this process. Instead of using gene annotations for inferring the genome content of the ancestral sequence, we identify genomic markers through a process called genome segmentation. This enables us to reconstruct the ancestral genome from hundreds of thousands of markers rather than the tens of thousands of annotated genes. We also introduce the concept of local genome rearrangement, through which we refine syntenic blocks before they are used in the reconstruction of contiguous ancestral regions. With the enhanced workflow at hand, we reconstruct the ancestral genome of eudicots, a major sub-clade of flowering plants, using whole genome sequences of five modern plants.
Our reconstructed genome is highly detailed, yet its layout agrees well with that reported in Badouin et al. (2017). Using local genome rearrangement, not only the marker-based, but also the gene-based reconstruction of the eudicot ancestor exhibited increased genome content, evidencing the power of this novel concept.
计算推断的祖先基因组在基因组研究的许多领域中发挥着重要作用。我们提出了一种改进的工作流程，用于重建高度分化的基因组，如植物基因组。
我们的工作依赖于重建祖先植物的既定工作流程，但改进了该过程的几个步骤。我们不是使用基因注释来推断祖先序列的基因组内容，而是通过称为基因组分割的过程来识别基因组标记。这使我们能够从数十万标记而不是数万注释基因中重建祖先基因组。我们还引入了局部基因组重排的概念，通过该概念，我们在用于重建连续祖先区域之前细化同线性块。有了增强的工作流程，我们使用五株现代植物的全基因组序列重建了真双子叶植物（开花植物的主要亚群）的祖先基因组。
我们重建的基因组非常详细，但它的布局与 Badouin 等人（2017 年）报道的非常吻合。使用局部基因组重排，不仅基于标记的，而且基于基因的真双子叶植物祖先重建都显示出增加的基因组含量，证明了这一新概念的强大功能。
