BACKGROUND Genomes are subjected to rearrangements that change the orientation and ordering of genes during evolution. The most common rearrangements that occur in uni-chromosomal genomes are inversions (or reversals) to adapt to the changing environment. Since genome rearrangements are rarer than point mutations, gene order with sequence data can facilitate more robust phylogenetic reconstruction. Helicobacter pylori is a good model because of its unique evolution in niche environment. RESULTS We have developed a method to identify genome rearrangements by comparing almost-conserved genes among closely related strains. Orthologous gene clusters, rather than the gene sequences, are used to align the gene order so that comparison of large number of genomes becomes easier. Comparison of 72 Helicobacter pylori strains revealed shared as well as strain-specific reversals, some of which were found in different geographical locations. CONCLUSION Degree of genome rearrangements increases with time. Therefore, gene orders can be used to study the evolutionary relationship among species and strains. Multiple genome comparison helps to identify the strain-specific as well as shared reversals. Identification of the time course of rearrangements can provide insights into evolutionary events.

中文翻译：

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多个细菌基因组的重排分析。

背景技术基因组经受重排，其在进化过程中改变了基因的方向和顺序。单染色体基因组中最常见的重排是倒置（或逆转）以适应不断变化的环境。由于基因组重排比点突变少，因此具有序列数据的基因顺序可以促进更稳健的系统发育重建。幽门螺杆菌是一个很好的模型，因为它在利基环境中具有独特的进化能力。结果我们开发了一种方法，可以通过在密切相关的菌株之间比较几乎保守的基因来鉴定基因组重排。使用直系同源基因簇而不是基因序列来比对基因顺序，以便比较大量基因组变得更加容易。比较了72株幽门螺杆菌菌株，发现它们具有共同的以及特定菌株的逆转，其中一些在不同的地理位置发现。结论基因组重排程度随时间增加。因此，基因顺序可用于研究物种和品系之间的进化关系。多基因组比较有助于确定菌株特异性以及共有的逆转。鉴定重排的时间过程可以提供对进化事件的见解。多基因组比较有助于鉴定菌株特异性以及共有的逆转。鉴定重排的时间过程可以提供对进化事件的见解。多基因组比较有助于鉴定菌株特异性以及共有的逆转。鉴定重排的时间过程可以提供对进化事件的见解。