BACKGROUND Horizontal Gene Transfer (HGT) refers to the transfer of genetic materials between organisms through mechanisms other than parent-offspring inheritance. HGTs may affect human health through a large number of microorganisms, especially the gut microbiomes which the human body harbors. The transferred segments may lead to complicated local genome structural variations. Details of the local genome structure can elucidate the effects of the HGTs. RESULTS In this work, we propose a graph-based method to reconstruct the local strains from the gut metagenomics data at the HGT sites. The method is implemented in a package named LEMON. The simulated results indicate that the method can identify transferred segments accurately on reference sequences of the microbiome. Simulation results illustrate that LEMON could recover local strains with complicated structure variation. Furthermore, the gene fusion points detected in real data near HGT breakpoints validate the accuracy of LEMON. Some strains reconstructed by LEMON have a replication time profile with lower standard error, which demonstrates HGT events recovered by LEMON is reliable. CONCLUSIONS Through LEMON we could reconstruct the sequence structure of bacteria, which harbors HGT events. This helps us to study gene flow among different microbial species.

中文翻译：

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LEMON：一种在肠道宏基因组中水平基因转移位点构建局部菌株的方法。

背景水平基因转移(HGT)是指通过亲子遗传以外的机制在生物体之间转移遗传物质。HGTs可能通过大量微生物，尤其是人体肠道微生物群影响人类健康。转移的片段可能导致复杂的局部基因组结构变异。局部基因组结构的细节可以阐明 HGT 的作用。结果在这项工作中，我们提出了一种基于图的方法，根据 HGT 位点的肠道宏基因组数据重建局部菌株。该方法在名为 LEMON 的包中实现。模拟结果表明，该方法可以在微生物组参考序列上准确识别转移片段。仿真结果表明，LEMON 可以恢复具有复杂结构变化的局部应变。此外，在 HGT 断点附近的真实数据中检测到的基因融合点验证了 LEMON 的准确性。LEMON 重建的一些菌株具有较低标准误差的复制时间曲线，这表明 LEMON 恢复的 HGT 事件是可靠的。结论 通过 LEMON，我们可以重建含有 HGT 事件的细菌的序列结构。这有助于我们研究不同微生物物种之间的基因流。