Development of a method for core genome identification as a basis for microbial comparative genomics

作为对经历了包括水平基因转移在内的复杂进化过程的微生物基因组进行比较分析的基本基础，我们研究了一种在相关基因组中识别主要通过垂直转移遗传的“基因组核心结构”的方法。我们的方法是基于提取相关基因组中具有保守基因顺序的区域。我们将我们的方法应用于各种基因组数据来测试其有效性，并建立了一个系统，将所得到的已发表数据的核心结构累积到数据库中。我们还开发了一个工具，实现了核心基因组分析的协议，包括核心结构的可视化，并将其应用于密切相关的微生物基因组的实际比较研究。

As a fundamental basis for comparative analysis of microbial genomes that have undergone complex evolutionary processes including horizontal gene transfers, we have investigated a method to identify a "genomic core structure" among related genomes that is mainly inherited through vertical transfers. Our method is based on extracting the regions that have conserved gene order among the related genomes. We applied our method to various genomic data to test its validity and established a system to accumulate the resulting core structures of the published data into a database. We also developed a tool that implements the protocol for core genome analysis including visualization of core structures, and applied it to actual comparative studies of closely related microbial genomes.