European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.
Department of Molecular Biology, University of Geneva, 1211 Geneva, Switzerland.
Nucleic Acids Res. 2022 Apr 8;50(6):3155-3168. doi: 10.1093/nar/gkac163.
Prokaryotic Mobile Genetic Elements (MGEs) such as transposons, integrons, phages and plasmids, play important roles in prokaryotic evolution and in the dispersal of cargo functions like antibiotic resistance. However, each of these MGE types is usually annotated and analysed individually, hampering a global understanding of phylogenetic and environmental patterns of MGE dispersal. We thus developed a computational framework that captures diverse MGE types, their cargos and MGE-mediated horizontal transfer events, using recombinases as ubiquitous MGE marker genes and pangenome information for MGE boundary estimation. Applied to ∼84k genomes with habitat annotation, we mapped 2.8 million MGE-specific recombinases to six operational MGE types, which together contain on average 13% of all the genes in a genome. Transposable elements (TEs) dominated across all taxa (∼1.7 million occurrences), outnumbering phages and phage-like elements (<0.4 million). We recorded numerous MGE-mediated horizontal transfer events across diverse phyla and habitats involving all MGE types, disentangled and quantified the extent of hitchhiking of TEs (17%) and integrons (63%) with other MGE categories, and established TEs as dominant carriers of antibiotic resistance genes. We integrated all these findings into a resource (proMGE.embl.de), which should facilitate future studies on the large mobile part of genomes and its horizontal dispersal.
原核移动遗传元件（MGE），如转座子、整合子、噬菌体和质粒，在原核进化和货物功能（如抗生素抗性）的传播中发挥重要作用。然而，这些 MGE 类型通常是单独注释和分析的，这阻碍了对 MGE 传播的系统发育和环境模式的全面理解。因此，我们开发了一种计算框架，使用重组酶作为普遍存在的 MGE 标记基因，并利用泛基因组信息来估计 MGE 边界，从而捕获多种 MGE 类型、它们的货物和 MGE 介导的水平转移事件。应用于具有栖息地注释的约 84k 个基因组，我们将 280 万个 MGE 特异性重组酶映射到六种操作 MGE 类型，这些类型总共包含基因组中平均 13%的基因。转座元件（TEs）在所有分类群中占主导地位（约 170 万次出现），超过了噬菌体和噬菌体样元件（<0.4 万次）。我们记录了在涉及所有 MGE 类型的多个门和栖息地之间发生的大量 MGE 介导的水平转移事件，解开并量化了 TEs（17%）和整合子（63%）与其他 MGE 类别的 hitchhiking 程度，并确定 TEs 是抗生素抗性基因的主要载体。我们将所有这些发现整合到一个资源（proMGE.embl.de）中，这应该有助于未来研究基因组的大型移动部分及其水平传播。
