Large-scale duplication events underpin population-level flexibility in bacterial tRNA gene copy number

<strong>ABSTRACT</strong> The complement of tRNA genes within a genome is typically regarded as a stable characteristic of an organism. Here we demonstrate that bacterial tRNA gene set composition can be more flexible than previously appreciated, particularly regarding tRNA gene copy number. We report the spontaneous, high-rate occurrence of large-scale, tandem duplication events in laboratory populations of the bacterium <em>Pseudomonas fluorescens </em>SBW25. The identified duplication fragments are up to 1 Mb in size (~15 % of the wildtype genome) and are predicted to change the copy number of up to 916 genes, including several tRNA genes. The observed duplication fragments are inherently unstable: they occur, and are subsequently lost, at extremely high rates. We propose that this unusually plastic type of mutation provides a mechanism that rapidly generates tRNA gene set diversity, while simultaneously preserving the underlying tRNA gene set in the absence of continued selection. That is, if a tRNA set variant provides no fitness advantage, then the high-rate segregation of the duplication fragment ensures the maintenance of the original tRNA gene set. However, if a tRNA gene set variant is selectively beneficial, the underlying duplication fragments persist and provide the raw material for further, more stable, evolutionary changes. <strong>REPOSITORY CONTENTS</strong> This entry contains additional raw data and background information for the above manuscript, organized into the following folders: <strong>data</strong>: this folder contains .xlsx sheets with the raw data, calculations, and statistics for several experiments (competition assays, growth curves in KB and M9, stability assays, YAMAT-seq sample preparation). <strong>background</strong>: this folder contains the background files for several experiments (colony images, gel images, Sanger sequences).<strong>摘要</strong> 基因组内的转运RNA（transfer RNA, tRNA）基因全集通常被认为是生物体的稳定特征之一。本研究表明，细菌的tRNA基因组成相较于此前认知更具可塑性，尤其是在tRNA基因拷贝数层面。我们在实验室培养的<em>荧光假单胞菌（Pseudomonas fluorescens）</em>SBW25种群中，观察到大规模串联重复事件以高频率自发发生。经鉴定的重复片段长度可达1 Mb（约占野生型基因组的15%），预计可改变多达916个基因的拷贝数，其中包含若干tRNA基因。所观察到的重复片段本身具有不稳定性：它们以极高的频率出现并随后丢失。我们提出，这种异常具有可塑性的突变类型提供了一种机制，可快速产生tRNA基因全集的多样性，同时在无持续选择压力的情况下保留原始的tRNA基因全集。换言之，若某一tRNA基因全集变体未带来适合度优势，则重复片段的高频率分离将确保原始tRNA基因全集得以保留。反之，若某一tRNA基因全集变体具有选择优势，则其对应的重复片段将得以保留，并为后续更稳定的进化改变提供原材料。<strong>数据集内容</strong> 本条目包含上述论文的补充原始数据与背景资料，按以下文件夹组织：<strong>data</strong>：该文件夹包含多个实验的原始数据、计算结果与统计分析表格（格式为.xlsx），实验涵盖竞争测定、KB与M9培养基中的生长曲线测定、稳定性测定以及YAMAT测序样本制备。<strong>background</strong>：该文件夹包含多个实验的背景资料文件，包括菌落图像、凝胶电泳图像以及桑格测序结果。