Mosaic plasmids, plasmids composed of genetic elements from distinct sources, are associated with the spread of antibiotic resistance genes. Transposons are considered the primary mechanism for mosaic plasmid formation, though other mechanisms have been observed in specific instances. The frequency with which mosaic plasmids have been described suggests they may play an important role in plasmid population dynamics. Our survey of the confirmed plasmid sequences available from complete and draft genomes in the RefSeq database shows that 46% of them fit a strict definition of mosaic. Mosaic plasmids are also not evenly distributed over the taxa represented in the database. Plasmids from some genera, including Piscirickettsia and Yersinia, are almost all mosaic, while plasmids from other genera, including Borrelia, are rarely mosaic. While some mosaic plasmids share identical regions with hundreds of others, the median mosaic plasmid only shares with 8 other plasmids. When considering only plasmids from finished genomes (51.6% of the total), mosaic plasmids have significantly higher proportions of transposase and antibiotic resistance genes. Conversely, only 56.6% of mosaic fragments (DNA fragments shared between mosaic plasmids) contain a recognizable transposase gene, and only 1.2% of mosaic fragments are flanked by inverted repeats. Mosaic fragments associated with the IS26 transposase gene are 3.8-fold more abundant than any other sequence shared between mosaic plasmids in the database, though this is at least partly due to overrepresentation of Enterobacteriaceae plasmids. Mosaic plasmids are a complicated trait of some plasmid populations, only partly explained by transposition. Though antibiotic resistance genes led to the identification of many mosaic plasmids, mosaic plasmids are a broad phenomenon encompassing many more traits than just antibiotic resistance. Further research will be required to determine the influence of ecology, host repair mechanisms, conjugation, and plasmid host range on the formation and influence of mosaic plasmids. AUTHOR SUMMARY: Plasmids are extrachromosomal genetic entities that are found in many prokaryotes. They serve as flexible storage for genes, and individual cells can make substantial changes to their characteristics by acquiring, losing, or modifying a plasmid. In some pathogenic bacteria, such as Escherichia coli, antibiotic resistance genes are known to spread primarily on plasmids. By analyzing a database of 8592 plasmid sequences we determined that many of these plasmids have exchanged genes with each other, becoming mosaics of genes from different sources. We next separated these plasmids into groups based on the organism they were isolated from and found that different groups had different fractions of mosaic plasmids. This result was unexpected and suggests that the mechanisms and selective pressures causing mosaic plasmids do not occur evenly over all species. It also suggests that plasmids may provide different levels of potential variation to different species. This work uncovers a previously unrecognized pattern in plasmids across prokaryotes, that could lead to new insights into the evolutionary role that plasmids play.

中文翻译：

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马赛克质粒丰富并且在原核生物分类中分布不均。

镶嵌质粒是由不同来源的遗传元件组成的质粒，与抗生素抗性基因的传播有关。转座子被认为是镶嵌质粒形成的主要机制，尽管在特定情况下还观察到其他机制。镶嵌质粒的描述频率表明它们可能在质粒种群动态中发挥重要作用。我们对RefSeq数据库中完整和草图基因组中可用的确认质粒序列的调查显示，其中46％符合严格的镶嵌定义。镶嵌质粒也不均匀分布在数据库中表示的分类单元上。包括Piscirickettsia和Yersinia在内的某些属的质粒几乎都是镶嵌的，而来自其他属（包括Borrelia）的属质粒则很少镶嵌。虽然一些镶嵌质粒与其他数百个质粒具有相同的区域，但中间镶嵌质粒仅与其他8个质粒共享。仅考虑来自完整基因组的质粒（占总数的51.6％）时，镶嵌质粒的转座酶和抗生素抗性基因的比例明显更高。相反，只有56.6％的镶嵌片段（镶嵌质粒之间共享的DNA片段）含有可识别的转座酶基因，只有1.2％的镶嵌片段的侧翼是反向重复。与IS26转座酶基因相关的镶嵌片段比数据库中镶嵌质粒之间共享的任何其他序列丰富3.8倍，尽管这至少部分是由于肠杆菌科细菌质粒的过量表达。镶嵌质粒是某些质粒种群的复杂特征，仅通过换位来部分解释。尽管抗生素抗性基因导致了许多镶嵌质粒的鉴定，但镶嵌质粒是一种广泛的现象，它不仅具有抗生素抗性，还具有更多的特征。需要进一步的研究以确定生态学，寄主修复机制，缀合和质粒寄主范围对镶嵌质粒形成和影响的影响。作者摘要：质粒是在许多原核生物中发现的染色体外遗传实体。它们可作为基因的灵活存储，单个细胞可通过获取，丢失或修饰质粒对其特性进行重大改变。在某些致病细菌（例如大肠杆菌）中，已知抗生素抗性基因主要在质粒上传播。通过分析8592个质粒序列的数据库，我们确定这些质粒中的许多已经相互交换了基因，成为了来自不同来源的基因的镶嵌图。接下来，我们基于分离出的生物体将这些质粒分为几类，发现不同的组具有不同比例的镶嵌质粒。该结果是出乎意料的，并表明引起镶嵌质粒的机制和选择压力并非在所有物种上均等发生。这也表明质粒可以为不同物种提供不同水平的潜在变异。这项工作揭示了原核生物质粒中以前无法识别的模式，这可能导致对质粒发挥进化作用的新见解。成为来自不同来源的基因的花叶。接下来，我们基于分离出的生物体将这些质粒分为几类，发现不同的组具有不同比例的镶嵌质粒。该结果是出乎意料的，并表明引起镶嵌质粒的机制和选择压力并非在所有物种上均等发生。这也表明质粒可以为不同物种提供不同水平的潜在变异。这项工作揭示了原核生物质粒中以前无法识别的模式，这可能导致对质粒发挥进化作用的新见解。成为来自不同来源的基因的花叶。接下来，我们基于分离出的生物体将这些质粒分为几类，发现不同的组具有不同比例的镶嵌质粒。该结果是出乎意料的，并表明引起镶嵌质粒的机制和选择压力并非在所有物种上均等发生。这也表明质粒可以为不同物种提供不同水平的潜在变异。这项工作揭示了原核生物质粒中以前无法识别的模式，这可能导致对质粒发挥进化作用的新见解。该结果是出乎意料的，并且表明引起镶嵌质粒的机制和选择压力并非在所有物种上均等发生。这也表明质粒可以为不同物种提供不同水平的潜在变异。这项工作揭示了原核生物质粒中以前无法识别的模式，这可能导致人们对质粒发挥的进化作用有了新的认识。该结果是出乎意料的，并表明引起镶嵌质粒的机制和选择压力并非在所有物种上均等发生。这也表明质粒可以为不同物种提供不同水平的潜在变异。这项工作揭示了原核生物质粒中以前无法识别的模式，这可能导致对质粒发挥进化作用的新见解。