Evidence for gene non-functionalization due to mutational processes is found in genomes in the form of pseudogenes. Pseudogenes are known to be rare in prokaryote chromosomes, with the exception of lineages that underwent an extreme genome reduction (e.g. obligatory symbionts). Much less is known about the frequency of pseudogenes in prokaryotic plasmids; those are genetic elements that can transfer between cells and may encode beneficial traits for their host. Non-functionalization of plasmid-encoded genes may alter the plasmid characteristics, e.g. mobility, or their effect on the host. Analyzing 10 832 prokaryotic genomes, we find that plasmid genomes are characterized by threefold-higher pseudogene density compared to chromosomes. The majority of plasmid pseudogenes correspond to deteriorated transposable elements. A detailed analysis of enterobacterial plasmids furthermore reveals frequent gene non-functionalization events associated with the loss of plasmid self-transmissibility. Reconstructing the evolution of closely related plasmids reveals that non-functionalization of the conjugation machinery led to the emergence of non-mobilizable plasmid types. Examples are virulence plasmids in Escherichia and Salmonella. Our study highlights non-functionalization of core plasmid mobility functions as one route for the evolution of domesticated plasmids. Pseudogenes in plasmids supply insights into past transitions in plasmid mobility that are akin to transitions in bacterial lifestyle.

中文翻译：

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质粒基因组中的假基因揭示了过去质粒迁移性的转变


在基因组中以假基因的形式发现了由于突变过程而导致基因非功能化的证据。已知假基因在原核生物染色体中很少见，除了经历了基因组极度减少的谱系（例如强制共生体）。对于原核质粒中假基因的频率知之甚少。这些是可以在细胞之间转移的遗传元件，并可能为其宿主编码有益的特征。质粒编码基因的非功能化可能会改变质粒特征，例如移动性或其对宿主的影响。通过分析 10 832 个原核生物基因组，我们发现质粒基因组的特点是假基因密度比染色体高三倍。大多数质粒假基因对应于恶化的转座元件。对肠细菌质粒的详细分析进一步揭示了与质粒自我传播性丧失相关的频繁的基因非功能化事件。重建密切相关的质粒的进化表明，接合机制的非功能化导致了不可移动质粒类型的出现。例如埃希氏菌和沙门氏菌中的毒力质粒。我们的研究强调核心质粒移动功能的非功能化是驯化质粒进化的一种途径。质粒中的假基因提供了对过去质粒迁移性转变的见解，这类似于细菌生活方式的转变。