Mobile genetic elements with circular genomes play a key role in the evolution of microbial communities. Their circular genomes correspond to circular walks in metagenome graphs, and yet, assemblies derived from natural microbial communities produce graphs riddled with spurious cycles, complicating the accurate reconstruction of circular genomes. We present DomCycle, an algorithm that reconstructs likely circular genomes based on the identification of so-called “dominant” graph cycles. In the implementation, we leverage paired reads to bridge assembly gaps and scrutinize cycles through a nucleotide-level analysis, making the approach robust to misassembly artifacts. We validated the approach using simulated and real sequencing data. Application of DomCycle to 32 publicly available DNA shotgun sequence data sets from diverse natural environments led to the reconstruction of hundreds of circular mobile genomes. Clustering revealed 20 highly prevalent and cryptic plasmids that have clonal population structures with recent common ancestors. This method facilitates the study of microbial communities that evolve through horizontal gene transfer.

中文翻译：

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从宏基因组数据中对环状移动元件进行精确基因分型揭示了与人类相关的质粒与最近的共同祖先

具有环状基因组的移动遗传元件在微生物群落的进化中发挥着关键作用。它们的循环基因组对应于宏基因组图中的循环游走，然而，源自天然微生物群落的组装产生的图充满了虚假循环，使循环基因组的准确重建变得复杂。我们提出了 DomCycle，一种基于所谓的“显性”图循环的识别重建可能的圆形基因组的算法。在实施过程中，我们利用成对的读取来弥合装配间隙并通过核苷酸水平分析仔细检查循环，从而使该方法对错误装配工件具有鲁棒性。我们使用模拟和真实测序数据验证了该方法。将 DomCycle 应用于来自不同自然环境的 32 个公开可用的 DNA 鸟枪序列数据集，导致重建了数百个圆形移动基因组。聚类揭示了 20 个高度流行和神秘的质粒，它们具有最近共同祖先的克隆种群结构。这种方法有助于研究通过水平基因转移进化的微生物群落。